HIVE Lab - User contributions [en]

Publications

2025-10-10T14:58:18Z

Rehmam:

All publications listed on this page should follow a modified National Library of Medicine (NLM) citation format, adapted for clarity and consistency. Here is the suggested format:<blockquote>''Author(s). Title of article. Journal Name. Year Month Day;Volume(Issue):Page range. PMID: [if available] DOI: [if no PMID]''</blockquote>Some guidelines:

* If a PubMed ID (PMID) is available, include it and omit the DOI.
* If no PMID is available, include the DOI instead.
* Journal names should be spelled out in full unless the journal is widely recognized by its acronym (e.g., ''PLoS'').
* Use full publication dates when available (e.g., 2025 Mar 28); if only the year is known, include the year alone.
* Include all author names in the order listed in the publication.
<h2>HIVE Platform Publications</h2>

<ul>
<p>Please cite use of HIVE with</p>
<li>Simonyan V and Mazumder R. High-performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. Genes, 2014 Sep 30;5(4): 957-981. [https://www.ncbi.nlm.nih.gov/pubmed/25271953 PMID: 25271953]</li>
<li>Simonyan V, Chumakov K, Dingerdissen H, et al. High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. Database (Oxford). 2016; 2016:baw022. [https://www.ncbi.nlm.nih.gov/pubmed/26989153 PMID: 26989153]</li>
</ul>

<h2>HIVE Team Publications</h2>
<ul>
<li>Krammer L, McNeely PM, Bhuiyan U, Singleton SS, Arethiya N, Argaw A, Aggarwal V, Basuchoudhary A, Mazumder M, David J, Agrawal S, Sen S, Mazumder R. PredictMod: A Platform for Predicting Medical Intervention Outcomes and Sharing Custom ML/AI Models. Network and Systems Medicine''.'' 2025. Vol. 1(1):57-66. [https://drugrepocentral.scienceopen.com/hosted-document?doi=10.14293/NSM.25.1.0007 DOI: 10.14293/NSM.25.1.0007]</li>
<li>Kahsay R, Bhuiyan U, Au CCH, Edwards N, Johnson L, Kulkarni S, Martinez K, Ranzinger R, Vijay-Shanker K, Vora J, Warner K, Tiemeyer M, Mazumder R. GlycoSiteMiner: an ML/AI-assisted literature mining-based pipeline for extracting glycosylation sites from PubMed abstracts. Glycobiology. 2025 May 22. [https://pubmed.ncbi.nlm.nih.gov/40401984/ PMID: 40401984].</li>
<li>Aoki-Kinoshita KF, Lisacek F, Mazumder R, Ranzinger R, Tiemeyer M, Yamada I, Packer NH. Meeting report of the GlySpace alliance and GaLSIC symposium. Glycobiology. 2025 Mar 28:cwaf019. [https://pubmed.ncbi.nlm.nih.gov/40156285/ PMID: 40156285].</li>
<li>Clarke DJB, Evangelista JE, Xie Z, Marino GB, Byrd AI, Maurya MR, Srinivasan S, Yu K, Petrosyan V, Roth ME, Milinkov M, King CH, Vora JK, Keeney J, Nemarich C, Khan W, Lachmann A, Ahmed N, Agris A, Pan J, Ramachandran S, Fahy E, Esquivel E, Mihajlovic A, Jevtic B, Milinovic V, Kim S, McNeely P, Wang T, Wenger E, Brown MA, Sickler A, Zhu Y, Jenkins SL, Blood PD, Taylor DM, Resnick AC, Mazumder R, Milosavljevic A, Subramaniam S, Ma'ayan A. Playbook workflow builder: Interactive construction of bioinformatics workflows. PLoS Comput Biol. 2025 Apr 3;21(4):e1012901. [https://pubmed.ncbi.nlm.nih.gov/40179105/ PMID: 40179105].</li>
<li>Keeney ''et al''. Olduvai domain expression downregulates mitochondrial pathways: implications for human brain evolution and neoteny. October 22, 2024. bioRxiv. https://doi.org/10.1101/2024.10.21.619278</li>
<li>Martinez K, Agirre J, Akune Y, Aoki-Kinoshita KF, Arighi C, Axelsen KB, Bolton E, Bordeleau E, Edwards NJ, Fadda E, Feizi T, Hayes C, Ives CM, Joshi HJ, Krishna Prasad K, Kossida S, Lisacek F, Liu Y, Lütteke T, Ma J, Malik A, Martin M, Mehta AY, Neelamegham S, Panneerselvam K, Ranzinger R, Ricard-Blum S, Sanou G, Shanker V, Thomas PD, Tiemeyer M, Urban J, Vita R, Vora J, Yamamoto Y, Mazumder R. Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. Database (Oxford). 2024 Aug 13;2024:baae073. [https://pubmed.ncbi.nlm.nih.gov/39137905/ PMID: 39137905].</li>
<li>Kim S, Mazumder R. Enhancing scientific reproducibility through automated BioCompute Object creation using Retrieval-Augmented Generation from publications. Computer Science, Computation and Language. https://doi.org/10.48550/arXiv.2409.15076</li>
<li>Wu J, Singleton SS, Bhuiyan U, Krammer L, Mazumder R. Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning. Front. Mol. Biosci.. 19 January 2024; Sec. Molecular Diagnostics and Therapeutics. Volume 10 – 2023. [https://www.ncbi.nlm.nih.gov/pubmed/38313584 PMID: 38313584].</li>
<li>Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS 4th, Patel JA, Duncan P, Mazumder R. Communicating computational workflows in a regulatory environment. Drug Discov Today. 2024 Jan 12; 103884. [https://www.ncbi.nlm.nih.gov/pubmed/38219969 PMID: 38219969].</li>
<li>Sylvetsky AC, Clement RA, Stearrett N, Issa NT, Dore FJ, Mazumder R, King CH, Hubal MJ, Walter PJ, Cai H, Sen S, Rother KI, Crandall KA. Consumption of sucralose and acesulfame-potassium containing diet soda alters the relative abundance of microbial taxa at the species level: findings of two pilot studies. Appl Physiol Nutr Metab. 2024 Jan 1; 49(1):125-134. [https://www.ncbi.nlm.nih.gov/pubmed/37902107 PMID: 37902107].</li>
<li>Vora J, Navelkar R, Vijay-Shanker K, Edwards N, Martinez K, Ding X, Wang T, Su P, Ross K, Lisacek F, Hayes C, Kahsay R, Ranzinger R, Tiemeyer M, Mazumder R. The glycan structure dictionary-a dictionary describing commonly used glycan structure terms. Glycobiology. 2023 Feb 17; cwad014 [https://www.ncbi.nlm.nih.gov/pubmed/36799723 PMID: 36799723].</li>
<li>Lisacek F, Tiemeyer M, Mazumder R, Aoki-Kinoshita KF. Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance. JACS Au. eCollection 2023 Jan 23; [https://www.ncbi.nlm.nih.gov/pubmed/36711080 PMID: 36711080].</li>
<li>Datta Chaudhuri R, Datta R, Rana S, Kar A, Vinh Nguyen Lam P, Mazumder R, Mohanty S, Sarkar S. Cardiomyocyte-specific regression of nitrosative stress-mediated S-Nitrosylation of IKKγ alleviates pathological cardiac hypertrophy. Cell Signal. 2022 Oct; 98:110403 [https://www.ncbi.nlm.nih.gov/pubmed/35835332 PMID: 35835332].</li>
<li>Dahlin M, Singleton SS, David JA, Basuchoudhary A, Wickström R, Mazumder R, Prast-Nielsen S. Higher levels of Bifidobacteria and tumour necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet. Cell Signal. 2022 ; eBioMedicine (part of The Lancet discovery science) [https://www.ncbi.nlm.nih.gov/pubmed/35598439 PMID: 35598439].</li>
<li>Lyman DF, Bell A, Black A, Dingerdissen H, Cauley E, Gogate N, Liu D, Joseph A, Kahsay R, Crichton DJ, Mehta A, Mazumder R. Modeling and integration of N-glycan biomarkers in a comprehensive biomarker data model. Glycobiology. August 2022; [https://academic.oup.com/glycob/article/32/10/855/6655823?login=false 35925813].</li>
<li>Torcivia J, Abdilleh K, Seidl F, Shahzada O, Rodriguez R, Pot D, Mazumder R. Whole Genome Variant Dataset for Enriching Studies across 18 Different Cancers. Onco (Basel). June 2022; 2(2):129-144. [https://www.ncbi.nlm.nih.gov/pubmed/37841494 PMID: 37841494].</li>
<li>Dahlin M, Singleton S, David J, Basuchoudhary A, Wickstrom, Mazumder R, Prast-Nielsen S. Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet. eBioMedicine. June 2022; vol: 80. [https://doi.org/10.1016/j.ebiom.2022.104061 https://doi.org/10.1016/j.ebiom.2022.104061].</li>
<li>King CH, Keeney J, Guimera N, Das S, Weber M, Fochtman B, Walderhaug MO, Talwar S, Patel JA, Mazumder R, Donaldson EF. Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today. 2022 Jan 22; [https://www.ncbi.nlm.nih.gov/pubmed/35077912 PMID: 35077912].</li>
<li>Wang Z, Hopson L, Singleton S, Yang X, Jogunoori W, Mazumder R, Obias V, Lin P, Nguyen BN, Yao M, Miller L, White J, Rao S, Mishra L. Mice with dysfunctional TGF-β signaling develop altered intestinal microbiome and colorectal cancer resistant to 5FU. Biochim Biophys Acta Mol Basis Dis. 2021 Oct 1; 1867(10):166179. [https://www.ncbi.nlm.nih.gov/pubmed/34082069 PMID: 34082069].</li>
<li>Lyman D, Natale D, Schriml L, Anton K, Crichton DC, Mazumder R. Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. Proceedings of the International Conference on Biomedical Ontologies 2021 (ICBO 2021) co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021) Bozen-Bolzano, Italy. 2021 Sep 16-18; [https://ceur-ws.org/Vol-3073/paper13.pdf https://ceur-ws.org/Vol-3073/paper13.pdf].</li>
<li>Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford). 2021 March 31; [https://www.ncbi.nlm.nih.gov/pubmed/33784373 PMID: 33784373].</li>
<li>Hora B, Gulzar N, Chen Y, Karagiannis K, Cai F, Su C, Smith K, Simonyan V, Shah SA, Ahmed M, Sanchez AM, Stone M, Cohen MS, Denny TN, Mazumder R, Gao F. Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing. mSphere. 2020 Oct 14; [https://www.ncbi.nlm.nih.gov/pubmed/33055255 PMID: 33055255].</li>
<li>Hopson L, Singleton S, David J, Basuchoudhary A, Prast-Nielsen S, Klein P, Sen S, Mazumder R. Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application. Prog Mol Biol Transl Sci. 2020 Sep 30; 176:141-178. [https://www.ncbi.nlm.nih.gov/pubmed/33814114 PMID: 33814114].</li>
<li>Torcivia J, Mazumder R. Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples. Briefings in Bioinformatics. 2020 Sep 17; [https://www.ncbi.nlm.nih.gov/pubmed/32940334 PMID: 32940334].</li>
<li>Gogate N, Lyman D, Bell A, Cauley E, Crandall KA, Joseph A, Kahsay R, Natale DA, Schriml LM, Sen S, Mazumder R. COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Brief Bioinform. 2021 May 20; bbab191. doi: 10.1093/bib/bbab191. [https://www.ncbi.nlm.nih.gov/pubmed/34015823 PMID: 34015823].</li>
<li>Kahsay R, Vora J, Navelkar R, Mousavi R, Fochtman BC, Holmes X, Pattabiraman N, Ranzinger R, Mahadik R, Williamson T, Kulkarni S, Agarwal G, Martin M, Vasudev P, Garcia L, Edwards N, Zhang W, Natale DA, Ross K, Aoki-Kinoshita KF, Campbell MP, York WS, Mazumder R. GlyGen data model and processing workflow. Bioinformatics. 2020; [https://www.ncbi.nlm.nih.gov/pubmed/32324859 PMID: 32324859].</li>
<li>Kurnat-Thoma E, Baranova A, Baird P, Brodsky E, Butte AJ, Cheema AK, Cheng F, Dutta S, Grant C, Giordano J, Maitland-van der Zee AH, Fridsma DB, Jarrin R, Kann MG, Keeney J, Loscalzo J, Madhavan G, Maron BA, McBride DK, McKean M, Mun SK, Palmer JC, Patel B, Parakh K, Pariser AR, Pristipino C, Radstake TRDJ, Rajasimha HK, Rouse WB, Rozman D, Saleh A, Schmidt HHHW, Schultz N, Sethi T, Silverman EK, Skopac J, Svab I, Trujillo S, Valentine JE, Verma D, West BJ, Vasudevan S. Recent Advances in Systems and Network Medicine: Meeting Report from the First International Conference in Systems and Network Medicine. Syst Med (New Rochelle). 2020; 3(1):22-35. [https://www.ncbi.nlm.nih.gov/pubmed/32226924 PMID: 32226924].</li>
<li>Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform. 2020; 4:210-220. [https://www.ncbi.nlm.nih.gov/pubmed/32142370 PMID: 32142370].</li>
<li>Aoki-Kinoshita KF, Lisacek F, Mazumder R, York WS, Packer NH. The GlySpace Alliance: toward a collaborative global glycoinformatics community. Glycobiology. 2020; 30(2):70-71. [https://www.ncbi.nlm.nih.gov/pubmed/31573039 PMID: 31573039].</li>
<li>York WS, Mazumder R, Ranzinger R, et al. GlyGen: Computational and Informatics Resources for Glycoscience. Glycobiology. 2019. https://doi.org/10.1093/glycob/cwz080 [https://www.ncbi.nlm.nih.gov/pubmed/31616925 PMID: 31616925].</li>
<li>King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall K, Fochtman B, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao M, Mazumder R. Baseline human gut microbiota profile in healthy people and standard reporting template. PLOS ONE. 2019. [https://www.ncbi.nlm.nih.gov/pubmed/31509535 PMID: 31509535].</li>
<li>Fan Y, Hu Y, Yan C, Goldman R, Pan Y, Mazumder R, Dingerdissen H. Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer. Scientific Reports. PLoS One. 2018; 8():4322. [https://www.ncbi.nlm.nih.gov/pubmed/29531238 PMID: 29531238].</li>
<li>Baekdoo Kim, Thahmina Ali, Changsu Dong, Carlos Lijeron, Raja Mazumder, Claudia Wultsch, and Konstantinos Krampis. miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines. Journal of Computational Biology. 2018. http://doi.org/10.1089/cmb.2018.0218</li>
<li>Alterovitz G, Dean D A, Goble C, Crusoe M R, Soiland-Reyes S, Bell A, Hayes A, King, C H S, Taylor D, Johanson E, Thompson E E, Donaldson E, Morizono H, Tsang H S, Goecks J, Yao J, Almeida J S, Krampis K, Guo L, Walderhaug M, Walsh P, Kahsay R, Gottipati S, Bloom T, Lai Y, Simonyan V, Mazumder R. Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results. PLOS Biology; 16(12): e3000099. 2018. https://doi.org/10.1371/journal.pbio.3000099</li>
<li>Hu Y, Dingerdissen H, Gupta S, Kahsay R, Shanker V, Wan Q, Yan C, Mazumder R. Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. Computers in Biology and Medicine 2018; vol: 103 pp: 183-197. [https://www.ncbi.nlm.nih.gov/pubmed/30384176 PMID: 30384176].</li>
<li>Dingerdissen H, Torcivia-Rodriguez J, Hu Y, Chang T-C, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. Nucleic Acids Research. 2017. [https://pubmed.ncbi.nlm.nih.gov/30053270/ PMID: 30053270].</li>
<li>Karagiannis K, Simonyan V, Chumakov K, Mazumder R. Separation and assembly of deep sequencing data into discrete sub-population genomes. Nucleic Acids Research. 45(19):10989-11003. 2017. [https://www.ncbi.nlm.nih.gov/pubmed/28977510 PMID: 28977510].</li>
<li>Chen J, Zaidi S, Rao S, Chen J-S, Phan L, Farci P, Su X, Shetty K, White J, Zamboni F, Wu X, Rashid A, Pattabiraman N, Mazumder R, Horvath A, Wu R-C, Li S, Xiao C, Deng C-X, Wheeler D A, Mishra B, Akbani R, Mishra L. Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor beta Pathway. Gastroenterology. 2017; S0016-5085(17)36144-9. [https://www.ncbi.nlm.nih.gov/pubmed/28918914 PMID: 28918914].</li>
<li>Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C. A new and updated resource for codon usage tables. BMC Bioinformatics. 2017; 18(1):391. [https://www.ncbi.nlm.nih.gov/pubmed/28865429 PMID: 28865429].</li>
<li>Gannavaram S, Torcivia J, Gasparyan L, Kaul A, Ismail N, Simonyan V, Nakhasi HL. Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization. Sci Rep. 2017; 7(1):4718. [https://www.ncbi.nlm.nih.gov/pubmed/28680050 PMID: 28680050].</li>
<li>Simonyan V, Chumakov K, Donaldson E, Karagiannis K, Lam PV, Dingerdissen H, Voskanian A. HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls. Genomics. 2017; 109(3-4):131-140. [https://www.ncbi.nlm.nih.gov/pubmed/28188908 PMID: 28188908].</li>
<li>Pan Y, Yan C, Fan Y, Pan Q, Wan Q, Torcivia-Rodriquez J, Mazumder R. Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids. Scientific Reports. 2017; 7:42169 [https://www.ncbi.nlm.nih.gov/pubmed/28176830 PMID: 28176830].</li>
<li>Gulzar N, Dingerdissen H, Yan C, Mazumder R. Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins. Methods Mol Biol. 2017; 1558:159-190. [https://www.ncbi.nlm.nih.gov/pubmed/28150238 PMID: 28150238].</li>
<li>Simonyan V, Goecks J, Mazumder R. BioCompute objects - a step towards evaluation and validation of bio-medical scientific computations. PDA J Pharm Sci Technol. 2017; 71(2):136-146 [https://www.ncbi.nlm.nih.gov/pubmed/27974626 PMID: 27974626].</li>
<li>Yan C, Pattabiraman N, Goecks J, Lam P, Nayak A, Pan Y, Torcivia-Rodriquez J, Voskanian A, Wan Q, Mazumder R. Impact of germline and somatic missense variations on drug binding sites. Pharmacogenomics J. 2017; 17(2):128-136 [https://www.ncbi.nlm.nih.gov/pubmed/26810135 PMID: 26810135].</li>
<li>Novatt H, Theisen TC, Massie T, Simonyan V, Voskanian-Kordi A, Renn LA, Rabin RL. Distinct Patterns of Expression of Transcription Factors in Response to Interferon Beta and Interferon lambda-1. J Interferon Cytokine Res. 2016; 36(10):589-598 [https://www.ncbi.nlm.nih.gov/pubmed/27447339 PMID: 27447339].</li>
<li>Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Poison SW, Wang Y, Wu CH, UniProt Consortium. Computational clustering for viral reference proteomes. Bioinformatics. 2016; 32(13):2041-3 [https://www.ncbi.nlm.nih.gov/pubmed/27153712 PMID: 27153712].</li>
<li>Mahmood AS, Wu TJ, Mazumder R, Vijay-Shanker K. DiMeX: A text-mining system for mutation-disease association extraction. PLoS One. 2016; 11(4):e0152725 [https://www.ncbi.nlm.nih.gov/pubmed/27073839 PMID: 27073839].</li>
<li>Goldweber S, Theodore J, Torcivia-Rodriquez J, Simonyan V, Mazumder R. Pubcast and Genecast: Browsing and exploring publications and associated curated content in biology through mobile devices. IEEE/ACM Trans Comput Biol Bioinform. 2016; 14(2):498-500 [https://www.ncbi.nlm.nih.gov/pubmed/28113865 PMID: 28113865].</li>
<li>Laassri M, Zagorodnyaya T, Plant EP, Petrovskaya S, Bidzhieva B, Ye Z, Simonyan V, Chumakov K. Deep Sequencing for Evaluation of Genetic Stability of Influenza A/California/07/2009 (H1N1) Vaccine Viruses. PLoS One. 2015; 10(9):e0138650. [https://www.ncbi.nlm.nih.gov/pubmed/26407068 PMID: 26407068].</li>
<li>Sauder CJ, Ngo L, Simonyan V, Cong Y, Zhang C, Link M, Malik T, Rubin SA. Generation and propagation of recombinant mumps viruses exhibiting an additional U residue in the homopolymeric U tract of the F gene-end signal. Virus Genes. 2015; 51(1):12-24. [https://www.ncbi.nlm.nih.gov/pubmed/25962759 PMID: 25962759].</li>
<li>Wu T-J, Schriml LM, Chen Q-R, Colbert M, Crichton DJ, Finney R, Hu Y, Kibbe WA, Kincaid H, Meerzaman D, Mitraka E, Pan Y, Smith KM, Srivastava S, Ward S, Yan C, Mazumder R. Generating a focused view of Disease Ontology cancer terms for pan-cancer data integration and analysis. Database (Oxford). 2015; 2015:bav032. [https://www.ncbi.nlm.nih.gov/pubmed/25841438 PMID: 25841438].</li>
<li>Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu T-J, Yang C, Zhang H, Mazumder R. BioXpress: An integrated RNA-seq derived gene expression database for pan-cancer analysis. Database (Oxford). 2015; 2015. pii: bav019 [https://www.ncbi.nlm.nih.gov/pubmed/25819073 PMID: 25819073].</li>
<li>Kumari P, Mazumder R, Simonyan V, Krampis K. Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly. F1000Research. 2015; 4(20). [https://hsrc.himmelfarb.gwu.edu/cgi/viewcontent.cgi?article=1167&context=smhs_biochem_facpubs https://hsrc.himmelfarb.gwu.edu/cgi/viewcontent.cgi?article=1167&context=smhs_biochem_facpubs].</li>
<li>Abunimer A, Dingerdissen H, Torcivia-Rodriguez J, Vinh Nguyen Lam P, Mazumder R. Non-synonymous Single-Nucleotide Variations as Cardiovascular System Disease Biomarkers and Their Roles in Bridging Genomic and Proteomic Technologies. Biomarkers in Cardiovascular Disease. 2015. [https://link.springer.com/referenceworkentry/10.1007/978-94-007-7741-5_40-1 Springer Nature link].</li>
<li>Adhikari S, Chetram MA, Woodrick J, Mitra PS, Manthena PV, Khatkar P, Dakshanamurthy S, Dixon M, Karmahapatra SK, Nuthalapati NK, Gupta S, Narasimhan G, Mazumder R, Loffredo CA, Uren A, Roy R. Germ-line variants of human N-methylpurine DNA glycosylase show impaired DNA repair activity and facilitate 1,N6 ethenoadenine induced mutations. J Biol Chem. 2014; 290(8):4966-80. [https://www.ncbi.nlm.nih.gov/pubmed/25538240 PMID: 25538240].</li>
<li>Wilson CA and Simonyan V. FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies. PDA J Pharm Sci Technol. 2014; 68(6):626-630. [https://www.ncbi.nlm.nih.gov/pubmed/25475637 PMID: 25475637].</li>
<li>Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R. Census-based rapid and accurate metagenome taxonomic profiling. BMC Genomics. 2014; 15(1):918. [https://www.ncbi.nlm.nih.gov/pubmed/25336203 PMID: 25336203].</li>
<li>Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, Mazumder R. Human germline and pan-cancer variomes and their distinct functional profiles. Nucleic Acids Research. 2014; 42(18):11570-88. [https://www.ncbi.nlm.nih.gov/pubmed/25232094 PMID: 25232094].</li>
<li>Nayak A, Pattabiraman N, Fadra N, Goldman R, Pond S, Mazumder R. Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2. J Biomol Struct Dyn. 2014; 33(8):1682-94. [https://www.ncbi.nlm.nih.gov/pubmed/25245635 PMID: 25245635].</li>
<li>Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R. Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. Genomics. 2014; 104(1):1-7. [https://www.ncbi.nlm.nih.gov/pubmed/24930720 PMID: 24930720].</li>
<li>Santana-Quintero L, Dingerdissen H, Thierry-Mieg J, Mazumder R, Simonyan V. HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis. PLOS One. 2014; 9(6):e99033. [https://www.ncbi.nlm.nih.gov/pubmed/24918764 PMID: 24918764].</li>
<li>Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, Mazumder R. A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. Biol Direct. 2014; 9:9. [https://www.ncbi.nlm.nih.gov/pubmed/24894379 PMID: 24894379].</li>
<li>Bidzhieva B, Zagorodnyaya T, Karagiannis K, Simonyan V, Laassri M, Chumakov K. Deep sequencing approach for genetic stability evaluation of influenza A viruses. J Virol Methods. 2014; 199(68):75. [https://www.ncbi.nlm.nih.gov/pubmed/24406624 PMID: 24406624].</li>
<li>Abunimer A, Smith K, Wu T-J, Lam P, Simonyan V, Mazumder R. Single-nucleotide variations in cardiac arrhythmias: prospects for genomics and proteomics based variation detection. Genes. 2014; 5(2):254-69. [https://www.ncbi.nlm.nih.gov/pubmed/24705329 PMID: 24705329].</li>
<li>Wu T-J, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R. A framework for organizing cancer related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). Database. 2014; 2014:bau022. [https://www.ncbi.nlm.nih.gov/pubmed/24667251 PMID: 24667251].</li>
<li>Dabrazhynetskaya A, Soika V, Volokhov D, Simonyan V, Chizhikov V. Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050. Genome Announce. 2014; 2(2):pii: e00127-14. [https://www.ncbi.nlm.nih.gov/pubmed/24604646 PMID: 24604646].</li>
<li>Cole C, Krampis K, Karagiannis K, Almeida J, Faison JW, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. BMC Bioinformatics. 2014; 15:28. [https://www.ncbi.nlm.nih.gov/pubmed/24467687 PMID: 24467687].</li>
<li>Mudvari P, Kowsari K, Cole C, Mazumder R, Horvath A. Extraction of molecular features through exome to transcriptome alignment. J Metabol Sys Biol. 2013; 1(1):7. [https://www.ncbi.nlm.nih.gov/pubmed/24791251 PMID: 24791251].</li>
<li>Basuchoudhary A, Simonyan V, Mazumder R. Community annotation and the evolution of cooperation: How patience matters. Open Bioinformatics Journal. 2013; 7:9-18.</li>
<li>Karagiannis K, Simonyan V, Mazumder R. SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways. Genomics Proteomics Bioinformatics. 2013; 11(2):122-126. [https://www.ncbi.nlm.nih.gov/pubmed/23618375 PMID: 23618375].</li>
<li>Lam PV, Goldman R, Karagiannis K, Narsule T, Simonyan V, Soika V, Mazumder R. Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes. Genomics Proteomics Bioinformatics. 2013; 11(2):96-104. [https://www.ncbi.nlm.nih.gov/pubmed/23459159 PMID: 23459159].</li>
<li>Dingerdissen H, Motwani M, Karagiannis K, Simonyan V, Mazumder R. Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins. FEBS J. 2013; 280(6):1542-1562. [https://www.ncbi.nlm.nih.gov/pubmed/23350563 PMID: 23350563].</li>
<li>Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R. Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference. Database (Oxford). 2012; 2012:bas036. [https://www.ncbi.nlm.nih.gov/pubmed/23110974 PMID: 23110974].</li>
<li>Volokhov DV, Simonyan V, Davidson MK, Chizhikov VE. RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene phylogenetic analysis and identification of the species of the family Mycoplasmataceae. Mol Phylogenet Evol. 2012; 62(1):515-28. [https://www.ncbi.nlm.nih.gov/pubmed/22115576 PMID: 22115576].</li>
<li>Mazumder R, Morampudi KS, Motwani M, Vasudevan S, Goldman R. Proteome-wide analysis of single-nucleotide variations in the N-glycosylation sequon of human genes. PLoS One. 2012; 7(5):e36212. [https://www.ncbi.nlm.nih.gov/pubmed/22586465 PMID: 22586465].</li>
</ul>

Getting Recommendations from HIVE Lab Faculty and Staff

2025-09-24T17:19:40Z

Rehmam: Created page with "If you are a current or former member of the HIVE Lab and would like to request a recommendation, please follow the steps below. Providing complete and accurate information will help us prepare a stronger and more personalized letter on your behalf. == Steps for Requesting a Recommendation == '''Step 1. Submit the Request''' Send all recommendation requests from each organization to: '''mazumder_lab@gwu.edu''' '''Step 2. Updated LinkedIn Profile''' Include a link to..."

If you are a current or former member of the HIVE Lab and would like to request a recommendation, please follow the steps below. Providing complete and accurate information will help us prepare a stronger and more personalized letter on your behalf.

== Steps for Requesting a Recommendation ==
'''Step 1. Submit the Request'''

Send all recommendation requests from each organization to: '''mazumder_lab@gwu.edu'''

'''Step 2. Updated LinkedIn Profile'''

Include a link to your updated LinkedIn profile. Please ensure that your profile shows you are a member of the '''GW Bioinfo & Biochem Students and Alumni''' group. This insures you stay informed and connected with the community.

'''Step 3. Relationship Details'''

Specify the dates you worked with the lab or were involved and in what capacity (e.g., student, colleague, collaborator).

* If you were a student, include the course number(s) and your grades.

'''Step 4. Key Achievements and Characteristics'''

List your major accomplishments while in the lab and indicate which traits or qualities you would like emphasized in your recommendation letter.

* Bullet points are welcome.

'''Step 5. Short Bio Paragraph'''

Provide a concise bio summarizing your background, interests, and experiences.

'''Step 6. Submission Details'''

Clearly outline how and where the recommendation should be submitted (e.g., online portal link, email address, mailing address).

People

2025-09-24T17:03:33Z

Rehmam:

<div style="text-align: center; width: 100%;">
[[File:staircasepic.jpg|center|950px]]
</div><h2>GW Faculty</h2>
<table>
<tr>
<td style="text-align: center; padding: 25px">
[[File:Raja-Mazumder.png|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Raja%20Mazumder&FacID=2067473740| Raja Mazumder]</span>, Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File:Robel.Kahsay.jpg|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Robel%20Kahsay&FacID=2051216059| Robel Kashay]</span>, Asst Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File:McNeely.Patrick.jpg|130px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Patrick%20McNeely&FacID=2065037504&show=1| Pat McNeely]</span>, Asst Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File: Jonathon.Keeney.png|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Jonathon%20Keeney&FacID=2056964816| Jonathon Keeney]</span>, Asst Professor]]
</td>
</tr>
</table>
<h2>PI</h2>
<p>
[https://orcid.org/0000-0001-8823-9945 Raja Mazumder] -
[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Raja%20Mazumder&FacID=2067473740 Faculty Bio]
</p>

<h2>Past FDA HIVE Project Lead/s</h2>

Vahan Simonyan (FDA-HIVE)<br>Konstantinos Karagiannis (FDA-HIVE)

<h2>Current GW HIVE Lab Members</h2>
<table>
<tr>
<td style="vertical-align: top;">
<ul>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Daniall Masood]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Kate Warner]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Tianyi Wang]</li>
<li>[https://orcid.org/0009-0000-7970-7815 Christie Woodside]</li> </ul>
</td>
<td style="padding-left: 20px; vertical-align: top;">
<ul>
<li>[https://orcid.org/0000-0002-5317-1458 Jeet Kiran Vora]</li>
<li>[https://orcid.org/0009-0007-4585-7314 Lori Krammer]</li>
<li>[https://orcid.org/0000-0001-8823-9945 Raja Mazumder]</li>
<li>[https://orcid.org/0000-0002-5381-9744 Urnisha Bhuiyan]</li> </ul>
</td>
<td style="padding-left: 20px; vertical-align: top;">
<ul>
<li>[https://orcid.org/0000-0002-7665-6204 Jonathon Keeney]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Patrick McNeely]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Robel Kahsay]</li><li>[https://orcid.org/0009-0002-5733-1495 Maria Kim]</li>
</ul>
</td>
</tr>
</table>
<h2>Current Volunteers and Part-time Members</h2>
<table>
<tr>
<td style="vertical-align: top;">
<ul>
<li>[https://www.linkedin.com/in/rehma-malik/ Rehma Malik]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Cyrus Chun Hong AU YEUNG]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Nikhil Aritheya]</li> </ul>
</td></tr>
</table>[[File:HIVE mini picnic.jpg|center|thumb|671x671px|Lab members enjoying a summer picnic with the extended HIVE community at the Seneca Creek State Park, MD on June 19, 2025.]]

Events

2025-09-23T16:32:23Z

Rehmam:

<h2>Current/Past Events</h2>
<ul>
<li style="margin-bottom: 15px;">
[https://wiki.glygen.org/GlySpace_Alliance_Webinar_Series GlySpace Alliance / GlyGen Webinar Series]<br>
Frequency: monthly
</li>
<li style="margin-bottom: 15px;">
[[Symposium 2025|HIVE Lab Summer Symposium]]<br>
July 31, 2025 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
[[2025 Bioinformatics Symposium]]<br>
April 29, 2025 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
[https://wiki.glygen.org/GlyGen_and_Foundation_for_Advanced_Education_in_the_Sciences_(FAES)_2024_Workshop 2024 GlyGen-FAES Workshop] <br>
Nov 4, 2024 at FAES-NIH in Bethesda, MD, USA
</li>
<li style="margin-bottom: 15px;">
[https://wiki.biocomputeobject.org/BioCompute_Conference_and_Workshop#Conference_Webinar 2024 BioCompute Conference and Workshop] <br>
May 10, 2024 at FDA in White Oak, MD, USA
</li>
<li style="margin-bottom: 15px;">
[https://www.biocomputeobject.org/ 2019 BioCompute Workshop] <br>
May 14, 2019 at FDA in White Oak, MD, USA
</li>
<li style="margin-bottom: 15px;">
2018 OncoMX Workshop <br>
May 22 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
2018 Glycoinformatics Tools Workshop <br>
Mar 16 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
2018 BioCompute PoC Workshop <br>
Mar 23 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
2017 HTS Computational Standards for Regulatory Sciences Workshop <br>
Mar 16-17 at NIH in Bethesda, MD, USA
</li>
<li style="margin-bottom: 15px;">
2014 Next Generation Sequencing Standards <br>
Sep 24-25 at NIH in Bethesda, MD, USA
</li>
</ul>

Opportunities

2025-09-19T13:28:55Z

Rehmam:

<h2>List of Open Positions</h2>
<p>We have several open positions. View the requirements, relevant projects, and how to [https://docs.google.com/document/d/1nwHVHqCMblQRNodHCsXMzKkvzo_LM7sHyAWYTkRUtFY/edit?tab=t.0#heading=h.oto5l8zzalb apply here].</p>

<h2>Research Opportunities Here at GW</h2>
<p>We usually have full-time and part-time positions open. Part-time positions are usually 20 hours/week. Individuals with bioinformatics, biocuration, and/or programming backgrounds are encouraged to contact mazumder_lab AT gwu.edu for details regarding part-time positions.</p>

<h2>Volunteer Positions</h2>
<p>Students interested in helping with biocuration and the testing of software and databases can apply. Primary responsibilities will be focused on routine biocuration and testing, but may be expanded to include a role in research projects depending on skill and interest level. Candidates do not necessarily need to have advanced knowledge of genomics or coding (previous experience is a plus), but should have a strong interest in bioinformatics and be dedicated to the role as a member of the team. May work remotely if necessary, but will be expected to join routine meetings virtually. All internships are a minimum of eight weeks.</p><p>Our lab runs volunteer cohorts during the fall, spring and summer semesters. Applications for the Spring 2025 cohort will open soon.</p><p>Interested candidates should email their resume to [mailto:mazumder_lab@gwu.edu HIVE Lab].</p>

<h2>Research Staff Positions</h2>
<h3>Research Assistant / Research Associate (Closed)</h3>
<p>The research assistant or associate should have knowledge of at least one of the following: glycobiology, biochemistry, genomics, proteomics, data science, and other informatics. This individual will be responsible for the maintenance and update of knowledgebase datasets and coordinating weekly, bi-weekly, monthly, and annual project meetings with collaborators and stakeholders. This individual will also be responsible for creating project reports, presentation slides, and posters along with maintaining the project’s Agile boards for our group. This position also requires an understanding of bioinformatics, and hands-on experience with bioinformatics tools and resources is a plus, as well as familiarity with data science technologies. For more information, please send a CV and cover letter to [mailto:mazumder_lab@gwu.edu HIVE Lab].</p>

<h2>Post-Doctoral Research Positions</h2>
<h3>Post-Doctoral Scientist - Glycobiology (Closed)</h3>
<p>The Post-Doctoral Scientist will work on an NIH-funded project. This individual will have extensive knowledge of data standardization, carbohydrate chemistry, biochemistry, proteomics, and existing glycobiology and protein-related resources. They will be responsible for the maintenance and update of datasets and attending and sometimes planning weekly, bi-weekly, monthly, and annual project meetings with collaborators and stakeholders. The Post-Doctoral Scientist will also be responsible for creating project reports, presentation slides, and posters along with drafting publications with key collaborators.</p>
<p><strong>Minimum Qualifications:</strong> Applicant must have a terminal degree (PhD, MD/PhD, or equivalent) at the time of appointment and demonstrable experience in glycobiology.<br>
For more information please visit https://www.gwu.jobs/postings/51870.</p>

<h3>Post-Doctoral Scientist - Computer Science</h3>
<p>The Post-Doctoral Scientist will work on government/commercial funded project involved in the development of glycoinformatics and cancer knowledge bases. This individual will have extensive knowledge of Python, MySQL, SPARQL, JavaScript, and RESTful APIs. They will be responsible for processing data using various pipelines that feed our HIVE Lab knowledgebase resources, and attending and sometimes planning weekly, bi-weekly, monthly, and annual project meetings with collaborators and stakeholders. The Post-Doctoral Scientist will also be responsible for creating project reports, presentation slides, and posters along with drafting publications with other key collaborators.</p>
<strong>Minimum Qualifications:</strong> Applicant must have a terminal degree (PhD, MD/PhD, or equivalent) at the time of appointment and demonstrable experience in Computer Science.<br>
For more information please send a CV and cover letter to [mailto:mazumder_lab@gwu.edu HIVE Lab]

<h2>Research Faculty Positions</h2>
<h3>Research Assistant Professor/Scientific Coordinator</h3>
<p>The Department of Biochemistry and Molecular Medicine at The George Washington University’s School of Medicine and Health Sciences is seeking applications for a full-time (12-month) faculty position to be filled at the rank of Assistant Professor (non-tenure). Salary will be commensurate with experience. The successful candidate will have an active role in the development of knowledgebases, coordinate data integration activities, develop detailed milestones, and lead other project members. They will be expected to regularly reach out to the scientific community (domestic and international) to develop new collaborations and pursue existing ones, while also attending and planning weekly, bi-weekly, monthly, and annual project meetings with collaborators and stakeholders. Conducting bioinformatics experiments on integrated data to showcase utility of integration will be part of developing and writing project reports, presentation slides, posters, manuscripts, and detailed read-me files. The development of new projects related to or complementary to the HIVE Lab interests is also a possibility.</p>
<strong>Minimum Qualifications:</strong> Applicant must have a terminal degree (PhD, MD/PhD, or equivalent) at the time of appointment and demonstrable experience in glycobiology and proven leadership capability.<br>
For more information please send a CV and cover letter to [mailto:mazumder_lab@gwu.edu HIVE Lab].

<h2>Visit the Department of Biochemistry</h2>
<p>[https://biochemistry.smhs.gwu.edu/ Visit the Department of Biochemistry and Molecular Medicine]</p>

Events

2025-09-19T13:21:45Z

Rehmam:

<h2>Current/Past Events</h2>
<ul>
<li style="margin-bottom: 15px;">
[https://wiki.glygen.org/GlySpace_Alliance_Webinar_Series GlySpace Alliance / GlyGen Webinar Series]<br>
Frequency: monthly
</li>
<li style="margin-bottom: 15px;">
[[2025 Bioinformatics Symposium|HIVE Lab Summer Symposium]]<br>
July 31, 2025 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
[[2025 Bioinformatics Symposium]]<br>
April 29, 2025 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
[https://wiki.glygen.org/GlyGen_and_Foundation_for_Advanced_Education_in_the_Sciences_(FAES)_2024_Workshop 2024 GlyGen-FAES Workshop] <br>
Nov 4, 2024 at FAES-NIH in Bethesda, MD, USA
</li>
<li style="margin-bottom: 15px;">
[https://wiki.biocomputeobject.org/BioCompute_Conference_and_Workshop#Conference_Webinar 2024 BioCompute Conference and Workshop] <br>
May 10, 2024 at FDA in White Oak, MD, USA
</li>
<li style="margin-bottom: 15px;">
[https://www.biocomputeobject.org/ 2019 BioCompute Workshop] <br>
May 14, 2019 at FDA in White Oak, MD, USA
</li>
<li style="margin-bottom: 15px;">
2018 OncoMX Workshop <br>
May 22 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
2018 Glycoinformatics Tools Workshop <br>
Mar 16 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
2018 BioCompute PoC Workshop <br>
Mar 23 at GW in Washington, DC, USA
</li>
<li style="margin-bottom: 15px;">
2017 HTS Computational Standards for Regulatory Sciences Workshop <br>
Mar 16-17 at NIH in Bethesda, MD, USA
</li>
<li style="margin-bottom: 15px;">
2014 Next Generation Sequencing Standards <br>
Sep 24-25 at NIH in Bethesda, MD, USA
</li>
</ul>

Volunteership 2025

2025-07-24T14:19:57Z

Rehmam:

For Fall opportunities, [[Volunteership Fall 2025|click here to view our Fall 2025 Volunteership Program]].<h2>2025 Volunteer Program Details</h2>

<h3>Dates</h3>
<strong>Volunteer Zoom Kick-Off Meeting</strong><br>
May 27, 2025 | 3:30 to 4:30 PM

<strong>Program Dates: June 2nd, 2025 – July 25th, 2025</strong> (8 weeks)<br>
Monday to Friday | Remote | No breaks

<hr>

<h3>Volunteer Expectations</h3>
<ol>
<li>Daily progress updates via Slack (scrum).</li>
<li>Regular Zoom meetings with the assigned project point of contact.</li><li>Expected to dedicate 5–6 hours per day to project work, with the remaining time focused on skill development or reading. </li>
</ol>
<p style="color: red;"><strong>Important:</strong> If the scrum is not updated for 2 consecutive days, the candidate will be <u>automatically dropped</u> from the program.</p>
<hr>

<h3>Potential Projects</h3>
<ol>
<li>BiomarkerKB ([https://biomarkerkb.org biomarkerkb.org]) project: Biomarker curation project. Involves reading papers and collecting biomarkers.</li>
<li>GlyGen ([https://glygen.org glygen.org]) project: Review glycomics and glycoproteomics data and curate tissue, disease, and other related information. </li><li>ARGOS ([https://argosdb.org argosdb.org]) project: Analyze genomics data using HIVE to identify reference genome assemblies. </li><li>PredictMod ([https://hivelab.biochemistry.gwu.edu/predictmod hivelab.biochemistry.gwu.edu/predictmod]) project. Identifying datasets and harmonizing them so that they can be used to generate ML models. </li></ol>''Note: Individuals involved in the above projects with a background in programming and/or machine learning may also undertake additional tasks to support the development of ML models, which can be integrated into PredictMod or used to enhance AI/ML-ready datasets within GlyGen.''<hr>

<h4>1. BiomarkerKB Biocuration Project Ideas</h4>POC: Daniall Masood, Maria Kim
# Curate biomarkers for a specific disease (Alzheimers)
## The student would be doing manual curation for about 4 weeks, with regular check-ins with me to ensure it is being done correctly.
## The next 4 weeks can be dedicated to developing an LLM or an automated process to extract biomarker details with data collected in the first 4 weeks as training data/example data.
# Top 50 biomarkers
## Curate the top 50 biomarkers for biomarkerkb.org.
## Define what constitutes a top 50 biomarker.
## Begin curating biomarkers from different sources and papers by collecting fields mentioned in the data model, as well as collecting cross-references.
# Biocuration of biomarkers from NLP/LLM work
## Use the biomarkers collected from NLP work.
## Curate biomarkers. Data provided was not provided in the biomarker data model.
## While curating the biomarkers, check if data collected from NLP is correct.
## After completion, the student can start using curated data to work on the NLP/LLM method.
# Curate biomarkers for a treatment
## See #1 above.

If the student has any other ideas, diseases, treatments, or methods they want to focus on, please reach out to daniallmasood@gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.

==== 2. GlyGen Biocuration Project Ideas ====
POC: Rene Ranzinger and Urnisha Bhuiyan

Over the last three decades, numerous glycomics database projects have been initiated to collect valuable information about glycans, proteins, and their interactions. Some of these databases have been discontinued due to the end of project funding. However, the data within these databases remains highly valuable to the community. Integrating these datasets into modern databases or knowledgebases, such as GlyGen, presents a challenge because much of the valuable metadata (e.g., species, tissue, disease, cell line) annotations are free-text terms that do not align with established standard dictionaries and ontologies used in modern resources. Automated matching of this information with dictionaries or ontologies is often not possible due to the use of synonyms, spelling errors, or abbreviations. For example, "human," "man," and "h. sapiens" all map to the scientific species name "Homo sapiens."

The GlyGen project aims to make datasets from two older databases (CarbBank, CFG) accessible by migrating the data and metadata into our database. For this project, we are seeking curators with a medical or biology background who are interested in helping map metadata terms from these old databases to standard dictionaries and ontologies.

The project involves:

# Using internet resources (e.g., Google, Wikipedia) to identify terms used in the old database.
# Mapping identified terms to corresponding dictionaries and ontologies using the webpages and search interfaces of these projects.
# Finding papers based on titles and author lists that may contain spelling errors.
# Interacting and discussing with other curators in case terms are mapped differently.

If you have any other ideas or methods you would like to focus on, please reach out to rene@ccrc.uga.edu to discuss them.

'''3. GlyGen Publication Analysis Project Ideas'''

POC: Rene Ranzinger and Urnisha Bhuiyan

One of the challenges for any bioinformatics project is understanding the size of its community, how well the project serves this community, and how widely its software/database is used. A potential solution is to analyze PubMed publication data. We are seeking applicants with programming skills (in Python or Java) to perform this analysis.

The project involves:

# Using the PubMed web API to filter publications based on keywords.
# Analyzing paper abstracts to identify research institutions and groups that form the community.
# Filtering the community list to exclude unrelated co-authors.
# Prioritize papers identified by GlycoSiteMiner for curation via TableMaker

A subproject will involve analyzing the full text of papers (when available) for keywords or resource and database names. The results of the analysis will be discussed with GlyGen project member who will suggest changes and improvements to the analysis and data presentation. Source code developed as part of this project will be documented and shared in a public GitHub repository. If you have any other ideas or methods you would like to explore, please reach out to rene@ccrc.uga.edu to discuss them.

==== 4. PredictMod Machine Learning Project Ideas ====
POC: Lori Krammer

Data Identification & Curation:

# Identify publicly-available datasets from scientific literature that can be used for intervention outcome prediction models.
# Curate indicators of useful ML publications that could be used to train an LLM to recommend relevant publications for cancer modeling.

Modeling & Integration (for those with experience in programming/ML)

# Conduct data harmonization and pre-processing following established project pipelines to make ML-ready dataset and data dictionary.
# Perform model training and document ML pipeline in a BioCompute Object (BCO).
# Integrate model into PredictMod platform.

Individuals with a background or interest in machine learning should reach out to lorikrammer@gwu.edu with a potential dataset to determine if it is a feasible project for the summer.

'''5. FDA-ARGOS Computation and Pathogen Curation Project'''

POC: Christie Woodside, Jonathon Keeney

# Update data tables for more efficient computations
## Student would review and input additional data and IDs in the tables/sheets used to perform computations. This would be manual work (but super important), but would require high attention to detail. ~1 week's worth of work
## Requires Python/shell coding background. Student would run scripts that prepare and format data tables that are pushed to data.argosdb.org. Coding knowledge is needed in case of errors, bugs, or other mishaps in the code. Ongoing work as computations are performed.
# Curate and report on current pathogens to upload to ARGOS
## Student would work on manual curation of circulating pathogens to be added to data.argosdb.org. Regular check-ins and reports of what was found. ~4-10 weeks worth of work
## Locate assembly IDs, reads, and metagenomic information for these pathogens to be used in computations and deposited into data.argosdb.org.
## Provide documentation on why they were curated, why they are important, how they were selected, and how data was collected.

If the student has any other ideas or methods they want to focus on, please reach out to christie.woodside@email.gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.<hr>
<h3>Requirements for Completion</h3>
<p><strong>Note:</strong> The following are <u>mandatory</u>. Failure to complete any will result in an incomplete volunteer record.</p>

<h4>Documentation</h4>
<p>All volunteers must maintain adequate documentation of their work, including written protocols and scripts submitted to GitHub.</p>

<h4>Written Report</h4>
<p>Submit a 1–2 page summary of your tasks and accomplishments to the Admin during the final week of your program.</p>

<h4>Presentation & Slide Submission</h4>
<p>Present your work last week of the 8-week period.</p>
<p>Slides must be submitted to the Admin Team and should include:</p>
<ul>
<li>See Symposium Slides Guidelines below</li></ul>
Contact the Admin Team to access previously submitted slides.
<hr>

=== Completion Certificate ===
A certificate of completion and a letter of recommendation will be provided to all participants who successfully complete the program.
<hr>
=== Contact ===
mazumder_lab@gwu.edu.
<hr>
=== Volunteers ===
{| class="wikitable"
|+
|-
! Name
!Project
!Projects Interested
|-
| [https://www.linkedin.com/in/gracesjchong/ Grace Chong]
|PredictMod
|
# PredictMod
# BiomarkerKB Biocuration
# GlyGen Biocuration
|-
|[https://www.linkedin.com/in/alma-ogunsina-4959072b1/ Alma Ogunsina]
|Biomarker curation
|
# BiomarkerKB
# ARGOS
# PredictMod
|-
|[https://www.linkedin.com/in/diya-kamalabharathy-62557935a/ Diya Kamalabharathy]
|PredictMod
|
# BiomarkerKB Biocuration
# PredictMod Machine Learning
# GlyGen Biocuration
|-
|[https://www.linkedin.com/in/harivinay-prasad-reddy-gujjula-a06ba71bb/ Harivinay P. Gujjula]
|GlyGen curation
|
# GlyGen Biocuration
# BioMarkerKB Biocuration
|-
|[https://www.linkedin.com/in/miao-wang-88b602290/Miao Wang Miao Wang]
|ARGOS
|
# BiomarkerKB Biocuration Project Ideas
# FDA-ARGOS Computation and Pathogen Curation Project
# PredictMod Machine Learning Project Ideas
|-
|[https://www.linkedin.com/in/nahom-gebreselassie-1545ab336/ Nahom Abel]
|GlyGen curation
|
# BiomarkerKB Biocuration
# GlyGen Biocuration
# PredictMod
|-
|[https://www.linkedin.com/in/kajal-patel-cs/ Kajal Sanjaykumar Patel]
|GlyGen and PubMed project
|
#PredictMod
#BiomarkerKB
#GlyGen
|-
|[https://www.linkedin.com/in/john-mccaffrey-b8850930a/ John McCaffrey]
|Biomarker curation
|
# PredictMod
# BiomarkerKB
# GlyGen Biocuration
|-
|[https://www.linkedin.com/in/nathan-ressom/ Nathan Ressom]
|BiomarkerKB
|
# PredictMod
# GlyGen Biocuration
# BiomarkerKB Biocuration
|-
|[https://www.linkedin.com/in/aaron-ressom/ Aaron Ressom]
|PredictMod
|
# BiomarkerKB
# PredictMod
# GlyGen
|-
|[https://www.linkedin.com/in/akale-kinfe/ Akale Kinfe]
|Biomarker curation
|
# BiomarkerKB Biocuration
# GlyGen Biocuration
# ARGOS
|-
|[https://www.linkedin.com/in/aise-arpinar-a8bb9b373/?original_referer= Aise Arpinar]
|GlyGen curation
|
# GlyGen Biocuration
# BiomarkerKB Biocuration
# GlyGen Publication Analysis
|-
|[https://www.linkedin.com/in/piyush-pandey-906b582b5/ Piyush Pandey]
|Biomarker curation
|
# BiomarkerKB Biocuration
# PredictMod
# GlyGen Biocuration
|-
|[http://www.linkedin.com/in/filmawit-zeru-203272363 Filmawit Zeru]
|GlycoSiteMiner project
|
# BiomarkerKB
# GlyGen
# ARGOS
|-
|[https://www.linkedin.com/in/mathias-belay-03b51a2a3/ Mathias Belay]
|Biomarker curation
|
# GlyGen
# PredictMod
# BiomarkerKB
|-
|[https://www.linkedin.com/in/isaac-kim-b644bb231/ Isaac Kim]
|Biomarker curation
|
# BiomarkerKB
# PredictMod
# GlyGen
|-
|[https://www.linkedin.com/in/sohana-bahl-6549a2376/ Sohana Bahl]
|Biomarker curation
|
# BiomarkerKB
|-
|[https://www.linkedin.com/in/ana-vohralikova-794a4433a?utm_source=share&utm_campaign=share_via&utm_content=profile&utm_medium=ios_app Ana Vohralikova]
|Biomarker curation
|
# BiomarkerKB Biocuration Project
# GlyGen Biocuration Project
# FDA-ARGOS Computation and Pathogen
|}

<hr>

=== Symposium Slide Guidelines ===
'''Content Clarity'''

   •   '''Keep It Simple:''' Use concise bullet points instead of long paragraphs. Aim for no more than 6 bullet points per slide.

•    '''Focus on Key Points:''' Highlight the main ideas or data you want your audience to remember.

•    '''Consistent Layout:''' Use a consistent layout for each slide, including fonts, colors, and background. This helps maintain a professional look.

•    '''High-Quality Images:''' Use high-resolution images and graphics to illustrate your points. Avoid using clip art.

•    '''Readable Fonts:''' Use easy-to-read fonts (e.g., Arial, Calibri) and ensure font sizes are large enough to be seen from a distance (24 pt or larger for main text).

•    '''Contrast:''' Ensure there is high contrast between text and background (e.g., dark text on a light background).

•    '''Citation:''' Cite a publication to support the information presented in proper citation format.

'''Outline for Symposium presentation'''

1. Introduction:

2. Project Descriptions

3. Objectives and Goals:

4. Methods, Results, Achievements and Contributions:

5. Future Plans:

6. Skills and Knowledge Gained:

7. Acknowledgments:

8. Q&A Session:

'''Outline'''

'''1. Introduction:''' (1 slide)

- Briefly introduce yourself.

- Add your picture and name on the introduction slide. If it is group add the group picture.

'''2. Project Descriptions:''' (1 slide)

- Provide context and background information about the project.

'''3. Project Objectives and Goals:''' (1 slide)

- Describe the main objectives of the project or initiative.

- Discuss any additional goals or desired outcomes.

- Explain why these objectives and goals are important.

'''4. Methods, Results, Achievements and Contributions:'''

- Highlight the methods/tools used in the project.

- Highlight the key results and outcomes of the project.

- Discuss the most significant achievements and milestones reached.

- Explain how each member of the team project contributed to the project (for group project)

''' '''

'''5. Future Plans'''

- Next steps or future plans for the project

'''6. Skills and Knowledge Gained:''' (1 slide)

- Detail any technical skills acquired or improved.

- Highlight any soft skills, such as communication or teamwork, that were developed.

- Discuss new knowledge gained in specific areas or subjects.

- Share any personal reflections on the experience and what was learned.

- Discuss any challenges or obstacles encountered and how they were overcome.

- Provide key insights or lessons learned from the project.

'''7. Acknowledgments:''' ''':''' (1 slide)

- Acknowledge the contributions of team members and collaborators.

- Recognize the guidance and support of mentors and advisors.

- Acknowledge the Project Funding. Eg. CFDE

'''8. Q&A Session:'''

- Invite the audience to ask questions and engage in discussion.

- Provide clear and thoughtful responses to audience questions.

- Offer closing remarks and thank the audience for their participation.

Note – If you have limited presentation time you can also merge few topics into one.

Volunteership 2025

2025-07-23T17:08:04Z

Rehmam:

For Fall opportunities, [[Volunteership Fall 2025|click here to view our Fall 2025 Volunteership Program]].<h2>2025 Volunteer Program Details</h2>

<h3>Dates</h3>
<strong>Volunteer Zoom Kick-Off Meeting</strong><br>
May 27, 2025 | 3:30 to 4:30 PM

<strong>Program Dates: June 2nd, 2025 – July 25th, 2025</strong> (8 weeks)<br>
Monday to Friday | Remote | No breaks

<hr>

<h3>Volunteer Expectations</h3>
<ol>
<li>Daily progress updates via Slack (scrum).</li>
<li>Regular Zoom meetings with the assigned project point of contact.</li><li>Expected to dedicate 5–6 hours per day to project work, with the remaining time focused on skill development or reading. </li>
</ol>
<p style="color: red;"><strong>Important:</strong> If the scrum is not updated for 2 consecutive days, the candidate will be <u>automatically dropped</u> from the program.</p>
<hr>

<h3>Potential Projects</h3>
<ol>
<li>BiomarkerKB ([https://biomarkerkb.org biomarkerkb.org]) project: Biomarker curation project. Involves reading papers and collecting biomarkers.</li>
<li>GlyGen ([https://glygen.org glygen.org]) project: Review glycomics and glycoproteomics data and curate tissue, disease, and other related information. </li><li>ARGOS ([https://argosdb.org argosdb.org]) project: Analyze genomics data using HIVE to identify reference genome assemblies. </li><li>PredictMod ([https://hivelab.biochemistry.gwu.edu/predictmod hivelab.biochemistry.gwu.edu/predictmod]) project. Identifying datasets and harmonizing them so that they can be used to generate ML models. </li></ol>''Note: Individuals involved in the above projects with a background in programming and/or machine learning may also undertake additional tasks to support the development of ML models, which can be integrated into PredictMod or used to enhance AI/ML-ready datasets within GlyGen.''<hr>

<h4>1. BiomarkerKB Biocuration Project Ideas</h4>POC: Daniall Masood, Maria Kim
# Curate biomarkers for a specific disease (Alzheimers)
## The student would be doing manual curation for about 4 weeks, with regular check-ins with me to ensure it is being done correctly.
## The next 4 weeks can be dedicated to developing an LLM or an automated process to extract biomarker details with data collected in the first 4 weeks as training data/example data.
# Top 50 biomarkers
## Curate the top 50 biomarkers for biomarkerkb.org.
## Define what constitutes a top 50 biomarker.
## Begin curating biomarkers from different sources and papers by collecting fields mentioned in the data model, as well as collecting cross-references.
# Biocuration of biomarkers from NLP/LLM work
## Use the biomarkers collected from NLP work.
## Curate biomarkers. Data provided was not provided in the biomarker data model.
## While curating the biomarkers, check if data collected from NLP is correct.
## After completion, the student can start using curated data to work on the NLP/LLM method.
# Curate biomarkers for a treatment
## See #1 above.

If the student has any other ideas, diseases, treatments, or methods they want to focus on, please reach out to daniallmasood@gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.

==== 2. GlyGen Biocuration Project Ideas ====
POC: Rene Ranzinger and Urnisha Bhuiyan

Over the last three decades, numerous glycomics database projects have been initiated to collect valuable information about glycans, proteins, and their interactions. Some of these databases have been discontinued due to the end of project funding. However, the data within these databases remains highly valuable to the community. Integrating these datasets into modern databases or knowledgebases, such as GlyGen, presents a challenge because much of the valuable metadata (e.g., species, tissue, disease, cell line) annotations are free-text terms that do not align with established standard dictionaries and ontologies used in modern resources. Automated matching of this information with dictionaries or ontologies is often not possible due to the use of synonyms, spelling errors, or abbreviations. For example, "human," "man," and "h. sapiens" all map to the scientific species name "Homo sapiens."

The GlyGen project aims to make datasets from two older databases (CarbBank, CFG) accessible by migrating the data and metadata into our database. For this project, we are seeking curators with a medical or biology background who are interested in helping map metadata terms from these old databases to standard dictionaries and ontologies.

The project involves:

# Using internet resources (e.g., Google, Wikipedia) to identify terms used in the old database.
# Mapping identified terms to corresponding dictionaries and ontologies using the webpages and search interfaces of these projects.
# Finding papers based on titles and author lists that may contain spelling errors.
# Interacting and discussing with other curators in case terms are mapped differently.

If you have any other ideas or methods you would like to focus on, please reach out to rene@ccrc.uga.edu to discuss them.

'''3. GlyGen Publication Analysis Project Ideas'''

POC: Rene Ranzinger and Urnisha Bhuiyan

One of the challenges for any bioinformatics project is understanding the size of its community, how well the project serves this community, and how widely its software/database is used. A potential solution is to analyze PubMed publication data. We are seeking applicants with programming skills (in Python or Java) to perform this analysis.

The project involves:

# Using the PubMed web API to filter publications based on keywords.
# Analyzing paper abstracts to identify research institutions and groups that form the community.
# Filtering the community list to exclude unrelated co-authors.
# Prioritize papers identified by GlycoSiteMiner for curation via TableMaker

A subproject will involve analyzing the full text of papers (when available) for keywords or resource and database names. The results of the analysis will be discussed with GlyGen project member who will suggest changes and improvements to the analysis and data presentation. Source code developed as part of this project will be documented and shared in a public GitHub repository. If you have any other ideas or methods you would like to explore, please reach out to rene@ccrc.uga.edu to discuss them.

==== 4. PredictMod Machine Learning Project Ideas ====
POC: Lori Krammer

Data Identification & Curation:

# Identify publicly-available datasets from scientific literature that can be used for intervention outcome prediction models.
# Curate indicators of useful ML publications that could be used to train an LLM to recommend relevant publications for cancer modeling.

Modeling & Integration (for those with experience in programming/ML)

# Conduct data harmonization and pre-processing following established project pipelines to make ML-ready dataset and data dictionary.
# Perform model training and document ML pipeline in a BioCompute Object (BCO).
# Integrate model into PredictMod platform.

Individuals with a background or interest in machine learning should reach out to lorikrammer@gwu.edu with a potential dataset to determine if it is a feasible project for the summer.

'''5. FDA-ARGOS Computation and Pathogen Curation Project'''

POC: Christie Woodside, Jonathon Keeney

# Update data tables for more efficient computations
## Student would review and input additional data and IDs in the tables/sheets used to perform computations. This would be manual work (but super important), but would require high attention to detail. ~1 week's worth of work
## Requires Python/shell coding background. Student would run scripts that prepare and format data tables that are pushed to data.argosdb.org. Coding knowledge is needed in case of errors, bugs, or other mishaps in the code. Ongoing work as computations are performed.
# Curate and report on current pathogens to upload to ARGOS
## Student would work on manual curation of circulating pathogens to be added to data.argosdb.org. Regular check-ins and reports of what was found. ~4-10 weeks worth of work
## Locate assembly IDs, reads, and metagenomic information for these pathogens to be used in computations and deposited into data.argosdb.org.
## Provide documentation on why they were curated, why they are important, how they were selected, and how data was collected.

If the student has any other ideas or methods they want to focus on, please reach out to christie.woodside@email.gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.<hr>
<h3>Requirements for Completion</h3>
<p><strong>Note:</strong> The following are <u>mandatory</u>. Failure to complete any will result in an incomplete volunteer record.</p>

<h4>Documentation</h4>
<p>All volunteers must maintain adequate documentation of their work, including written protocols and scripts submitted to GitHub.</p>

<h4>Written Report</h4>
<p>Submit a 1–2 page summary of your tasks and accomplishments to the Admin during the final week of your program.</p>

<h4>Presentation & Slide Submission</h4>
<p>Present your work last week of the 8-week period.</p>
<p>Slides must be submitted to the Admin Team and should include:</p>
<ul>
<li>See Symposium Slides Guidelines below</li></ul>
Contact the Admin Team to access previously submitted slides.
<hr>

=== Completion Certificate ===
A certificate of completion and a letter of recommendation will be provided to all participants who successfully complete the program.
<hr>
=== Contact ===
mazumder_lab@gwu.edu.
<hr>
=== Volunteers ===
{| class="wikitable"
|+
|-
! Name
!Project
!Projects Interested
|-
| [https://www.linkedin.com/in/gracesjchong/ Grace Chong]
|PredictMod
|
# PredictMod
# BiomarkerKB Biocuration
# GlyGen Biocuration
|-
|[https://www.linkedin.com/in/alma-ogunsina-4959072b1/ Alma Ogunsina]
|Biomarker curation
|
# BiomarkerKB
# ARGOS
# PredictMod
|-
|[https://www.linkedin.com/in/diya-kamalabharathy-62557935a/ Diya Kamalabharathy]
|PredictMod
|
# BiomarkerKB Biocuration
# PredictMod Machine Learning
# GlyGen Biocuration
|-
|[https://www.linkedin.com/in/harivinay-prasad-reddy-gujjula-a06ba71bb/ Harivinay P. Gujjula]
|GlyGen curation
|
# GlyGen Biocuration
# BioMarkerKB Biocuration
|-
|[https://www.linkedin.com/in/miao-wang-88b602290/Miao Wang Miao Wang]
|ARGOS
|
# BiomarkerKB Biocuration Project Ideas
# FDA-ARGOS Computation and Pathogen Curation Project
# PredictMod Machine Learning Project Ideas
|-
|[https://www.linkedin.com/in/nahom-gebreselassie-1545ab336/ Nahom Abel]
|GlyGen curation
|
# BiomarkerKB Biocuration
# GlyGen Biocuration
# PredictMod
|-
|[https://www.linkedin.com/in/kajal-patel-cs/ Kajal Sanjaykumar Patel]
|GlyGen and PubMed project
|
#PredictMod
#BiomarkerKB
#GlyGen
|-
|[https://www.linkedin.com/in/john-mccaffrey-b8850930a/ John McCaffrey]
|Biomarker curation
|
# PredictMod
# BiomarkerKB
# GlyGen Biocuration
|-
|[https://www.linkedin.com/in/nathan-ressom/ Nathan Ressom]
|BiomarkerKB
|
# PredictMod
# GlyGen Biocuration
# BiomarkerKB Biocuration
|-
|[https://www.linkedin.com/in/aaron-ressom/ Aaron Ressom]
|PredictMod
|
# BiomarkerKB
# PredictMod
# GlyGen
|-
|[https://www.linkedin.com/in/akale-kinfe/ Akale Kinfe]
|Biomarker curation
|
# BiomarkerKB Biocuration
# GlyGen Biocuration
# ARGOS
|-
|[https://www.linkedin.com/in/aise-arpinar-a8bb9b373/?original_referer= Aise Arpinar]
|GlyGen curation
|
# GlyGen Biocuration
# BiomarkerKB Biocuration
# GlyGen Publication Analysis
|-
|[https://www.linkedin.com/in/piyush-pandey-906b582b5/ Piyush Pandey]
|Biomarker curation
|
# BiomarkerKB Biocuration
# PredictMod
# GlyGen Biocuration
|-
|[http://www.linkedin.com/in/filmawit-zeru-203272363 Filmawit Zeru]
|GlycoSiteMiner project
|
# BiomarkerKB
# GlyGen
# ARGOS
|-
|[https://www.linkedin.com/in/mathias-belay-03b51a2a3/ Mathias Belay]
|Biomarker curation
|
# GlyGen
# PredictMod
# BiomarkerKB
|-
|[https://www.linkedin.com/in/isaac-kim-b644bb231/ Isaac Kim]
|Biomarker curation
|
# BiomarkerKB
# PredictMod
# GlyGen
|-
|Sohana Bahl
|Biomarker curation
|
# BiomarkerKB
|-
|[https://www.linkedin.com/in/ana-vohralikova-794a4433a?utm_source=share&utm_campaign=share_via&utm_content=profile&utm_medium=ios_app Ana Vohralikova]
|Biomarker curation
|
# BiomarkerKB Biocuration Project
# GlyGen Biocuration Project
# FDA-ARGOS Computation and Pathogen
|}

<hr>

=== Symposium Slide Guidelines ===
'''Content Clarity'''

   •   '''Keep It Simple:''' Use concise bullet points instead of long paragraphs. Aim for no more than 6 bullet points per slide.

•    '''Focus on Key Points:''' Highlight the main ideas or data you want your audience to remember.

•    '''Consistent Layout:''' Use a consistent layout for each slide, including fonts, colors, and background. This helps maintain a professional look.

•    '''High-Quality Images:''' Use high-resolution images and graphics to illustrate your points. Avoid using clip art.

•    '''Readable Fonts:''' Use easy-to-read fonts (e.g., Arial, Calibri) and ensure font sizes are large enough to be seen from a distance (24 pt or larger for main text).

•    '''Contrast:''' Ensure there is high contrast between text and background (e.g., dark text on a light background).

•    '''Citation:''' Cite a publication to support the information presented in proper citation format.

'''Outline for Symposium presentation'''

1. Introduction:

2. Project Descriptions

3. Objectives and Goals:

4. Methods, Results, Achievements and Contributions:

5. Future Plans:

6. Skills and Knowledge Gained:

7. Acknowledgments:

8. Q&A Session:

'''Outline'''

'''1. Introduction:''' (1 slide)

- Briefly introduce yourself.

- Add your picture and name on the introduction slide. If it is group add the group picture.

'''2. Project Descriptions:''' (1 slide)

- Provide context and background information about the project.

'''3. Project Objectives and Goals:''' (1 slide)

- Describe the main objectives of the project or initiative.

- Discuss any additional goals or desired outcomes.

- Explain why these objectives and goals are important.

'''4. Methods, Results, Achievements and Contributions:'''

- Highlight the methods/tools used in the project.

- Highlight the key results and outcomes of the project.

- Discuss the most significant achievements and milestones reached.

- Explain how each member of the team project contributed to the project (for group project)

''' '''

'''5. Future Plans'''

- Next steps or future plans for the project

'''6. Skills and Knowledge Gained:''' (1 slide)

- Detail any technical skills acquired or improved.

- Highlight any soft skills, such as communication or teamwork, that were developed.

- Discuss new knowledge gained in specific areas or subjects.

- Share any personal reflections on the experience and what was learned.

- Discuss any challenges or obstacles encountered and how they were overcome.

- Provide key insights or lessons learned from the project.

'''7. Acknowledgments:''' ''':''' (1 slide)

- Acknowledge the contributions of team members and collaborators.

- Recognize the guidance and support of mentors and advisors.

- Acknowledge the Project Funding. Eg. CFDE

'''8. Q&A Session:'''

- Invite the audience to ask questions and engage in discussion.

- Provide clear and thoughtful responses to audience questions.

- Offer closing remarks and thank the audience for their participation.

Note – If you have limited presentation time you can also merge few topics into one.

Volunteership Fall 2025

2025-07-23T15:33:09Z

Rehmam:

== 2025 Volunteer Program Details ==

=== Dates ===
'''Volunteer Zoom Kick-Off Meeting'''

August 25, 2025 | 4:00 to 5:00 PM

'''Program Dates: September 1st, 2025 – November 30th, 2025''' (13 weeks)

Remote
----

=== Volunteer Expectations ===

# Minimum commitment of 10 hours per week.
# Progress updates via Slack at least 3 days per week (scrum).
# Regular Zoom meetings with the assigned project point of contact.

'''Important:''' If the scrum is not updated for 2 consecutive working days, the candidate will be automatically dropped from the program.
----

=== Potential Projects ===

# BiomarkerKB (biomarkerkb.org) project: Biomarker curation project. Involves reading papers and collecting biomarkers.
# GlyGen (glygen.org) project: Review glycomics and glycoproteomics data and curate tissue, disease, and other related information.
# ARGOS (argosdb.org) project: Analyze genomics data using HIVE to identify reference genome assemblies.
# PredictMod (hivelab.biochemistry.gwu.edu/predictmod) project. Identifying datasets and harmonizing them so that they can be used to generate ML models.

''Note: Individuals involved in the above projects with a background in programming and/or machine learning may also undertake additional tasks to support the development of ML models, which can be integrated into PredictMod or used to enhance AI/ML-ready datasets within GlyGen.''
----

==== 1. BiomarkerKB Biocuration Project Ideas ====
POC: Daniall Masood, Maria Kim

# Curate biomarkers for a specific disease (Alzheimers)
## The student would be doing manual curation for about 4 weeks, with regular check-ins with me to ensure it is being done correctly.
## The next 4 weeks can be dedicated to developing an LLM or an automated process to extract biomarker details with data collected in the first 4 weeks as training data/example data.
# Top 50 biomarkers
## Curate the top 50 biomarkers for biomarkerkb.org.
## Define what constitutes a top 50 biomarker.
## Begin curating biomarkers from different sources and papers by collecting fields mentioned in the data model, as well as collecting cross-references.
# Biocuration of biomarkers from NLP/LLM work
## Use the biomarkers collected from NLP work.
## Curate biomarkers. Data provided was not provided in the biomarker data model.
## While curating the biomarkers, check if data collected from NLP is correct.
## After completion, the student can start using curated data to work on the NLP/LLM method.
# Curate biomarkers for a treatment
## See #1 above.

If the student has any other ideas, diseases, treatments, or methods they want to focus on, please reach out to daniallmasood@gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.

==== 2. GlyGen Biocuration Project Ideas[edit | edit source] ====
POC: Rene Ranzinger and Urnisha Bhuiyan

Over the last three decades, numerous glycomics database projects have been initiated to collect valuable information about glycans, proteins, and their interactions. Some of these databases have been discontinued due to the end of project funding. However, the data within these databases remains highly valuable to the community. Integrating these datasets into modern databases or knowledgebases, such as GlyGen, presents a challenge because much of the valuable metadata (e.g., species, tissue, disease, cell line) annotations are free-text terms that do not align with established standard dictionaries and ontologies used in modern resources. Automated matching of this information with dictionaries or ontologies is often not possible due to the use of synonyms, spelling errors, or abbreviations. For example, "human," "man," and "h. sapiens" all map to the scientific species name "Homo sapiens."

The GlyGen project aims to make datasets from two older databases (CarbBank, CFG) accessible by migrating the data and metadata into our database. For this project, we are seeking curators with a medical or biology background who are interested in helping map metadata terms from these old databases to standard dictionaries and ontologies.

The project involves:

# Using internet resources (e.g., Google, Wikipedia) to identify terms used in the old database.
# Mapping identified terms to corresponding dictionaries and ontologies using the webpages and search interfaces of these projects.
# Finding papers based on titles and author lists that may contain spelling errors.
# Interacting and discussing with other curators in case terms are mapped differently.

If you have any other ideas or methods you would like to focus on, please reach out to rene@ccrc.uga.edu to discuss them.

'''3. GlyGen Publication Analysis Project Ideas'''

POC: Rene Ranzinger and Urnisha Bhuiyan

One of the challenges for any bioinformatics project is understanding the size of its community, how well the project serves this community, and how widely its software/database is used. A potential solution is to analyze PubMed publication data. We are seeking applicants with programming skills (in Python or Java) to perform this analysis.

The project involves:

# Using the PubMed web API to filter publications based on keywords.
# Analyzing paper abstracts to identify research institutions and groups that form the community.
# Filtering the community list to exclude unrelated co-authors.
# Prioritize papers identified by GlycoSiteMiner for curation via TableMaker

A subproject will involve analyzing the full text of papers (when available) for keywords or resource and database names. The results of the analysis will be discussed with GlyGen project member who will suggest changes and improvements to the analysis and data presentation. Source code developed as part of this project will be documented and shared in a public GitHub repository. If you have any other ideas or methods you would like to explore, please reach out to rene@ccrc.uga.edu to discuss them.

==== 4. PredictMod Machine Learning Project Ideas[edit | edit source] ====
POC: Lori Krammer

Data Identification & Curation:

# Identify publicly-available datasets from scientific literature that can be used for intervention outcome prediction models.
# Curate indicators of useful ML publications that could be used to train an LLM to recommend relevant publications for cancer modeling.

Modeling & Integration (for those with experience in programming/ML)

# Conduct data harmonization and pre-processing following established project pipelines to make ML-ready dataset and data dictionary.
# Perform model training and document ML pipeline in a BioCompute Object (BCO).
# Integrate model into PredictMod platform.

Individuals with a background or interest in machine learning should reach out to lorikrammer@gwu.edu with a potential dataset to determine if it is a feasible project for the summer.

'''5. FDA-ARGOS Computation and Pathogen Curation Project'''

POC: Christie Woodside, Jonathon Keeney

# Update data tables for more efficient computations
## Student would review and input additional data and IDs in the tables/sheets used to perform computations. This would be manual work (but super important), but would require high attention to detail. ~1 week's worth of work
## Requires Python/shell coding background. Student would run scripts that prepare and format data tables that are pushed to data.argosdb.org. Coding knowledge is needed in case of errors, bugs, or other mishaps in the code. Ongoing work as computations are performed.
# Curate and report on current pathogens to upload to ARGOS
## Student would work on manual curation of circulating pathogens to be added to data.argosdb.org. Regular check-ins and reports of what was found. ~4-10 weeks worth of work
## Locate assembly IDs, reads, and metagenomic information for these pathogens to be used in computations and deposited into data.argosdb.org.
## Provide documentation on why they were curated, why they are important, how they were selected, and how data was collected.

If the student has any other ideas or methods they want to focus on, please reach out to christie.woodside@email.gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.
----

=== Requirements for Completion ===
'''Note:''' The following are mandatory. Failure to complete any will result in an incomplete volunteer record.

==== Documentation ====
All volunteers must maintain adequate documentation of their work, including written protocols and scripts submitted to GitHub.

==== Written Report ====
Submit a 1–2 page summary of your tasks and accomplishments to the Admin during the final week of your program.

==== Presentation & Slide Submission ====
Present your work last week of the 13-week period.

Slides must be submitted to the Admin Team.

Contact the Admin Team to access previously submitted slides.
----

=== Completion Certificate ===
A certificate of completion and a letter of recommendation will be provided to all participants who successfully complete the program.
----

=== Contact ===
mazumder_lab@gwu.edu.
----

=== Volunteers (TBD) ===
{| class="wikitable"
|+
!Name
!Project
!Projects Interested
|-
|''will be updated''
|
|
#
|}

Volunteership Fall 2025

2025-07-23T15:23:50Z

Rehmam:

== 2025 Volunteer Program Details ==

=== Dates ===
'''Volunteer Zoom Kick-Off Meeting'''

TBD

'''Program Dates: September 1st, 2025 – November 30th, 2025''' (13 weeks)

Remote
----

=== Volunteer Expectations ===

# Minimum commitment of 10 hours per week.
# Progress updates via Slack at least 3 days per week (scrum).
# Regular Zoom meetings with the assigned project point of contact.

'''Important:''' If the scrum is not updated for 2 consecutive working days, the candidate will be automatically dropped from the program.
----

=== Potential Projects ===

# BiomarkerKB (biomarkerkb.org) project: Biomarker curation project. Involves reading papers and collecting biomarkers.
# GlyGen (glygen.org) project: Review glycomics and glycoproteomics data and curate tissue, disease, and other related information.
# ARGOS (argosdb.org) project: Analyze genomics data using HIVE to identify reference genome assemblies.
# PredictMod (hivelab.biochemistry.gwu.edu/predictmod) project. Identifying datasets and harmonizing them so that they can be used to generate ML models.

''Note: Individuals involved in the above projects with a background in programming and/or machine learning may also undertake additional tasks to support the development of ML models, which can be integrated into PredictMod or used to enhance AI/ML-ready datasets within GlyGen.''
----

==== 1. BiomarkerKB Biocuration Project Ideas ====
POC: Daniall Masood, Maria Kim

# Curate biomarkers for a specific disease (Alzheimers)
## The student would be doing manual curation for about 4 weeks, with regular check-ins with me to ensure it is being done correctly.
## The next 4 weeks can be dedicated to developing an LLM or an automated process to extract biomarker details with data collected in the first 4 weeks as training data/example data.
# Top 50 biomarkers
## Curate the top 50 biomarkers for biomarkerkb.org.
## Define what constitutes a top 50 biomarker.
## Begin curating biomarkers from different sources and papers by collecting fields mentioned in the data model, as well as collecting cross-references.
# Biocuration of biomarkers from NLP/LLM work
## Use the biomarkers collected from NLP work.
## Curate biomarkers. Data provided was not provided in the biomarker data model.
## While curating the biomarkers, check if data collected from NLP is correct.
## After completion, the student can start using curated data to work on the NLP/LLM method.
# Curate biomarkers for a treatment
## See #1 above.

If the student has any other ideas, diseases, treatments, or methods they want to focus on, please reach out to daniallmasood@gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.

==== 2. GlyGen Biocuration Project Ideas[edit | edit source] ====
POC: Rene Ranzinger and Urnisha Bhuiyan

Over the last three decades, numerous glycomics database projects have been initiated to collect valuable information about glycans, proteins, and their interactions. Some of these databases have been discontinued due to the end of project funding. However, the data within these databases remains highly valuable to the community. Integrating these datasets into modern databases or knowledgebases, such as GlyGen, presents a challenge because much of the valuable metadata (e.g., species, tissue, disease, cell line) annotations are free-text terms that do not align with established standard dictionaries and ontologies used in modern resources. Automated matching of this information with dictionaries or ontologies is often not possible due to the use of synonyms, spelling errors, or abbreviations. For example, "human," "man," and "h. sapiens" all map to the scientific species name "Homo sapiens."

The GlyGen project aims to make datasets from two older databases (CarbBank, CFG) accessible by migrating the data and metadata into our database. For this project, we are seeking curators with a medical or biology background who are interested in helping map metadata terms from these old databases to standard dictionaries and ontologies.

The project involves:

# Using internet resources (e.g., Google, Wikipedia) to identify terms used in the old database.
# Mapping identified terms to corresponding dictionaries and ontologies using the webpages and search interfaces of these projects.
# Finding papers based on titles and author lists that may contain spelling errors.
# Interacting and discussing with other curators in case terms are mapped differently.

If you have any other ideas or methods you would like to focus on, please reach out to rene@ccrc.uga.edu to discuss them.

'''3. GlyGen Publication Analysis Project Ideas'''

POC: Rene Ranzinger and Urnisha Bhuiyan

One of the challenges for any bioinformatics project is understanding the size of its community, how well the project serves this community, and how widely its software/database is used. A potential solution is to analyze PubMed publication data. We are seeking applicants with programming skills (in Python or Java) to perform this analysis.

The project involves:

# Using the PubMed web API to filter publications based on keywords.
# Analyzing paper abstracts to identify research institutions and groups that form the community.
# Filtering the community list to exclude unrelated co-authors.
# Prioritize papers identified by GlycoSiteMiner for curation via TableMaker

A subproject will involve analyzing the full text of papers (when available) for keywords or resource and database names. The results of the analysis will be discussed with GlyGen project member who will suggest changes and improvements to the analysis and data presentation. Source code developed as part of this project will be documented and shared in a public GitHub repository. If you have any other ideas or methods you would like to explore, please reach out to rene@ccrc.uga.edu to discuss them.

==== 4. PredictMod Machine Learning Project Ideas[edit | edit source] ====
POC: Lori Krammer

Data Identification & Curation:

# Identify publicly-available datasets from scientific literature that can be used for intervention outcome prediction models.
# Curate indicators of useful ML publications that could be used to train an LLM to recommend relevant publications for cancer modeling.

Modeling & Integration (for those with experience in programming/ML)

# Conduct data harmonization and pre-processing following established project pipelines to make ML-ready dataset and data dictionary.
# Perform model training and document ML pipeline in a BioCompute Object (BCO).
# Integrate model into PredictMod platform.

Individuals with a background or interest in machine learning should reach out to lorikrammer@gwu.edu with a potential dataset to determine if it is a feasible project for the summer.

'''5. FDA-ARGOS Computation and Pathogen Curation Project'''

POC: Christie Woodside, Jonathon Keeney

# Update data tables for more efficient computations
## Student would review and input additional data and IDs in the tables/sheets used to perform computations. This would be manual work (but super important), but would require high attention to detail. ~1 week's worth of work
## Requires Python/shell coding background. Student would run scripts that prepare and format data tables that are pushed to data.argosdb.org. Coding knowledge is needed in case of errors, bugs, or other mishaps in the code. Ongoing work as computations are performed.
# Curate and report on current pathogens to upload to ARGOS
## Student would work on manual curation of circulating pathogens to be added to data.argosdb.org. Regular check-ins and reports of what was found. ~4-10 weeks worth of work
## Locate assembly IDs, reads, and metagenomic information for these pathogens to be used in computations and deposited into data.argosdb.org.
## Provide documentation on why they were curated, why they are important, how they were selected, and how data was collected.

If the student has any other ideas or methods they want to focus on, please reach out to christie.woodside@email.gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.
----

=== Requirements for Completion ===
'''Note:''' The following are mandatory. Failure to complete any will result in an incomplete volunteer record.

==== Documentation ====
All volunteers must maintain adequate documentation of their work, including written protocols and scripts submitted to GitHub.

==== Written Report ====
Submit a 1–2 page summary of your tasks and accomplishments to the Admin during the final week of your program.

==== Presentation & Slide Submission ====
Present your work last week of the 13-week period.

Slides must be submitted to the Admin Team.

Contact the Admin Team to access previously submitted slides.
----

=== Completion Certificate ===
A certificate of completion and a letter of recommendation will be provided to all participants who successfully complete the program.
----

=== Contact ===
mazumder_lab@gwu.edu.
----

=== Volunteers (TBD) ===
{| class="wikitable"
|+
!Name
!Project
!Projects Interested
|-
|''will be updated''
|
|
#
|}

Volunteership Fall 2025

2025-07-23T15:13:35Z

Rehmam: Created page with "== 2025 Volunteer Program Details == === Dates === '''Volunteer Zoom Kick-Off Meeting''' TBD '''Program Dates: September 1st, 2025 – November 30th, 2025''' (13 weeks) Monday to Friday | Remote | No breaks ---- === Volunteer Expectations === # Minimum commitment of 10 hours per week. # Progress updates via Slack at least 3 days per week (scrum). # Regular Zoom meetings with the assigned project point of contact. '''Important:''' If the scrum is not updated for 2..."

== 2025 Volunteer Program Details ==

=== Dates ===
'''Volunteer Zoom Kick-Off Meeting'''

TBD

'''Program Dates: September 1st, 2025 – November 30th, 2025''' (13 weeks)

Monday to Friday | Remote | No breaks
----

=== Volunteer Expectations ===

# Minimum commitment of 10 hours per week.
# Progress updates via Slack at least 3 days per week (scrum).
# Regular Zoom meetings with the assigned project point of contact.

'''Important:''' If the scrum is not updated for 2 consecutive working days, the candidate will be automatically dropped from the program.
----

=== Potential Projects ===

# BiomarkerKB (biomarkerkb.org) project: Biomarker curation project. Involves reading papers and collecting biomarkers.
# GlyGen (glygen.org) project: Review glycomics and glycoproteomics data and curate tissue, disease, and other related information.
# ARGOS (argosdb.org) project: Analyze genomics data using HIVE to identify reference genome assemblies.
# PredictMod (hivelab.biochemistry.gwu.edu/predictmod) project. Identifying datasets and harmonizing them so that they can be used to generate ML models.

''Note: Individuals involved in the above projects with a background in programming and/or machine learning may also undertake additional tasks to support the development of ML models, which can be integrated into PredictMod or used to enhance AI/ML-ready datasets within GlyGen.''
----

==== 1. BiomarkerKB Biocuration Project Ideas ====
POC: Daniall Masood, Maria Kim

# Curate biomarkers for a specific disease (Alzheimers)
## The student would be doing manual curation for about 4 weeks, with regular check-ins with me to ensure it is being done correctly.
## The next 4 weeks can be dedicated to developing an LLM or an automated process to extract biomarker details with data collected in the first 4 weeks as training data/example data.
# Top 50 biomarkers
## Curate the top 50 biomarkers for biomarkerkb.org.
## Define what constitutes a top 50 biomarker.
## Begin curating biomarkers from different sources and papers by collecting fields mentioned in the data model, as well as collecting cross-references.
# Biocuration of biomarkers from NLP/LLM work
## Use the biomarkers collected from NLP work.
## Curate biomarkers. Data provided was not provided in the biomarker data model.
## While curating the biomarkers, check if data collected from NLP is correct.
## After completion, the student can start using curated data to work on the NLP/LLM method.
# Curate biomarkers for a treatment
## See #1 above.

If the student has any other ideas, diseases, treatments, or methods they want to focus on, please reach out to daniallmasood@gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.

==== 2. GlyGen Biocuration Project Ideas[edit | edit source] ====
POC: Rene Ranzinger and Urnisha Bhuiyan

Over the last three decades, numerous glycomics database projects have been initiated to collect valuable information about glycans, proteins, and their interactions. Some of these databases have been discontinued due to the end of project funding. However, the data within these databases remains highly valuable to the community. Integrating these datasets into modern databases or knowledgebases, such as GlyGen, presents a challenge because much of the valuable metadata (e.g., species, tissue, disease, cell line) annotations are free-text terms that do not align with established standard dictionaries and ontologies used in modern resources. Automated matching of this information with dictionaries or ontologies is often not possible due to the use of synonyms, spelling errors, or abbreviations. For example, "human," "man," and "h. sapiens" all map to the scientific species name "Homo sapiens."

The GlyGen project aims to make datasets from two older databases (CarbBank, CFG) accessible by migrating the data and metadata into our database. For this project, we are seeking curators with a medical or biology background who are interested in helping map metadata terms from these old databases to standard dictionaries and ontologies.

The project involves:

# Using internet resources (e.g., Google, Wikipedia) to identify terms used in the old database.
# Mapping identified terms to corresponding dictionaries and ontologies using the webpages and search interfaces of these projects.
# Finding papers based on titles and author lists that may contain spelling errors.
# Interacting and discussing with other curators in case terms are mapped differently.

If you have any other ideas or methods you would like to focus on, please reach out to rene@ccrc.uga.edu to discuss them.

'''3. GlyGen Publication Analysis Project Ideas'''

POC: Rene Ranzinger and Urnisha Bhuiyan

One of the challenges for any bioinformatics project is understanding the size of its community, how well the project serves this community, and how widely its software/database is used. A potential solution is to analyze PubMed publication data. We are seeking applicants with programming skills (in Python or Java) to perform this analysis.

The project involves:

# Using the PubMed web API to filter publications based on keywords.
# Analyzing paper abstracts to identify research institutions and groups that form the community.
# Filtering the community list to exclude unrelated co-authors.
# Prioritize papers identified by GlycoSiteMiner for curation via TableMaker

A subproject will involve analyzing the full text of papers (when available) for keywords or resource and database names. The results of the analysis will be discussed with GlyGen project member who will suggest changes and improvements to the analysis and data presentation. Source code developed as part of this project will be documented and shared in a public GitHub repository. If you have any other ideas or methods you would like to explore, please reach out to rene@ccrc.uga.edu to discuss them.

==== 4. PredictMod Machine Learning Project Ideas[edit | edit source] ====
POC: Lori Krammer

Data Identification & Curation:

# Identify publicly-available datasets from scientific literature that can be used for intervention outcome prediction models.
# Curate indicators of useful ML publications that could be used to train an LLM to recommend relevant publications for cancer modeling.

Modeling & Integration (for those with experience in programming/ML)

# Conduct data harmonization and pre-processing following established project pipelines to make ML-ready dataset and data dictionary.
# Perform model training and document ML pipeline in a BioCompute Object (BCO).
# Integrate model into PredictMod platform.

Individuals with a background or interest in machine learning should reach out to lorikrammer@gwu.edu with a potential dataset to determine if it is a feasible project for the summer.

'''5. FDA-ARGOS Computation and Pathogen Curation Project'''

POC: Christie Woodside, Jonathon Keeney

# Update data tables for more efficient computations
## Student would review and input additional data and IDs in the tables/sheets used to perform computations. This would be manual work (but super important), but would require high attention to detail. ~1 week's worth of work
## Requires Python/shell coding background. Student would run scripts that prepare and format data tables that are pushed to data.argosdb.org. Coding knowledge is needed in case of errors, bugs, or other mishaps in the code. Ongoing work as computations are performed.
# Curate and report on current pathogens to upload to ARGOS
## Student would work on manual curation of circulating pathogens to be added to data.argosdb.org. Regular check-ins and reports of what was found. ~4-10 weeks worth of work
## Locate assembly IDs, reads, and metagenomic information for these pathogens to be used in computations and deposited into data.argosdb.org.
## Provide documentation on why they were curated, why they are important, how they were selected, and how data was collected.

If the student has any other ideas or methods they want to focus on, please reach out to christie.woodside@email.gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.
----

=== Requirements for Completion ===
'''Note:''' The following are mandatory. Failure to complete any will result in an incomplete volunteer record.

==== Documentation ====
All volunteers must maintain adequate documentation of their work, including written protocols and scripts submitted to GitHub.

==== Written Report ====
Submit a 1–2 page summary of your tasks and accomplishments to the Admin during the final week of your program.

==== Presentation & Slide Submission ====
Present your work last week of the 13-week period.

Slides must be submitted to the Admin Team and should include:

* See Symposium Slides Guidelines below

Contact the Admin Team to access previously submitted slides.
----

=== Completion Certificate ===
A certificate of completion and a letter of recommendation will be provided to all participants who successfully complete the program.
----

=== Contact ===
mazumder_lab@gwu.edu.

People

2025-06-25T16:27:32Z

Rehmam:

<div style="text-align: center; width: 100%;">
[[File:staircasepic.jpg|center|950px]]
</div><h2>GW Faculty</h2>
<table>
<tr>
<td style="text-align: center; padding: 25px">
[[File:Raja-Mazumder.png|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Raja%20Mazumder&FacID=2067473740| Raja Mazumder]</span>, Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File:Robel.Kahsay.jpg|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Robel%20Kahsay&FacID=2051216059| Robel Kashay]</span>, Asst Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File:McNeely.Patrick.jpg|130px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Patrick%20McNeely&FacID=2065037504&show=1| Pat McNeely]</span>, Asst Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File: Jonathon.Keeney.png|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Jonathon%20Keeney&FacID=2056964816| Jonathon Keeney]</span>, Asst Professor]]
</td>
</tr>
</table>
<h2>PI</h2>
<p>
[https://orcid.org/0000-0001-8823-9945 Raja Mazumder] -
[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Raja%20Mazumder&FacID=2067473740 Faculty Bio]
</p>

<h2>Past FDA HIVE Project Lead/s</h2>

Vahan Simonyan (FDA-HIVE)<br>Konstantinos Karagiannis (FDA-HIVE)

<h2>Current GW HIVE Lab Members</h2>
<table>
<tr>
<td style="vertical-align: top;">
<ul>
<li>[https://orcid.org/0009-0006-1223-1895 Sean Kim]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Daniall Masood]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Kate Warner]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Tianyi Wang]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Emily Pennington]</li>
</ul>
</td>
<td style="padding-left: 20px; vertical-align: top;">
<ul>
<li>[https://orcid.org/0000-0002-5317-1458 Jeet Kiran Vora]</li>
<li>[https://orcid.org/0009-0007-4585-7314 Lori Krammer]</li>
<li>[https://orcid.org/0000-0001-8823-9945 Raja Mazumder]</li>
<li>[https://orcid.org/0000-0002-5381-9744 Urnisha Bhuiyan]</li>
<li>[https://orcid.org/0009-0000-7970-7815 Christie Woodside]</li>
</ul>
</td>
<td style="padding-left: 20px; vertical-align: top;">
<ul>
<li>[https://orcid.org/0000-0002-7665-6204 Jonathon Keeney]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Patrick McNeely]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Robel Kahsay]</li>
</ul>
</td>
</tr>
</table>
<h2>Current Volunteers and Part-time Members</h2>
<table>
<tr>
<td style="vertical-align: top;">
<ul>
<li>[https://www.linkedin.com/in/vishal-bakshi/ Vishal Bakshi]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Miguel Mazumder]</li>
<li>[https://orcid.org/0009-0002-5733-1495 Maria Kim]</li>
<li>[https://www.linkedin.com/in/swathimuralisrinivasan/ Swathi Murali Srinivasan]</li>
</ul>
</td>
<td style="padding-left: 20px; vertical-align: top;">
<ul>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Reeya Gupta]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Cyrus Chun Hong AU YEUNG]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Nikhil Aritheya]</li>
<li>[https://www.linkedin.com/in/srivarshiniy/ Sri Varshini Yaddanpudi]</li>
</ul>
</td>
</tr>
</table>[[File:HIVE mini picnic.jpg|center|thumb|671x671px|Lab members enjoying a summer picnic with the extended HIVE community at the Seneca Creek State Park, MD on June 19, 2025.]]

People

2025-06-25T16:26:33Z

Rehmam: I added a photo from a social event as per Dr. Mazumder's request

<div style="text-align: center; width: 100%;">
[[File:staircasepic.jpg|center|950px]]
</div><h2>GW Faculty</h2>
<table>
<tr>
<td style="text-align: center; padding: 25px">
[[File:Raja-Mazumder.png|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Raja%20Mazumder&FacID=2067473740| Raja Mazumder]</span>, Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File:Robel.Kahsay.jpg|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Robel%20Kahsay&FacID=2051216059| Robel Kashay]</span>, Asst Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File:McNeely.Patrick.jpg|130px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Patrick%20McNeely&FacID=2065037504&show=1| Pat McNeely]</span>, Asst Professor]]
</td>
<td style="text-align: center; padding: 25px">
[[File: Jonathon.Keeney.png|150px|thumb|<span style="font-weight:bold;">[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Jonathon%20Keeney&FacID=2056964816| Jonathon Keeney]</span>, Asst Professor]]
</td>
</tr>
</table>
<h2>PI</h2>
<p>
[https://orcid.org/0000-0001-8823-9945 Raja Mazumder] -
[https://apps.smhs.gwu.edu/smhs/facultydirectory/profile.cfm?empName=Raja%20Mazumder&FacID=2067473740 Faculty Bio]
</p>

<h2>Past FDA HIVE Project Lead/s</h2>

Vahan Simonyan (FDA-HIVE)<br>Konstantinos Karagiannis (FDA-HIVE)

<h2>Current GW HIVE Lab Members</h2>
<table>
<tr>
<td style="vertical-align: top;">
<ul>
<li>[https://orcid.org/0009-0006-1223-1895 Sean Kim]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Daniall Masood]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Kate Warner]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Tianyi Wang]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Emily Pennington]</li>
</ul>
</td>
<td style="padding-left: 20px; vertical-align: top;">
<ul>
<li>[https://orcid.org/0000-0002-5317-1458 Jeet Kiran Vora]</li>
<li>[https://orcid.org/0009-0007-4585-7314 Lori Krammer]</li>
<li>[https://orcid.org/0000-0001-8823-9945 Raja Mazumder]</li>
<li>[https://orcid.org/0000-0002-5381-9744 Urnisha Bhuiyan]</li>
<li>[https://orcid.org/0009-0000-7970-7815 Christie Woodside]</li>
</ul>
</td>
<td style="padding-left: 20px; vertical-align: top;">
<ul>
<li>[https://orcid.org/0000-0002-7665-6204 Jonathon Keeney]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Patrick McNeely]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Robel Kahsay]</li>
</ul>
</td>
</tr>
</table>
<h2>Current Volunteers and Part-time Members</h2>
<table>
<tr>
<td style="vertical-align: top;">
<ul>
<li>[https://www.linkedin.com/in/vishal-bakshi/ Vishal Bakshi]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Miguel Mazumder]</li>
<li>[https://orcid.org/0009-0002-5733-1495 Maria Kim]</li>
<li>[https://www.linkedin.com/in/swathimuralisrinivasan/ Swathi Murali Srinivasan]</li>
</ul>
</td>
<td style="padding-left: 20px; vertical-align: top;">
<ul>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Reeya Gupta]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Cyrus Chun Hong AU YEUNG]</li>
<li>[https://hivelab.biochemistry.gwu.edu/wiki/people Nikhil Aritheya]</li>
<li>[https://www.linkedin.com/in/srivarshiniy/ Sri Varshini Yaddanpudi]</li>
</ul>
</td>
</tr>
</table>
[[File:HIVE mini picnic.jpg|center|thumb|522x522px|Lab members enjoying a summer picnic with the extended HIVE community at the Seneca Creek State Park, MD on June 19, 2025.]]

File:HIVE mini picnic.jpg

2025-06-25T16:23:48Z

Rehmam:

Lab members with the extended HIVE community enjoying a summer picnic at the Seneca Creek State Park, June 19, 2025.