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<h2>HIVE Team Publications</h2>
<h2>HIVE Team Publications</h2>
<ul>
<ul>
   <li>Wu J, Singleton SS, Bhuiyan, 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. PMID: [[38313584]].</li>
   <li>Wu J, Singleton SS, Bhuiyan, 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. PMID: [[38219969]].</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. PMID: [[37902107]].</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 PMID: [[36799723]].</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; PMID: [[36711080]].</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 PMID: [[35835332]].</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) PMID: [[35598439]].</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; PMID: [[35925813]].</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://www.ncbi.nlm.nih.gov/pubmed/35925813 PMID: 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. PMID: [[37841494]].</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. PMID: [[35598439]].</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://www.ncbi.nlm.nih.gov/pubmed/35598439 PMID: 35598439].</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; PMID: [[35077912]].</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. PMID: [[34082069]].</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; ceur-ws.org.</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; ceur-ws.org.</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; PMID: [[33784373]].</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; PMID: [[33055255]].</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. PMID: [[33814114]].</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; PMID: [[32940334]].</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. PMID: [[34015823]].</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; PMID: [[32324859]].</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. PMID: [[32226924]].</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. PMID: [[32142370]].</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. PMID: [[31573039]].</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 PMID: [[31616925]].</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://0.1371/journal.pone.0206484 PMID: [[31509535]].</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://0.1371/journal.pone.0206484 [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. PMID: [[29531238]].</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>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>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. PMID: [[30384176]].</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. PMCID: [[5753215]].</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. PMCID: [[5753215]].</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. PMID: [[28977510]].</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. PMID: [[28918914]].</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. PMID: [[28865429]].</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. PMID: [[28680050]].</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. PMID: [[28188908]].</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 PMID: [[28176830]].</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. PMID: [[28150238]].</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 PMID: [[27974626]].</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 PMID: [[26810135]].</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 PMID: [[27447339]].</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 PMID: [[27153712]].</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 PMID: [[27073839]].</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 PMID: [[28113865]].</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. PMID: [[26407068]].</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. PMID: [[25962759]].</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. PMID: [[25841438]].</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 PMID: [[25819073]].</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).</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).</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.</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.</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. PMID: [[25538240]].</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. PMID: [[25475637]].</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. PMID: [[25336203]].</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. PMID: [[25232094]].</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. PMID: [[25245635]].</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. PMID: [[24930720]].</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. PMID: [[24918764]].</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. PMID: [[24894379]].</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. PMID: [[24406624]].</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. PMID: [[24705329]].</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. PMID: [[24667251]].</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. PMID: [[24604646]].</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. PMID: [[24467687]].</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. PMID: [[24791251]].</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>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. PMID: [[23618375]].</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. PMID: [[23459159]].</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. PMID: [[23350563]].</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. PMID: [[23110974]].</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. PMID: [[22115576]].</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. PMID: [[22586465]].</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>
</ul>


Revision as of 20:58, 26 November 2024

HIVE Lab Publications

    Please cite use of HIVE with

  • 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. PMID: 25271953
  • 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. PMID: 26989153

HIVE Team Publications

  • Wu J, Singleton SS, Bhuiyan, 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. PMID: 38313584.
  • 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. PMID: 38219969.
  • 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. PMID: 37902107.
  • 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 PMID: 36799723.
  • Lisacek F, Tiemeyer M, Mazumder R, Aoki-Kinoshita KF. Worldwide Glycoscience Informatics Infrastructure: The GlySpace Alliance. JACS Au. eCollection 2023 Jan 23; PMID: 36711080.
  • 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 PMID: 35835332.
  • 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) PMID: 35598439.
  • 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; PMID: 35925813.
  • 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. PMID: 37841494.
  • 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. PMID: 35598439.
  • 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; PMID: 35077912.
  • 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. PMID: 34082069.
  • 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; ceur-ws.org.
  • 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; PMID: 33784373.
  • 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; PMID: 33055255.
  • 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. PMID: 33814114.
  • Torcivia J, Mazumder R. Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples. Briefings in Bioinformatics. 2020 Sep 17; PMID: 32940334.
  • 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. PMID: 34015823.
  • 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; PMID: 32324859.
  • 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. PMID: 32226924.
  • 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. PMID: 32142370.
  • 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. PMID: 31573039.
  • York WS, Mazumder R, Ranzinger R, et al. GlyGen: Computational and Informatics Resources for Glycoscience. Glycobiology. 2019. https://doi.org/10.1093/glycob/cwz080 PMID: 31616925.
  • 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://0.1371/journal.pone.0206484 PMID: 31509535.
  • 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. PMID: 29531238.
  • 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
  • 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
  • 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. PMID: 30384176.
  • 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. PMCID: 5753215.
  • 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. PMID: 28977510.
  • 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. PMID: 28918914.
  • 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. PMID: 28865429.
  • 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. PMID: 28680050.
  • 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. PMID: 28188908.
  • 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 PMID: 28176830.
  • 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. PMID: 28150238.
  • 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 PMID: 27974626.
  • 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 PMID: 26810135.
  • 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 PMID: 27447339.
  • 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 PMID: 27153712.
  • 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 PMID: 27073839.
  • 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 PMID: 28113865.
  • 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. PMID: 26407068.
  • 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. PMID: 25962759.
  • 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. PMID: 25841438.
  • 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 PMID: 25819073.
  • 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).
  • 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.
  • 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. PMID: 25538240.
  • 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. PMID: 25475637.
  • 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. PMID: 25336203.
  • 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. PMID: 25232094.
  • 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. PMID: 25245635.
  • 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. PMID: 24930720.
  • 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. PMID: 24918764.
  • 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. PMID: 24894379.
  • 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. PMID: 24406624.
  • 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. PMID: 24705329.
  • 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. PMID: 24667251.
  • 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. PMID: 24604646.
  • 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. PMID: 24467687.
  • 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. PMID: 24791251.
  • Basuchoudhary A, Simonyan V, Mazumder R. Community annotation and the evolution of cooperation: How patience matters. Open Bioinformatics Journal. 2013; 7:9-18.
  • 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. PMID: 23618375.
  • 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. PMID: 23459159.
  • 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. PMID: 23350563.
  • 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. PMID: 23110974.
  • 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. PMID: 22115576.
  • 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. PMID: 22586465.

HIVE Team Multimedia

  • 2024 BioCompute Conference and Workshop
    Presented by: Hadley King, Jonathon Keeney, Tianyi Wang, Sean Kim, Raja Mazumder.
    Watch on YouTube
  • BioCompute Workshop 2022
    Presented by: Charles Hadley King, Jonathon Keeney, Dennis Dean, et al.
    Watch on YouTube

HIVE Team Selected Posters

  • Publication of BioCompute Objects (IEEE-2791-2020) created from Galaxy workflow invocations, presented by Charles Hadley King at the 2021 Galaxy Community Conference (GCC2021). Link
  • HIVE Pathogen Detection Pipeline, presented by Ekaterina Osipova at the 1st Annual Office of Biostatistics and Epidemiology (OBE) Research Day. View as PDF

HIVE Team Other Works

  • BioCompute Objects (BCO) White Paper, updated 2024. Link
  • HIVE White Paper, updated October 2015. Link
  • HIVE Brochure, updated October 2015. Link
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