Publications

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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.

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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