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GlyGen: Computational and Informatics Resources for Glycoscience.

York WS, Mazumder R, Ranzinger R, Edwards N, Kahsay R, Aoki-Kinoshita KF, Campbell MP, Cummings RD, Feizi T, Martin M, Natale DA, Packer NH, Woods RJ, Agarwal G, Arpinar S, Bhat S, Blake J, Castro LJG, Fochtman B, Gildersleeve J, Goldman R, Holmes X, Jain V, Kulkarni S, Mahadik R, Mehta A, Mousavi R, Nakarakommula S, Navelkar R, Pattabiraman N, Pierce MJ, Ross K, Vasudev P, Vora J, Williamson T, Zhang W.

Glycobiology. 2019 Oct 16. pii: cwz080. doi: 10.1093/glycob/cwz080. [Epub ahead of print] No abstract available.


Mutated CEACAMs Disrupt Transforming Growth Factor Beta Signaling and Alter the Intestinal Microbiome to Promote Colorectal Carcinogenesis.

Gu S, Zaidi S, Hassan MI, Mohammad T, Malta TM, Noushmehr H, Nguyen B, Crandall KA, Srivastav J, Obias V, Lin P, Nguyen BN, Yao M, Yao R, King CH, Mazumder R, Mishra B, Rao S, Mishra L.

Gastroenterology. 2019 Oct 1. pii: S0016-5085(19)41365-6. doi: 10.1053/j.gastro.2019.09.023. [Epub ahead of print]


The GlySpace Alliance: towards a collaborative global glycoinformatics community.

Aoki-Kinoshita KF, Lisacek F, Mazumder R, York WS, Packer NH.

Glycobiology. 2019 Oct 1. pii: cwz078. doi: 10.1093/glycob/cwz078. [Epub ahead of print] No abstract available.


Baseline human gut microbiota profile in healthy people and standard reporting template.

King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, 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 MD, Mazumder R.

PLoS One. 2019 Sep 11;14(9):e0206484. doi: 10.1371/journal.pone.0206484. eCollection 2019.


Updates to the Symbol Nomenclature for Glycans guidelines.

Neelamegham S, Aoki-Kinoshita K, Bolton E, Frank M, Lisacek F, Lütteke T, O'Boyle N, Packer NH, Stanley P, Toukach P, Varki A, Woods RJ; SNFG Discussion Group.

Glycobiology. 2019 Aug 20;29(9):620-624. doi: 10.1093/glycob/cwz045.


Investigation of somatic single nucleotide variations in human endogenous retrovirus elements and their potential association with cancer.

Chang TC, Goud S, Torcivia-Rodriguez J, Hu Y, Pan Q, Kahsay R, Blomberg J, Mazumder R.

PLoS One. 2019 Apr 1;14(4):e0213770. doi: 10.1371/journal.pone.0213770. eCollection 2019.


miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines.

Kim B, Ali T, Dong C, Lijeron C, Mazumder R, Wultsch C, Krampis K.

J Comput Biol. 2019 Mar;26(3):280-284. doi: 10.1089/cmb.2018.0218. Epub 2019 Jan 17.


Enabling precision medicine via standard communication of HTS provenance, analysis, and results.

Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R.

PLoS Biol. 2018 Dec 31;16(12):e3000099. doi: 10.1371/journal.pbio.3000099. eCollection 2018 Dec.


Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis.

Hu Y, Dingerdissen H, Gupta S, Kahsay R, Shanker V, Wan Q, Yan C, Mazumder R.

Comput Biol Med. 2018 Dec 1;103:183-197. doi: 10.1016/j.compbiomed.2018.10.021. Epub 2018 Oct 22.


A Primer for Access to Repositories of Cancer-Related Genomic Big Data.

Torcivia-Rodriguez J, Dingerdissen H, Chang TC, Mazumder R.

Methods Mol Biol. 2019;1878:1-37. doi: 10.1007/978-1-4939-8868-6_1. Review.


BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery.

Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1128-D1136. doi: 10.1093/nar/gkx907.


DEXTER: Disease-Expression Relation Extraction from Text.

Gupta S, Dingerdissen H, Ross KE, Hu Y, Wu CH, Mazumder R, Vijay-Shanker K.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay045.


Loss and gain of N-linked glycosylation sequons due to single-nucleotide variation in cancer.

Fan Y, Hu Y, Yan C, Goldman R, Pan Y, Mazumder R, Dingerdissen HM.

Sci Rep. 2018 Mar 12;8(1):4322. doi: 10.1038/s41598-018-22345-2.


Separation and assembly of deep sequencing data into discrete sub-population genomes.

Karagiannis K, Simonyan V, Chumakov K, Mazumder R.

Nucleic Acids Res. 2017 Nov 2;45(19):10989-11003. doi: 10.1093/nar/gkx755.


Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor-β Pathway.

Chen J, Zaidi S, Rao S, Chen JS, Phan L, Farci P, Su X, Shetty K, White J, Zamboni F, Wu X, Rashid A, Pattabiraman N, Mazumder R, Horvath A, Wu RC, Li S, Xiao C, Deng CX, Wheeler DA, Mishra B, Akbani R, Mishra L.

Gastroenterology. 2018 Jan;154(1):195-210. doi: 10.1053/j.gastro.2017.09.007. Epub 2017 Sep 15.


Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids.

Pan Y, Yan C, Hu Y, Fan Y, Pan Q, Wan Q, Torcivia-Rodriguez J, Mazumder R.

Sci Rep. 2017 Feb 8;7:42169. doi: 10.1038/srep42169.


Impact of Nonsynonymous Single-Nucleotide Variations on Post-Translational Modification Sites in Human Proteins.

Gulzar N, Dingerdissen H, Yan C, Mazumder R.

Methods Mol Biol. 2017;1558:159-190. doi: 10.1007/978-1-4939-6783-4_8.


Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices.

Goldweber S, Theodore J, Torcivia-Rodriguez J, Simonyan V, Mazumder R.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):498-500. doi: 10.1109/TCBB.2016.2542802. Epub 2016 Mar 23.


Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations.

Simonyan V, Goecks J, Mazumder R.

PDA J Pharm Sci Technol. 2017 Mar-Apr;71(2):136-146. doi: 10.5731/pdajpst.2016.006734. Epub 2016 Dec 14.


Computational clustering for viral reference proteomes.

Chen C, Huang H, Mazumder R, Natale DA, McGarvey PB, Zhang J, Polson SW, Wang Y, Wu CH; UniProt Consortium.

Bioinformatics. 2016 Jul 1;32(13):2041-3. doi: 10.1093/bioinformatics/btw110. Epub 2016 Feb 26.

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