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Items: 1 to 20 of 43


Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection.

Smith AD, Foss ED, Zhang I, Hastie JL, Giordano NP, Gasparyan L, VinhNguyen LP, Schubert AM, Prasad D, McMichael HL, Sun J, Beger RD, Simonyan V, Cowley SC, Carlson PE Jr.

PLoS One. 2019 Sep 27;14(9):e0223025. doi: 10.1371/journal.pone.0223025. eCollection 2019.


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.


Novel reference genes in colorectal cancer identify a distinct subset of high stage tumors and their associated histologically normal colonic tissues.

Xu L, Luo H, Wang R, Wu WW, Phue JN, Shen RF, Juhl H, Wu L, Alterovitz WL, Simonyan V, Pelosof L, Rosenberg AS.

BMC Med Genet. 2019 Aug 13;20(1):138. doi: 10.1186/s12881-019-0867-y.


Development of an Integrated Platform Using Multidisciplinary Real-World Data to Facilitate Biomarker Discovery for Medical Products.

Dabic S, Azarbaijani Y, Karapetyan T, Loyo-Berrios N, Simonyan V, Kitchner T, Brilliant M, Torosyan Y.

Clin Transl Sci. 2019 Aug 6. doi: 10.1111/cts.12685. [Epub ahead of print]


Identification and quantification of defective virus genomes in high throughput sequencing data using DVG-profiler, a novel post-sequence alignment processing algorithm.

Bosma TJ, Karagiannis K, Santana-Quintero L, Ilyushina N, Zagorodnyaya T, Petrovskaya S, Laassri M, Donnelly RP, Rubin S, Simonyan V, Sauder CJ.

PLoS One. 2019 May 17;14(5):e0216944. doi: 10.1371/journal.pone.0216944. eCollection 2019.


Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design.

Alexaki A, Kames J, Holcomb DD, Athey J, Santana-Quintero LV, Lam PVN, Hamasaki-Katagiri N, Osipova E, Simonyan V, Bar H, Komar AA, Kimchi-Sarfaty C.

J Mol Biol. 2019 Jun 14;431(13):2434-2441. doi: 10.1016/j.jmb.2019.04.021. Epub 2019 Apr 26.


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.


A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence.

Lypaczewski P, Hoshizaki J, Zhang WW, McCall LI, Torcivia-Rodriguez J, Simonyan V, Kaur A, Dewar K, Matlashewski G.

Sci Rep. 2018 Nov 8;8(1):16549. doi: 10.1038/s41598-018-34812-x.


Sequence comparison of Francisella tularensis LVS, LVS-G and LVS-R.

Kurtz SL, Voskanian-Kordi A, Simonyan V, Elkins KL.

Pathog Dis. 2018 Oct 1;76(7). doi: 10.1093/femspd/fty067.


Evolution of echovirus 11 in a chronically infected immunodeficient patient.

Laassri M, Zagorodnyaya T, Hassin-Baer S, Handsher R, Sofer D, Weil M, Karagiannis K, Simonyan V, Chumakov K, Shulman L.

PLoS Pathog. 2018 Mar 19;14(3):e1006943. doi: 10.1371/journal.ppat.1006943. eCollection 2018 Mar.


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.


A new and updated resource for codon usage tables.

Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C.

BMC Bioinformatics. 2017 Sep 2;18(1):391. doi: 10.1186/s12859-017-1793-7.


Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization.

Gannavaram S, Torcivia J, Gasparyan L, Kaul A, Ismail N, Simonyan V, Nakhasi HL.

Sci Rep. 2017 Jul 5;7(1):4718. doi: 10.1038/s41598-017-05088-4.


HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls.

Simonyan V, Chumakov K, Donaldson E, Karagiannis K, Lam PV, Dingerdissen H, Voskanian A.

Genomics. 2017 Jul;109(3-4):131-140. doi: 10.1016/j.ygeno.2017.01.002. Epub 2017 Feb 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.


Distinct Patterns of Expression of Transcription Factors in Response to Interferon╬▓ and Interferon╬╗1.

Novatt H, Theisen TC, Massie T, Massie T, Simonyan V, Voskanian-Kordi A, Renn LA, Rabin RL.

J Interferon Cytokine Res. 2016 Oct;36(10):589-598. Epub 2016 Jul 22.


Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine.

Xiao W, Wu L, Yavas G, Simonyan V, Ning B, Hong H.

Pharmaceutics. 2016 Apr 22;8(2). pii: E15. doi: 10.3390/pharmaceutics8020015. Review.


Evidence that a polyhexameric genome length is preferred, but not strictly required, for efficient mumps virus replication.

Sauder CJ, Simonyan V, Ngo L, Karagiannis K, Cong Y, Zhang C, Wang R, Wu WW, Malik T, Rubin SA.

Virology. 2016 Jun;493:173-88. doi: 10.1016/j.virol.2016.03.021. Epub 2016 Apr 6.


High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.

Simonyan V, Chumakov K, Dingerdissen H, Faison W, Goldweber S, Golikov A, Gulzar N, Karagiannis K, Vinh Nguyen Lam P, Maudru T, Muravitskaja O, Osipova E, Pan Y, Pschenichnov A, Rostovtsev A, Santana-Quintero L, Smith K, Thompson EE, Tkachenko V, Torcivia-Rodriguez J, Voskanian A, Wan Q, Wang J, Wu TJ, Wilson C, Mazumder R.

Database (Oxford). 2016 Mar 17;2016. pii: baw022. doi: 10.1093/database/baw022. Print 2016.

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