Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 38

1.

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.

2.

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.

3.

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.

PMID:
30137434
4.

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.

5.

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.

6.

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.

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.

8.

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.

PMID:
28188908
9.

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.

PMID:
28113865
10.

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.

11.

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.

PMID:
27447339
12.

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.

13.

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.

14.

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.

15.

Deep Sequencing for Evaluation of Genetic Stability of Influenza A/California/07/2009 (H1N1) Vaccine Viruses.

Laassri M, Zagorodnyaya T, Plant EP, Petrovskaya S, Bidzhieva B, Ye Z, Simonyan V, Chumakov K.

PLoS One. 2015 Sep 25;10(9):e0138650. doi: 10.1371/journal.pone.0138650. eCollection 2015. Erratum in: PLoS One. 2015;10(11):e0142248. Majid, Laassri [corrected to Laassri, Majid].

16.

Generation and propagation of recombinant mumps viruses exhibiting an additional U residue in the homopolymeric U tract of the F gene-end signal.

Sauder CJ, Ngo L, Simonyan V, Cong Y, Zhang C, Link M, Malik T, Rubin SA.

Virus Genes. 2015 Aug;51(1):12-24. doi: 10.1007/s11262-015-1204-y. Epub 2015 May 12.

PMID:
25962759
17.

FDA's Activities Supporting Regulatory Application of "Next Gen" Sequencing Technologies.

Wilson CA, Simonyan V.

PDA J Pharm Sci Technol. 2014 Nov-Dec;68(6):626-30. doi: 10.5731/pdajpst.2014.01024.

PMID:
25475637
18.

Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing.

Zhang W, Soika V, Meehan J, Su Z, Ge W, Ng HW, Perkins R, Simonyan V, Tong W, Hong H.

Pharmacogenomics J. 2015 Aug;15(4):298-309. doi: 10.1038/tpj.2014.70. Epub 2014 Nov 11.

PMID:
25384574
19.

Census-based rapid and accurate metagenome taxonomic profiling.

Shamsaddini A, Pan Y, Johnson WE, Krampis K, Shcheglovitova M, Simonyan V, Zanne A, Mazumder R.

BMC Genomics. 2014 Oct 21;15:918. doi: 10.1186/1471-2164-15-918.

20.

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis.

Simonyan V, Mazumder R.

Genes (Basel). 2014 Sep 30;5(4):957-81. doi: 10.3390/genes5040957.

21.

Human germline and pan-cancer variomes and their distinct functional profiles.

Pan Y, Karagiannis K, Zhang H, Dingerdissen H, Shamsaddini A, Wan Q, Simonyan V, Mazumder R.

Nucleic Acids Res. 2014 Oct;42(18):11570-88. doi: 10.1093/nar/gku772. Epub 2014 Sep 17.

22.

Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes.

Faison WJ, Rostovtsev A, Castro-Nallar E, Crandall KA, Chumakov K, Simonyan V, Mazumder R.

Genomics. 2014 Jul;104(1):1-7. doi: 10.1016/j.ygeno.2014.06.001. Epub 2014 Jun 12.

23.

HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis.

Santana-Quintero L, Dingerdissen H, Thierry-Mieg J, Mazumder R, Simonyan V.

PLoS One. 2014 Jun 11;9(6):e99033. doi: 10.1371/journal.pone.0099033. eCollection 2014.

24.

A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs.

Dingerdissen H, Weaver DS, Karp PD, Pan Y, Simonyan V, Mazumder R.

Biol Direct. 2014 Jun 3;9:9. doi: 10.1186/1745-6150-9-9.

25.

Single-nucleotide variations in cardiac arrhythmias: prospects for genomics and proteomics based biomarker discovery and diagnostics.

Abunimer A, Smith K, Wu TJ, Lam P, Simonyan V, Mazumder R.

Genes (Basel). 2014 Mar 27;5(2):254-69. doi: 10.3390/genes5020254.

26.

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

Wu TJ, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R.

Database (Oxford). 2014 Mar 25;2014:bau022. doi: 10.1093/database/bau022. Print 2014.

27.

Genome Sequence of Mycoplasma hyorhinis Strain DBS 1050.

Dabrazhynetskaya A, Soika V, Volokhov D, Simonyan V, Chizhikov V.

Genome Announc. 2014 Mar 6;2(2). pii: e00127-14. doi: 10.1128/genomeA.00127-14.

28.

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

Cole C, Krampis K, Karagiannis K, Almeida JS, Faison WJ, Motwani M, Wan Q, Golikov A, Pan Y, Simonyan V, Mazumder R.

BMC Bioinformatics. 2014 Jan 27;15:28. doi: 10.1186/1471-2105-15-28.

29.

Deep sequencing approach for genetic stability evaluation of influenza A viruses.

Bidzhieva B, Zagorodnyaya T, Karagiannis K, Simonyan V, Laassri M, Chumakov K.

J Virol Methods. 2014 Apr;199:68-75. doi: 10.1016/j.jviromet.2013.12.018. Epub 2014 Jan 7.

PMID:
24406624
30.

SNVDis: a proteome-wide analysis service for evaluating nsSNVs in protein functional sites and pathways.

Karagiannis K, Simonyan V, Mazumder R.

Genomics Proteomics Bioinformatics. 2013 Apr;11(2):122-6. doi: 10.1016/j.gpb.2012.10.003. Epub 2012 Dec 5.

31.

Structure-based comparative analysis and prediction of N-linked glycosylation sites in evolutionarily distant eukaryotes.

Lam PV, Goldman R, Karagiannis K, Narsule T, Simonyan V, Soika V, Mazumder R.

Genomics Proteomics Bioinformatics. 2013 Apr;11(2):96-104. doi: 10.1016/j.gpb.2012.11.003. Epub 2013 Feb 28.

32.

Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins.

Dingerdissen H, Motwani M, Karagiannis K, Simonyan V, Mazumder R.

FEBS J. 2013 Mar;280(6):1542-62. doi: 10.1111/febs.12155. Epub 2013 Feb 24.

33.

N-glycans in liver-secreted and immunoglogulin-derived protein fractions.

Bekesova S, Kosti O, Chandler KB, Wu J, Madej HL, Brown KC, Simonyan V, Goldman R.

J Proteomics. 2012 Apr 3;75(7):2216-24. doi: 10.1016/j.jprot.2012.01.024. Epub 2012 Feb 3.

35.

PubChem3D: a new resource for scientists.

Bolton EE, Chen J, Kim S, Han L, He S, Shi W, Simonyan V, Sun Y, Thiessen PA, Wang J, Yu B, Zhang J, Bryant SH.

J Cheminform. 2011 Sep 20;3(1):32. doi: 10.1186/1758-2946-3-32.

36.

CDD: a Conserved Domain Database for protein classification.

Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D192-6.

37.

MMDB: Entrez's 3D-structure database.

Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, Mazumder R, Nikolskaya AN, Rao BS, Panchenko AR, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH.

Nucleic Acids Res. 2003 Jan 1;31(1):474-7.

38.

CDD: a curated Entrez database of conserved domain alignments.

Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, Nikolskaya AN, Panchenko AR, Rao BS, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Vasudevan S, Wang Y, Yamashita RA, Yin JJ, Bryant SH.

Nucleic Acids Res. 2003 Jan 1;31(1):383-7.

Supplemental Content

Loading ...
Support Center