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Items: 1 to 50 of 538

1.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

PMID:
29979655
2.

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.

Harmanci A, Gerstein M.

Nat Commun. 2018 Jun 22;9(1):2453. doi: 10.1038/s41467-018-04875-5.

3.

Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions.

Barber KW, Muir P, Szeligowski RV, Rogulina S, Gerstein M, Sampson JR, Isaacs FJ, Rinehart J.

Nat Biotechnol. 2018 Aug;36(7):638-644. doi: 10.1038/nbt.4150. Epub 2018 Jun 11.

PMID:
29889213
4.

Cost-effectiveness of an Evidence-Based Childhood Asthma Intervention in Real-World Primary Care Settings.

Dor A, Luo Q, Gerstein MT, Malveaux F, Mitchell H, Markus AR.

J Ambul Care Manage. 2018 Jul/Sep;41(3):213-224. doi: 10.1097/JAC.0000000000000231.

PMID:
29847408
5.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P.

Genome Res. 2018 Apr;28(4):448-459. doi: 10.1101/gr.234096.117. Epub 2018 Mar 21.

6.

A comprehensive catalog of predicted functional upstream open reading frames in humans.

McGillivray P, Ault R, Pawashe M, Kitchen R, Balasubramanian S, Gerstein M.

Nucleic Acids Res. 2018 Apr 20;46(7):3326-3338. doi: 10.1093/nar/gky188.

PMID:
29562350
7.

FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods.

Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A.

Genome Biol. 2018 Mar 20;19(1):38. doi: 10.1186/s13059-018-1404-6.

8.

Gene names can confound most-searched listings.

Gerstein MB, Navarro FCP.

Nature. 2018 Jan 25;553(7689):405. doi: 10.1038/d41586-018-01077-3. No abstract available.

PMID:
29368714
9.

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP.

Cell Syst. 2018 Feb 28;6(2):157-170.e8. doi: 10.1016/j.cels.2017.12.013. Epub 2018 Jan 17.

PMID:
29361466
10.

Features, Treatment, and Outcomes of Macrophage Activation Syndrome in Childhood-Onset Systemic Lupus Erythematosus.

Borgia RE, Gerstein M, Levy DM, Silverman ED, Hiraki LT.

Arthritis Rheumatol. 2018 Apr;70(4):616-624. doi: 10.1002/art.40417. Epub 2018 Mar 2.

PMID:
29342508
11.

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors.

Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston RH.

Genetics. 2018 Mar;208(3):937-949. doi: 10.1534/genetics.117.300657. Epub 2017 Dec 28.

PMID:
29284660
12.

A multiregional proteomic survey of the postnatal human brain.

Carlyle BC, Kitchen RR, Kanyo JE, Voss EZ, Pletikos M, Sousa AMM, Lam TT, Gerstein MB, Sestan N, Nairn AC.

Nat Neurosci. 2017 Dec;20(12):1787-1795. doi: 10.1038/s41593-017-0011-2. Epub 2017 Nov 13.

13.

Molecular and cellular reorganization of neural circuits in the human lineage.

Sousa AMM, Zhu Y, Raghanti MA, Kitchen RR, Onorati M, Tebbenkamp ATN, Stutz B, Meyer KA, Li M, Kawasawa YI, Liu F, Perez RG, Mele M, Carvalho T, Skarica M, Gulden FO, Pletikos M, Shibata A, Stephenson AR, Edler MK, Ely JJ, Elsworth JD, Horvath TL, Hof PR, Hyde TM, Kleinman JE, Weinberger DR, Reimers M, Lifton RP, Mane SM, Noonan JP, State MW, Lein ES, Knowles JA, Marques-Bonet T, Sherwood CC, Gerstein MB, Sestan N.

Science. 2017 Nov 24;358(6366):1027-1032. doi: 10.1126/science.aan3456.

14.

MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.

Lochovsky L, Zhang J, Gerstein M.

Bioinformatics. 2018 Mar 15;34(6):1031-1033. doi: 10.1093/bioinformatics/btx700.

15.

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

Kaczor-Urbanowicz KE, Kim Y, Li F, Galeev T, Kitchen RR, Gerstein M, Koyano K, Jeong SH, Wang X, Elashoff D, Kang SY, Kim SM, Kim K, Kim S, Chia D, Xiao X, Rozowsky J, Wong DTW.

Bioinformatics. 2018 Jan 1;34(1):1-8. doi: 10.1093/bioinformatics/btx504.

PMID:
28961734
16.

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines.

Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY.

Nat Genet. 2017 Oct;49(10):1428-1436. doi: 10.1038/ng.3950. Epub 2017 Sep 4.

PMID:
28869592
17.

Using ALoFT to determine the impact of putative loss-of-function variants in protein-coding genes.

Balasubramanian S, Fu Y, Pawashe M, McGillivray P, Jin M, Liu J, Karczewski KJ, MacArthur DG, Gerstein M.

Nat Commun. 2017 Aug 29;8(1):382. doi: 10.1038/s41467-017-00443-5.

18.

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.

Yan KK, Lou S, Gerstein M.

PLoS Comput Biol. 2017 Jul 24;13(7):e1005647. doi: 10.1371/journal.pcbi.1005647. eCollection 2017 Jul.

19.

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis.

Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK.

Nat Commun. 2017 Jul 5;8(1):59. doi: 10.1038/s41467-017-00050-4.

20.

Landscape and variation of novel retroduplications in 26 human populations.

Zhang Y, Li S, Abyzov A, Gerstein MB.

PLoS Comput Biol. 2017 Jun 29;13(6):e1005567. doi: 10.1371/journal.pcbi.1005567. eCollection 2017 Jun.

21.

Cancer genomics: Less is more in the hunt for driver mutations.

Kumar S, Gerstein M.

Nature. 2017 Jul 6;547(7661):40-41. doi: 10.1038/nature23085. Epub 2017 Jun 28. No abstract available.

PMID:
28658210
22.

Effectiveness of Evidence-Based Asthma Interventions.

Kennedy S, Bailey R, Jaffee K, Markus A, Gerstein M, Stevens DM, Lesch JK, Malveaux FJ, Mitchell H.

Pediatrics. 2017 Jun;139(6). pii: e20164221. doi: 10.1542/peds.2016-4221. Epub 2017 May 9.

23.

Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.

Dhingra P, Fu Y, Gerstein M, Khurana E.

Curr Protoc Bioinformatics. 2017 May 2;57:15.11.1-15.11.17. doi: 10.1002/cpbi.23.

PMID:
28463398
24.

Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology.

Alves P, Liu S, Wang D, Gerstein M.

IEEE/ACM Trans Comput Biol Bioinform. 2018 May-Jun;15(3):926-933. doi: 10.1109/TCBB.2017.2691329. Epub 2017 Apr 5.

PMID:
28391206
25.

Dynamic RNA-protein interactions underlie the zebrafish maternal-to-zygotic transition.

Despic V, Dejung M, Gu M, Krishnan J, Zhang J, Herzel L, Straube K, Gerstein MB, Butter F, Neugebauer KM.

Genome Res. 2017 Jul;27(7):1184-1194. doi: 10.1101/gr.215954.116. Epub 2017 Apr 5.

26.

Structuring supplemental materials in support of reproducibility.

Greenbaum D, Rozowsky J, Stodden V, Gerstein M.

Genome Biol. 2017 Apr 5;18(1):64. doi: 10.1186/s13059-017-1205-3.

27.

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.

Yan KK, Yardimci GG, Yan C, Noble WS, Gerstein M.

Bioinformatics. 2017 Jul 15;33(14):2199-2201. doi: 10.1093/bioinformatics/btx152.

28.

Whole-genome analysis of papillary kidney cancer finds significant noncoding alterations.

Li S, Shuch BM, Gerstein MB.

PLoS Genet. 2017 Mar 30;13(3):e1006685. doi: 10.1371/journal.pgen.1006685. eCollection 2017 Mar.

29.

MicroRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos.

Kasper DM, Moro A, Ristori E, Narayanan A, Hill-Teran G, Fleming E, Moreno-Mateos M, Vejnar CE, Zhang J, Lee D, Gu M, Gerstein M, Giraldez A, Nicoli S.

Dev Cell. 2017 Mar 27;40(6):552-565.e5. doi: 10.1016/j.devcel.2017.02.021.

30.

Stroke and Circulating Extracellular RNAs.

Mick E, Shah R, Tanriverdi K, Murthy V, Gerstein M, Rozowsky J, Kitchen R, Larson MG, Levy D, Freedman JE.

Stroke. 2017 Apr;48(4):828-834. doi: 10.1161/STROKEAHA.116.015140. Epub 2017 Mar 13.

31.

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.

Abyzov A, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, Urban AE, Vaccarino FM.

Genome Res. 2017 Apr;27(4):512-523. doi: 10.1101/gr.215517.116. Epub 2017 Feb 24.

32.

Intensification: A Resource for Amplifying Population-Genetic Signals with Protein Repeats.

Chen J, Wang B, Regan L, Gerstein M.

J Mol Biol. 2017 Feb 3;429(3):435-445. doi: 10.1016/j.jmb.2016.12.003. Epub 2016 Dec 7.

33.

Localized structural frustration for evaluating the impact of sequence variants.

Kumar S, Clarke D, Gerstein M.

Nucleic Acids Res. 2016 Dec 1;44(21):10062-10073. Epub 2016 Oct 18.

34.

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.

Wang D, He F, Maslov S, Gerstein M.

PLoS Comput Biol. 2016 Oct 19;12(10):e1005146. doi: 10.1371/journal.pcbi.1005146. eCollection 2016 Oct.

35.

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

Yang CC, Andrews EH, Chen MH, Wang WY, Chen JJ, Gerstein M, Liu CC, Cheng C.

BMC Genomics. 2016 Aug 12;17(1):632. doi: 10.1186/s12864-016-2963-0.

36.

Pangolin genomes and the evolution of mammalian scales and immunity.

Choo SW, Rayko M, Tan TK, Hari R, Komissarov A, Wee WY, Yurchenko AA, Kliver S, Tamazian G, Antunes A, Wilson RK, Warren WC, Koepfli KP, Minx P, Krasheninnikova K, Kotze A, Dalton DL, Vermaak E, Paterson IC, Dobrynin P, Sitam FT, Rovie-Ryan JJ, Johnson WE, Yusoff AM, Luo SJ, Karuppannan KV, Fang G, Zheng D, Gerstein MB, Lipovich L, O'Brien SJ, Wong GJ.

Genome Res. 2016 Oct;26(10):1312-1322. Epub 2016 Aug 10.

37.

Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma.

Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, Murthy V, Tanriverdi SE, Koupenova M, Mikhalev E, Tanriverdi K.

Nat Commun. 2016 Jun 3;7:11902. doi: 10.1038/ncomms11902. No abstract available.

38.

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation.

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M.

Genome Biol. 2016 Apr 28;17:78. doi: 10.1186/s13059-016-0961-9. No abstract available.

39.

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources.

Shah R, Tanriverdi K, Levy D, Larson M, Gerstein M, Mick E, Rozowsky J, Kitchen R, Murthy V, Mikalev E, Freedman JE.

PLoS One. 2016 Apr 28;11(4):e0153691. doi: 10.1371/journal.pone.0153691. eCollection 2016.

40.

Diverse human extracellular RNAs are widely detected in human plasma.

Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, Murthy V, Tanriverdi SE, Koupenova-Zamor M, Mikhalev E, Tanriverdi K.

Nat Commun. 2016 Apr 26;7:11106. doi: 10.1038/ncomms11106.

41.

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M.

Nat Commun. 2016 Apr 18;7:11101. doi: 10.1038/ncomms11101.

42.

Extending gene ontology in the context of extracellular RNA and vesicle communication.

Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC.

J Biomed Semantics. 2016 Apr 12;7:19. doi: 10.1186/s13326-016-0061-5. eCollection 2016.

43.

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation.

Clarke D, Sethi A, Li S, Kumar S, Chang RWF, Chen J, Gerstein M.

Structure. 2016 May 3;24(5):826-837. doi: 10.1016/j.str.2016.03.008. Epub 2016 Apr 7.

44.

Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.

Yan KK, Wang D, Sethi A, Muir P, Kitchen R, Cheng C, Gerstein M.

Cell Syst. 2016 Mar 23;2(3):147-157.

45.

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

He F, Yoo S, Wang D, Kumari S, Gerstein M, Ware D, Maslov S.

Plant J. 2016 Jun;86(6):472-80. doi: 10.1111/tpj.13175.

46.

The real cost of sequencing: scaling computation to keep pace with data generation.

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M.

Genome Biol. 2016 Mar 23;17:53. doi: 10.1186/s13059-016-0917-0. Erratum in: Genome Biol. 2016;17:78.

47.

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

Wang D, Yan KK, Rozowsky J, Pan E, Gerstein M.

Trends Genet. 2016 May;32(5):251-253. doi: 10.1016/j.tig.2016.02.006. Epub 2016 Mar 20.

PMID:
27005445
48.

Quantification of private information leakage from phenotype-genotype data: linking attacks.

Harmanci A, Gerstein M.

Nat Methods. 2016 Mar;13(3):251-6. doi: 10.1038/nmeth.3746. Epub 2016 Feb 1.

49.

Role of non-coding sequence variants in cancer.

Khurana E, Fu Y, Chakravarty D, Demichelis F, Rubin MA, Gerstein M.

Nat Rev Genet. 2016 Feb;17(2):93-108. doi: 10.1038/nrg.2015.17. Epub 2016 Jan 19. Review.

PMID:
26781813
50.

Reads meet rotamers: structural biology in the age of deep sequencing.

Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M.

Curr Opin Struct Biol. 2015 Dec;35:125-34. doi: 10.1016/j.sbi.2015.11.003. Epub 2015 Dec 1. Review.

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