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Items: 1 to 50 of 561

1.

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.

Navarro FC, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB.

PLoS Comput Biol. 2019 Aug 19;15(8):e1007293. doi: 10.1371/journal.pcbi.1007293. [Epub ahead of print]

2.

Whole exome sequencing in childhood-onset lupus frequently detects single gene etiologies.

Tirosh I, Spielman S, Barel O, Ram R, Stauber T, Paret G, Rubinsthein M, Pessach IM, Gerstein M, Anikster Y, Shukrun R, Dagan A, Adler K, Pode-Shakked B, Volkov A, Perelman M, Greenberger S, Somech R, Lahav E, Majmundar AJ, Padeh S, Hildebrandt F, Vivante A.

Pediatr Rheumatol Online J. 2019 Jul 30;17(1):52. doi: 10.1186/s12969-019-0349-y.

3.

A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.

Polioudakis D, de la Torre-Ubieta L, Langerman J, Elkins AG, Shi X, Stein JL, Vuong CK, Nichterwitz S, Gevorgian M, Opland CK, Lu D, Connell W, Ruzzo EK, Lowe JK, Hadzic T, Hinz FI, Sabri S, Lowry WE, Gerstein MB, Plath K, Geschwind DH.

Neuron. 2019 Jul 3. pii: S0896-6273(19)30561-6. doi: 10.1016/j.neuron.2019.06.011. [Epub ahead of print]

PMID:
31303374
4.

Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions.

Wang B, Yan C, Lou S, Emani P, Li B, Xu M, Kong X, Meyerson W, Yang YT, Lee D, Gerstein M.

Structure. 2019 Jun 26. pii: S0969-2126(19)30200-X. doi: 10.1016/j.str.2019.06.001. [Epub ahead of print]

PMID:
31279629
5.

Genomics and data science: an application within an umbrella.

Navarro FCP, Mohsen H, Yan C, Li S, Gu M, Meyerson W, Gerstein M.

Genome Biol. 2019 May 29;20(1):109. doi: 10.1186/s13059-019-1724-1. Review.

6.

Multi-platform discovery of haplotype-resolved structural variation in human genomes.

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C.

Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z.

7.

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Rozowsky J, Kitchen RR, Park JJ, Galeev TR, Diao J, Warrell J, Thistlethwaite W, Subramanian SL, Milosavljevic A, Gerstein M.

Cell Syst. 2019 Apr 24;8(4):352-357.e3. doi: 10.1016/j.cels.2019.03.004. Epub 2019 Apr 4.

8.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A.

Cell. 2019 Apr 4;177(2):463-477.e15. doi: 10.1016/j.cell.2019.02.018.

9.

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research.

Das S; Extracellular RNA Communication Consortium, Ansel KM, Bitzer M, Breakefield XO, Charest A, Galas DJ, Gerstein MB, Gupta M, Milosavljevic A, McManus MT, Patel T, Raffai RL, Rozowsky J, Roth ME, Saugstad JA, Van Keuren-Jensen K, Weaver AM, Laurent LC.

Cell. 2019 Apr 4;177(2):231-242. doi: 10.1016/j.cell.2019.03.023. Review.

PMID:
30951667
10.

Shaping the nebulous enhancer in the era of high-throughput assays and genome editing.

Ho EY, Cao Q, Gu M, Chan RW, Wu Q, Gerstein M, Yip KY.

Brief Bioinform. 2019 Mar 20. pii: bbz030. doi: 10.1093/bib/bbz030. [Epub ahead of print]

PMID:
30895290
11.

Measuring the reproducibility and quality of Hi-C data.

Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS.

Genome Biol. 2019 Mar 19;20(1):57. doi: 10.1186/s13059-019-1658-7.

12.

MicroRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis.

Moro A, Driscoll TP, Boraas LC, Armero W, Kasper DM, Baeyens N, Jouy C, Mallikarjun V, Swift J, Ahn SJ, Lee D, Zhang J, Gu M, Gerstein M, Schwartz M, Nicoli S.

Nat Cell Biol. 2019 Mar;21(3):348-358. doi: 10.1038/s41556-019-0272-y. Epub 2019 Feb 11.

13.

Insights into genetics, human biology and disease gleaned from family based genomic studies.

Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR; Centers for Mendelian Genomics.

Genet Med. 2019 Apr;21(4):798-812. doi: 10.1038/s41436-018-0408-7. Epub 2019 Jan 18. Review.

PMID:
30655598
14.

Next-Generation Sequencing to Diagnose Suspected Genetic Disorders.

Li S, Gerstein MB.

N Engl J Med. 2019 Jan 10;380(2):200. doi: 10.1056/NEJMc1814955. No abstract available.

PMID:
30628427
15.

Comprehensive functional genomic resource and integrative model for the human brain.

Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE; PsychENCODE Consortium, Roussos P, Akbarian S, Jaffe AE, White KP, Weng Z, Sestan N, Geschwind DH, Knowles JA, Gerstein MB.

Science. 2018 Dec 14;362(6420). pii: eaat8464. doi: 10.1126/science.aat8464.

16.

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.

Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE; PsychENCODE Consortium, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH.

Science. 2018 Dec 14;362(6420). pii: eaat8127. doi: 10.1126/science.aat8127.

17.

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.

Li M, Santpere G, Imamura Kawasawa Y, Evgrafov OV, Gulden FO, Pochareddy S, Sunkin SM, Li Z, Shin Y, Zhu Y, Sousa AMM, Werling DM, Kitchen RR, Kang HJ, Pletikos M, Choi J, Muchnik S, Xu X, Wang D, Lorente-Galdos B, Liu S, Giusti-Rodríguez P, Won H, de Leeuw CA, Pardiñas AF; BrainSpan Consortium; PsychENCODE Consortium; PsychENCODE Developmental Subgroup, Hu M, Jin F, Li Y, Owen MJ, O'Donovan MC, Walters JTR, Posthuma D, Reimers MA, Levitt P, Weinberger DR, Hyde TM, Kleinman JE, Geschwind DH, Hawrylycz MJ, State MW, Sanders SJ, Sullivan PF, Gerstein MB, Lein ES, Knowles JA, Sestan N.

Science. 2018 Dec 14;362(6420). pii: eaat7615. doi: 10.1126/science.aat7615.

18.

Transcriptome and epigenome landscape of human cortical development modeled in organoids.

Amiri A, Coppola G, Scuderi S, Wu F, Roychowdhury T, Liu F, Pochareddy S, Shin Y, Safi A, Song L, Zhu Y, Sousa AMM; PsychENCODE Consortium, Gerstein M, Crawford GE, Sestan N, Abyzov A, Vaccarino FM.

Science. 2018 Dec 14;362(6420). pii: eaat6720. doi: 10.1126/science.aat6720.

19.

Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.

Shi W, Ng CKY, Lim RS, Jiang T, Kumar S, Li X, Wali VB, Piscuoglio S, Gerstein MB, Chagpar AB, Weigelt B, Pusztai L, Reis-Filho JS, Hatzis C.

Cell Rep. 2018 Nov 6;25(6):1446-1457. doi: 10.1016/j.celrep.2018.10.046.

20.

GENCODE reference annotation for the human and mouse genomes.

Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P.

Nucleic Acids Res. 2019 Jan 8;47(D1):D766-D773. doi: 10.1093/nar/gky955.

21.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM.

Nat Genet. 2018 Nov;50(11):1574-1583. doi: 10.1038/s41588-018-0223-8. Epub 2018 Oct 1.

22.

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci.

Onuchic V, Lurie E, Carrero I, Pawliczek P, Patel RY, Rozowsky J, Galeev T, Huang Z, Altshuler RC, Zhang Z, Harris RA, Coarfa C, Ashmore L, Bertol JW, Fakhouri WD, Yu F, Kellis M, Gerstein M, Milosavljevic A.

Science. 2018 Sep 28;361(6409). pii: eaar3146. doi: 10.1126/science.aar3146. Epub 2018 Aug 23.

23.

Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.

Carlyle BC, Kitchen RR, Zhang J, Wilson RS, Lam TT, Rozowsky JS, Williams KR, Sestan N, Gerstein MB, Nairn AC.

J Proteome Res. 2018 Oct 5;17(10):3431-3444. doi: 10.1021/acs.jproteome.8b00310. Epub 2018 Sep 6.

PMID:
30125121
24.

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.

25.

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.

26.

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.

27.

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
28.

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.

29.

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.

30.

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.

31.

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
32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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
40.

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.

41.

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.

42.

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.

43.

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.

44.

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
45.

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.

46.

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
47.

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
48.

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.

49.

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.

50.

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.

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