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Items: 1 to 20 of 402

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.

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.

5.

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
6.

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.

7.

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
8.

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
9.

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
10.

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.

11.

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
12.

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
13.

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.

14.

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.

15.

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
16.

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.

17.

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
18.

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
19.

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.

20.

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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