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Items: 1 to 20 of 213

1.

Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization.

Liu D, Davila-Velderrain J, Zhang Z, Kellis M.

Nucleic Acids Res. 2019 Jul 2. pii: gkz538. doi: 10.1093/nar/gkz538. [Epub ahead of print]

PMID:
31265076
2.

A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS).

Wu MR, Nissim L, Stupp D, Pery E, Binder-Nissim A, Weisinger K, Enghuus C, Palacios SR, Humphrey M, Zhang Z, Maria Novoa E, Kellis M, Weiss R, Rabkin SD, Tabach Y, Lu TK.

Nat Commun. 2019 Jun 28;10(1):2880. doi: 10.1038/s41467-019-10912-8.

3.

Corrigendum: Loss of LDAH associated with prostate cancer and hearing loss.

Currall BB, Chen M, Sallari RC, Cotter M, Wong KE, Robertson NG, Penney KL, Lunardi A, Reschke M, Hickox AE, Yin Y, Wong GT, Fung J, Brown KK, Williamson RE, Sinnott-Armstrong NA, Kammin T, Ivanov A, Zepeda-Mendoza CJ, Shen J, Quade BJ, Signoretti S, Arnos KS, Banks AS, Patsopoulos N, Liberman MC, Kellis M, Pandolfi PP, Morton CC.

Hum Mol Genet. 2019 May 15;28(10):1753-1754. doi: 10.1093/hmg/ddz036. No abstract available.

4.

Elucidation of Codon Usage Signatures across the Domains of Life.

Novoa EM, Jungreis I, Jaillon O, Kellis M.

Mol Biol Evol. 2019 May 20. pii: msz124. doi: 10.1093/molbev/msz124. [Epub ahead of print]

PMID:
31220870
5.

Author Correction: Single-cell transcriptomic analysis of Alzheimer's disease.

Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ, Ransohoff RM, Hafler BP, Bennett DA, Kellis M, Tsai LH.

Nature. 2019 Jul;571(7763):E1. doi: 10.1038/s41586-019-1329-6.

PMID:
31209304
6.

Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer's disease.

Glorioso CA, Pfenning AR, Lee SS, Bennett DA, Sibille EL, Kellis M, Guarente LP.

Life Sci Alliance. 2019 May 27;2(3). pii: e201900303. doi: 10.26508/lsa.201900303. Print 2019 Jun.

7.

Challenges in IBD Research: Environmental Triggers.

Ho SM, Lewis JD, Mayer EA, Plevy SE, Chuang E, Rappaport SM, Croitoru K, Korzenik JR, Krischer J, Hyams JS, Judson R, Kellis M, Jerrett M, Miller GW, Grant ML, Shtraizent N, Honig G, Hurtado-Lorenzo A, Wu GD.

Inflamm Bowel Dis. 2019 May 16;25(Supplement_2):S13-S23. doi: 10.1093/ibd/izz076.

PMID:
31095702
8.

Single-cell transcriptomic analysis of Alzheimer's disease.

Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ, Ransohoff RM, Hafler BP, Bennett DA, Kellis M, Tsai LH.

Nature. 2019 Jun;570(7761):332-337. doi: 10.1038/s41586-019-1195-2. Epub 2019 May 1. Erratum in: Nature. 2019 Jun 17;:.

PMID:
31042697
9.

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP.

Development. 2019 Mar 28;146(6). pii: dev175265. doi: 10.1242/dev.175265.

10.

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use.

Liu M, Jiang Y, Wedow R, Li Y, Brazel DM, Chen F, Datta G, Davila-Velderrain J, McGuire D, Tian C, Zhan X; 23andMe Research Team; HUNT All-In Psychiatry, Choquet H, Docherty AR, Faul JD, Foerster JR, Fritsche LG, Gabrielsen ME, Gordon SD, Haessler J, Hottenga JJ, Huang H, Jang SK, Jansen PR, Ling Y, Mägi R, Matoba N, McMahon G, Mulas A, Orrù V, Palviainen T, Pandit A, Reginsson GW, Skogholt AH, Smith JA, Taylor AE, Turman C, Willemsen G, Young H, Young KA, Zajac GJM, Zhao W, Zhou W, Bjornsdottir G, Boardman JD, Boehnke M, Boomsma DI, Chen C, Cucca F, Davies GE, Eaton CB, Ehringer MA, Esko T, Fiorillo E, Gillespie NA, Gudbjartsson DF, Haller T, Harris KM, Heath AC, Hewitt JK, Hickie IB, Hokanson JE, Hopfer CJ, Hunter DJ, Iacono WG, Johnson EO, Kamatani Y, Kardia SLR, Keller MC, Kellis M, Kooperberg C, Kraft P, Krauter KS, Laakso M, Lind PA, Loukola A, Lutz SM, Madden PAF, Martin NG, McGue M, McQueen MB, Medland SE, Metspalu A, Mohlke KL, Nielsen JB, Okada Y, Peters U, Polderman TJC, Posthuma D, Reiner AP, Rice JP, Rimm E, Rose RJ, Runarsdottir V, Stallings MC, Stančáková A, Stefansson H, Thai KK, Tindle HA, Tyrfingsson T, Wall TL, Weir DR, Weisner C, Whitfield JB, Winsvold BS, Yin J, Zuccolo L, Bierut LJ, Hveem K, Lee JJ, Munafò MR, Saccone NL, Willer CJ, Cornelis MC, David SP, Hinds DA, Jorgenson E, Kaprio J, Stitzel JA, Stefansson K, Thorgeirsson TE, Abecasis G, Liu DJ, Vrieze S.

Nat Genet. 2019 Feb;51(2):237-244. doi: 10.1038/s41588-018-0307-5. Epub 2019 Jan 14.

11.

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.

Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E.

Genome Res. 2019 Feb;29(2):223-235. doi: 10.1101/gr.230243.117. Epub 2019 Jan 3.

PMID:
30606742
12.

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human.

Wang X, He L, Goggin SM, Saadat A, Wang L, Sinnott-Armstrong N, Claussnitzer M, Kellis M.

Nat Commun. 2018 Dec 19;9(1):5380. doi: 10.1038/s41467-018-07746-1.

13.

Corrigendum: Loose ends: almost one in five human genes still have unresolved coding status.

Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML.

Nucleic Acids Res. 2018 Dec 14;46(22):12194. doi: 10.1093/nar/gky1146. No abstract available.

14.

Target site specificity and in vivo complexity of the mammalian arginylome.

Wang J, Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A.

Sci Rep. 2018 Nov 1;8(1):16177. doi: 10.1038/s41598-018-34639-6.

15.

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.

16.

Loss of LDAH associated with prostate cancer and hearing loss.

Currall BB, Chen M, Sallari RC, Cotter M, Wong KE, Robertson NG, Penney KL, Lunardi A, Reschke M, Hickox AE, Yin Y, Wong GT, Fung J, Brown KK, Williamson RE, Sinnott-Armstrong NA, Kammin T, Ivanov A, Zepeda-Mendoza CJ, Shen J, Quade BJ, Signoretti S, Arnos KS, Banks AS, Patsopoulos N, Liberman MC, Kellis M, Pandolfi PP, Morton CC.

Hum Mol Genet. 2018 Dec 15;27(24):4194-4203. doi: 10.1093/hmg/ddy310. Erratum in: Hum Mol Genet. 2019 May 15;28(10):1753-1754.

PMID:
30169630
17.

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Vasan RS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P; NHLBI TOPMed Lipids Working Group.

Nat Commun. 2018 Aug 23;9(1):3493. doi: 10.1038/s41467-018-05975-y.

18.

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals.

Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S; NHLBI TOPMed Lipids Working Group.

Nat Commun. 2018 Aug 23;9(1):3391. doi: 10.1038/s41467-018-05747-8.

19.

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.

20.

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.

Beaudoin JD, Novoa EM, Vejnar CE, Yartseva V, Takacs CM, Kellis M, Giraldez AJ.

Nat Struct Mol Biol. 2018 Aug;25(8):677-686. doi: 10.1038/s41594-018-0091-z. Epub 2018 Jul 30.

PMID:
30061596

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