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Items: 1 to 50 of 176

1.

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
2.

Chromatin Accessibility Impacts Transcriptional Reprogramming in Oocytes.

Miyamoto K, Nguyen KT, Allen GE, Jullien J, Kumar D, Otani T, Bradshaw CR, Livesey FJ, Kellis M, Gurdon JB.

Cell Rep. 2018 Jul 10;24(2):304-311. doi: 10.1016/j.celrep.2018.06.030.

3.

Salmonella enterica Serotype Javiana Infections Linked to a Seafood Restaurant in Maricopa County, Arizona, 2016.

Venkat H, Matthews J, Lumadao P, Caballero B, Collins J, Fowle N, Kellis M, Tewell M, White S, Hassan R, Classon A, Joung Y, Komatsu K, Weiss J, Zusy S, Sunenshine R.

J Food Prot. 2018 Aug;81(8):1283-1292. doi: 10.4315/0362-028X.JFP-17-494.

PMID:
29985066
4.

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, Ramachandran VS, 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 Jul 4;9(1):2606. doi: 10.1038/s41467-018-04668-w.

5.

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation.

Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J; GTEx Consortium, Nicolae DL, Eskin E, Kellis M, Getz G, McCarthy MI, Dermitzakis ET, Cox NJ, Ardlie KG.

Nat Genet. 2018 Jul;50(7):956-967. doi: 10.1038/s41588-018-0154-4. Epub 2018 Jun 28.

PMID:
29955180
6.

ncdDetect2: Improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation.

Juul M, Madsen T, Guo Q, Bertl J, Hobolth A, Kellis M, Pedersen JS.

Bioinformatics. 2018 Jun 26. doi: 10.1093/bioinformatics/bty511. [Epub ahead of print]

PMID:
29945188
7.

Outbreak of E. coli O157:H7 Infections Associated with Exposure to Animal Manure in a Rural Community - Arizona and Utah, June-July 2017.

Luna S, Krishnasamy V, Saw L, Smith L, Wagner J, Weigand J, Tewell M, Kellis M, Penev R, McCullough L, Eason J, McCaffrey K, Burnett C, Oakeson K, Dimond M, Nakashima A, Barlow D, Scherzer A, Sarino M, Schroeder M, Hassan R, Basler C, Wise M, Gieraltowski L.

MMWR Morb Mortal Wkly Rep. 2018 Jun 15;67(23):659-662. doi: 10.15585/mmwr.mm6723a2.

8.

Publisher Correction: N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, Zhang Z, Ogawa Y, Kellis M, Duester G, Zhao JC.

Nat Neurosci. 2018 Jun 7. doi: 10.1038/s41593-018-0169-2. [Epub ahead of print]

PMID:
29880878
9.

Multistate outbreak of Salmonella Paratyphi B variant L(+) tartrate(+) and Salmonella Weltevreden infections linked to imported frozen raw tuna: USA, March-July 2015.

Hassan R, Tecle S, Adcock B, Kellis M, Weiss J, Saupe A, Sorenson A, Klos R, Blankenship J, Blessington T, Whitlock L, Carleton HA, Concepción-Acevedo J, Tolar B, Wise M, Neil KP.

Epidemiol Infect. 2018 Aug;146(11):1461-1467. doi: 10.1017/S0950268818001462. Epub 2018 Jun 8.

PMID:
29880080
10.

Notes from the Field: Investigation of an Outbreak of Salmonella Paratyphi B Variant L(+) tartrate + (Java) Associated with Ball Python Exposure - United States, 2017.

Krishnasamy V, Stevenson L, Koski L, Kellis M, Schroeder B, Sundararajan M, Ladd-Wilson S, Sampsel A, Mannell M, Classon A, Wagner D, Hise K, Carleton H, Trees E, Schlater L, Lantz K, Nichols M.

MMWR Morb Mortal Wkly Rep. 2018 May 19;67(19):562-563. doi: 10.15585/mmwr.mm6719a7. No abstract available.

11.

RANGER-DTL 2.0: Rigorous Reconstruction of Gene-Family Evolution by Duplication, Transfer, and Loss.

Bansal MS, Kellis M, Kordi M, Kundu S.

Bioinformatics. 2018 Apr 24. doi: 10.1093/bioinformatics/bty314. [Epub ahead of print]

PMID:
29688310
12.

Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response.

Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF.

J Biol Chem. 2018 Mar 23;293(12):4434-4444. doi: 10.1074/jbc.M117.818526. Epub 2018 Jan 31.

13.

Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival.

Hornshøj H, Nielsen MM, Sinnott-Armstrong NA, Świtnicki MP, Juul M, Madsen T, Sallari R, Kellis M, Ørntoft T, Hobolth A, Pedersen JS.

NPJ Genom Med. 2018 Jan 11;3:1. doi: 10.1038/s41525-017-0040-5. eCollection 2018.

14.

N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

Wang Y, Li Y, Yue M, Wang J, Kumar S, Wechsler-Reya RJ, Zhang Z, Ogawa Y, Kellis M, Duester G, Zhao JC.

Nat Neurosci. 2018 Feb;21(2):195-206. doi: 10.1038/s41593-017-0057-1. Epub 2018 Jan 15. Erratum in: Nat Neurosci. 2018 Jun 7;:.

PMID:
29335608
15.

Chromatin-state discovery and genome annotation with ChromHMM.

Ernst J, Kellis M.

Nat Protoc. 2017 Dec;12(12):2478-2492. doi: 10.1038/nprot.2017.124. Epub 2017 Nov 9. Review.

16.

Evidence of reduced recombination rate in human regulatory domains.

Liu Y, Sarkar A, Kheradpour P, Ernst J, Kellis M.

Genome Biol. 2017 Oct 20;18(1):193. doi: 10.1186/s13059-017-1308-x.

17.

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.

Day FR, Thompson DJ, Helgason H, Chasman DI, Finucane H, Sulem P, Ruth KS, Whalen S, Sarkar AK, Albrecht E, Altmaier E, Amini M, Barbieri CM, Boutin T, Campbell A, Demerath E, Giri A, He C, Hottenga JJ, Karlsson R, Kolcic I, Loh PR, Lunetta KL, Mangino M, Marco B, McMahon G, Medland SE, Nolte IM, Noordam R, Nutile T, Paternoster L, Perjakova N, Porcu E, Rose LM, Schraut KE, Segrè AV, Smith AV, Stolk L, Teumer A, Andrulis IL, Bandinelli S, Beckmann MW, Benitez J, Bergmann S, Bochud M, Boerwinkle E, Bojesen SE, Bolla MK, Brand JS, Brauch H, Brenner H, Broer L, Brüning T, Buring JE, Campbell H, Catamo E, Chanock S, Chenevix-Trench G, Corre T, Couch FJ, Cousminer DL, Cox A, Crisponi L, Czene K, Davey Smith G, de Geus EJCN, de Mutsert R, De Vivo I, Dennis J, Devilee P, Dos-Santos-Silva I, Dunning AM, Eriksson JG, Fasching PA, Fernández-Rhodes L, Ferrucci L, Flesch-Janys D, Franke L, Gabrielson M, Gandin I, Giles GG, Grallert H, Gudbjartsson DF, Guénel P, Hall P, Hallberg E, Hamann U, Harris TB, Hartman CA, Heiss G, Hooning MJ, Hopper JL, Hu F, Hunter DJ, Ikram MA, Im HK, Järvelin MR, Joshi PK, Karasik D, Kellis M, Kutalik Z, LaChance G, Lambrechts D, Langenberg C, Launer LJ, Laven JSE, Lenarduzzi S, Li J, Lind PA, Lindstrom S, Liu Y, Luan J, Mägi R, Mannermaa A, Mbarek H, McCarthy MI, Meisinger C, Meitinger T, Menni C, Metspalu A, Michailidou K, Milani L, Milne RL, Montgomery GW, Mulligan AM, Nalls MA, Navarro P, Nevanlinna H, Nyholt DR, Oldehinkel AJ, O'Mara TA, Padmanabhan S, Palotie A, Pedersen N, Peters A, Peto J, Pharoah PDP, Pouta A, Radice P, Rahman I, Ring SM, Robino A, Rosendaal FR, Rudan I, Rueedi R, Ruggiero D, Sala CF, Schmidt MK, Scott RA, Shah M, Sorice R, Southey MC, Sovio U, Stampfer M, Steri M, Strauch K, Tanaka T, Tikkanen E, Timpson NJ, Traglia M, Truong T, Tyrer JP, Uitterlinden AG, Edwards DRV, Vitart V, Völker U, Vollenweider P, Wang Q, Widen E, van Dijk KW, Willemsen G, Winqvist R, Wolffenbuttel BHR, Zhao JH, Zoledziewska M, Zygmunt M, Alizadeh BZ, Boomsma DI, Ciullo M, Cucca F, Esko T, Franceschini N, Gieger C, Gudnason V, Hayward C, Kraft P, Lawlor DA, Magnusson PKE, Martin NG, Mook-Kanamori DO, Nohr EA, Polasek O, Porteous D, Price AL, Ridker PM, Snieder H, Spector TD, Stöckl D, Toniolo D, Ulivi S, Visser JA, Völzke H, Wareham NJ, Wilson JF; LifeLines Cohort Study; InterAct Consortium; kConFab/AOCS Investigators; Endometrial Cancer Association Consortium; Ovarian Cancer Association Consortium; PRACTICAL consortium, Spurdle AB, Thorsteindottir U, Pollard KS, Easton DF, Tung JY, Chang-Claude J, Hinds D, Murray A, Murabito JM, Stefansson K, Ong KK, Perry JRB.

Nat Genet. 2017 Jun;49(6):834-841. doi: 10.1038/ng.3841. Epub 2017 Apr 24.

18.

Multi-scale chromatin state annotation using a hierarchical hidden Markov model.

Marco E, Meuleman W, Huang J, Glass K, Pinello L, Wang J, Kellis M, Yuan GC.

Nat Commun. 2017 Apr 7;8:15011. doi: 10.1038/ncomms15011.

19.

Predicting gene expression in massively parallel reporter assays: A comparative study.

Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N.

Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9.

PMID:
28220625
20.

Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo.

Le Gros MA, Clowney EJ, Magklara A, Yen A, Markenscoff-Papadimitriou E, Colquitt B, Myllys M, Kellis M, Lomvardas S, Larabell CA.

Cell Rep. 2016 Nov 15;17(8):2125-2136. doi: 10.1016/j.celrep.2016.10.060.

21.

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.

Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M.

Nat Biotechnol. 2016 Nov;34(11):1180-1190. doi: 10.1038/nbt.3678. Epub 2016 Oct 3.

22.

SwiSpot: modeling riboswitches by spotting out switching sequences.

Barsacchi M, Novoa EM, Kellis M, Bechini A.

Bioinformatics. 2016 Nov 1;32(21):3252-3259. Epub 2016 Jul 4.

PMID:
27378291
23.

52 Genetic Loci Influencing Myocardial Mass.

van der Harst P, van Setten J, Verweij N, Vogler G, Franke L, Maurano MT, Wang X, Mateo Leach I, Eijgelsheim M, Sotoodehnia N, Hayward C, Sorice R, Meirelles O, Lyytikäinen LP, Polašek O, Tanaka T, Arking DE, Ulivi S, Trompet S, Müller-Nurasyid M, Smith AV, Dörr M, Kerr KF, Magnani JW, Del Greco M F, Zhang W, Nolte IM, Silva CT, Padmanabhan S, Tragante V, Esko T, Abecasis GR, Adriaens ME, Andersen K, Barnett P, Bis JC, Bodmer R, Buckley BM, Campbell H, Cannon MV, Chakravarti A, Chen LY, Delitala A, Devereux RB, Doevendans PA, Dominiczak AF, Ferrucci L, Ford I, Gieger C, Harris TB, Haugen E, Heinig M, Hernandez DG, Hillege HL, Hirschhorn JN, Hofman A, Hubner N, Hwang SJ, Iorio A, Kähönen M, Kellis M, Kolcic I, Kooner IK, Kooner JS, Kors JA, Lakatta EG, Lage K, Launer LJ, Levy D, Lundby A, Macfarlane PW, May D, Meitinger T, Metspalu A, Nappo S, Naitza S, Neph S, Nord AS, Nutile T, Okin PM, Olsen JV, Oostra BA, Penninger JM, Pennacchio LA, Pers TH, Perz S, Peters A, Pinto YM, Pfeufer A, Pilia MG, Pramstaller PP, Prins BP, Raitakari OT, Raychaudhuri S, Rice KM, Rossin EJ, Rotter JI, Schafer S, Schlessinger D, Schmidt CO, Sehmi J, Silljé HHW, Sinagra G, Sinner MF, Slowikowski K, Soliman EZ, Spector TD, Spiering W, Stamatoyannopoulos JA, Stolk RP, Strauch K, Tan ST, Tarasov KV, Trinh B, Uitterlinden AG, van den Boogaard M, van Duijn CM, van Gilst WH, Viikari JS, Visscher PM, Vitart V, Völker U, Waldenberger M, Weichenberger CX, Westra HJ, Wijmenga C, Wolffenbuttel BH, Yang J, Bezzina CR, Munroe PB, Snieder H, Wright AF, Rudan I, Boyer LA, Asselbergs FW, van Veldhuisen DJ, Stricker BH, Psaty BM, Ciullo M, Sanna S, Lehtimäki T, Wilson JF, Bandinelli S, Alonso A, Gasparini P, Jukema JW, Kääb S, Gudnason V, Felix SB, Heckbert SR, de Boer RA, Newton-Cheh C, Hicks AA, Chambers JC, Jamshidi Y, Visel A, Christoffels VM, Isaacs A, Samani NJ, de Bakker PIW.

J Am Coll Cardiol. 2016 Sep 27;68(13):1435-1448. doi: 10.1016/j.jacc.2016.07.729.

24.

Evolutionary Dynamics of Abundant Stop Codon Readthrough.

Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M.

Mol Biol Evol. 2016 Dec;33(12):3108-3132. Epub 2016 Sep 7.

25.
26.

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures.

Wang X, Tucker NR, Rizki G, Mills R, Krijger PH, de Wit E, Subramanian V, Bartell E, Nguyen XX, Ye J, Leyton-Mange J, Dolmatova EV, van der Harst P, de Laat W, Ellinor PT, Newton-Cheh C, Milan DJ, Kellis M, Boyer LA.

Elife. 2016 May 10;5. pii: e10557. doi: 10.7554/eLife.10557.

27.

Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure.

Smith JG, Felix JF, Morrison AC, Kalogeropoulos A, Trompet S, Wilk JB, Gidlöf O, Wang X, Morley M, Mendelson M, Joehanes R, Ligthart S, Shan X, Bis JC, Wang YA, Sjögren M, Ngwa J, Brandimarto J, Stott DJ, Aguilar D, Rice KM, Sesso HD, Demissie S, Buckley BM, Taylor KD, Ford I, Yao C, Liu C; CHARGE-SCD consortium; EchoGen consortium; QT-IGC consortium; CHARGE-QRS consortium, Sotoodehnia N, van der Harst P, Stricker BH, Kritchevsky SB, Liu Y, Gaziano JM, Hofman A, Moravec CS, Uitterlinden AG, Kellis M, van Meurs JB, Margulies KB, Dehghan A, Levy D, Olde B, Psaty BM, Cupples LA, Jukema JW, Djousse L, Franco OH, Boerwinkle E, Boyer LA, Newton-Cheh C, Butler J, Vasan RS, Cappola TP, Smith NL.

PLoS Genet. 2016 May 5;12(5):e1006034. doi: 10.1371/journal.pgen.1006034. eCollection 2016 May.

28.

Survey of variation in human transcription factors reveals prevalent DNA binding changes.

Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML.

Science. 2016 Mar 25;351(6280):1450-1454. doi: 10.1126/science.aad2257. Epub 2016 Mar 24.

29.

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides.

Ma J, Diedrich JK, Jungreis I, Donaldson C, Vaughan J, Kellis M, Yates JR 3rd, Saghatelian A.

Anal Chem. 2016 Apr 5;88(7):3967-75. doi: 10.1021/acs.analchem.6b00191. Epub 2016 Mar 24.

30.

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases.

Marbach D, Lamparter D, Quon G, Kellis M, Kutalik Z, Bergmann S.

Nat Methods. 2016 Apr;13(4):366-70. doi: 10.1038/nmeth.3799. Epub 2016 Mar 7.

31.

MicroRNA and gene expression changes in unruptured human cerebral aneurysms.

Bekelis K, Kerley-Hamilton JS, Teegarden A, Tomlinson CR, Kuintzle R, Simmons N, Singer RJ, Roberts DW, Kellis M, Hendrix DA.

J Neurosurg. 2016 Dec;125(6):1390-1399. Epub 2016 Feb 26.

32.

FTO Obesity Variant and Adipocyte Browning in Humans.

Claussnitzer M, Hui CC, Kellis M.

N Engl J Med. 2016 Jan 14;374(2):192-3. doi: 10.1056/NEJMc1513316. No abstract available.

PMID:
26760096
33.

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease.

Ward LD, Kellis M.

Nucleic Acids Res. 2016 Jan 4;44(D1):D877-81. doi: 10.1093/nar/gkv1340. Epub 2015 Dec 10.

34.

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells.

Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH.

Cell Rep. 2015 Sep 1;12(9):1456-70. doi: 10.1016/j.celrep.2015.07.053. Epub 2015 Aug 20.

35.

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.

Claussnitzer M, Dankel SN, Kim KH, Quon G, Meuleman W, Haugen C, Glunk V, Sousa IS, Beaudry JL, Puviindran V, Abdennur NA, Liu J, Svensson PA, Hsu YH, Drucker DJ, Mellgren G, Hui CC, Hauner H, Kellis M.

N Engl J Med. 2015 Sep 3;373(10):895-907. doi: 10.1056/NEJMoa1502214. Epub 2015 Aug 19.

36.
37.

Deep learning for regulatory genomics.

Park Y, Kellis M.

Nat Biotechnol. 2015 Aug;33(8):825-6. doi: 10.1038/nbt.3313. No abstract available.

PMID:
26252139
38.

Alzheimer's loci: epigenetic associations and interaction with genetic factors.

Chibnik LB, Yu L, Eaton ML, Srivastava G, Schneider JA, Kellis M, Bennett DA, De Jager PL.

Ann Clin Transl Neurol. 2015 Jun;2(6):636-47. doi: 10.1002/acn3.201. Epub 2015 Apr 24.

39.

Context influences on TALE-DNA binding revealed by quantitative profiling.

Rogers JM, Barrera LA, Reyon D, Sander JD, Kellis M, Joung JK, Bulyk ML.

Nat Commun. 2015 Jun 11;6:7440. doi: 10.1038/ncomms8440.

40.

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes.

Madabhushi R, Gao F, Pfenning AR, Pan L, Yamakawa S, Seo J, Rueda R, Phan TX, Yamakawa H, Pao PC, Stott RT, Gjoneska E, Nott A, Cho S, Kellis M, Tsai LH.

Cell. 2015 Jun 18;161(7):1592-605. doi: 10.1016/j.cell.2015.05.032. Epub 2015 Jun 4.

41.

Sharing and Specificity of Co-expression Networks across 35 Human Tissues.

Pierson E; GTEx Consortium, Koller D, Battle A, Mostafavi S, Ardlie KG, Getz G, Wright FA, Kellis M, Volpi S, Dermitzakis ET.

PLoS Comput Biol. 2015 May 13;11(5):e1004220. doi: 10.1371/journal.pcbi.1004220. eCollection 2015 May.

42.

FRESCo: finding regions of excess synonymous constraint in diverse viruses.

Sealfon RS, Lin MF, Jungreis I, Wolf MY, Kellis M, Sabeti PC.

Genome Biol. 2015 Feb 17;16:38. doi: 10.1186/s13059-015-0603-7.

43.

Corrigendum: Network deconvolution as a general method to distinguish direct dependencies in networks.

Feizi S, Marbach D, Médard M, Kellis M.

Nat Biotechnol. 2015 Apr;33(4):424. doi: 10.1038/nbt0415-424. No abstract available.

PMID:
25850062
44.

Preface: RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2014 Special Issue.

Califano A, Kellis M, Stolovitzky G.

J Comput Biol. 2015 Apr;22(4):251-2. doi: 10.1089/cmb.2015.020P. No abstract available.

PMID:
25844665
45.

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.

Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P; Type 1 Diabetes Genetics Consortium, Todd JA, Wallace C, Concannon P, Rich SS.

Nat Genet. 2015 Apr;47(4):381-6. doi: 10.1038/ng.3245. Epub 2015 Mar 9.

46.

BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair.

Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, Dimitrov S, Pathania S, McKinney KM, Eaton ML, Kellis M, Hill SJ, Parmigiani G, Proudfoot NJ, Livingston DM.

Mol Cell. 2015 Feb 19;57(4):636-647. doi: 10.1016/j.molcel.2015.01.011.

47.

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease.

Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M.

Nature. 2015 Feb 19;518(7539):365-9. doi: 10.1038/nature14252.

48.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

49.

Intermediate DNA methylation is a conserved signature of genome regulation.

Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJ, Maire CL, Ligon KL, Sigaroudinia M, Gascard P, Tlsty TD, Harris RA, Schalkwyk LC, Bilenky M, Mill J, Farnham PJ, Kellis M, Marra MA, Milosavljevic A, Hirst M, Stormo GD, Wang T, Costello JF.

Nat Commun. 2015 Feb 18;6:6363. doi: 10.1038/ncomms7363.

50.

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues.

Ernst J, Kellis M.

Nat Biotechnol. 2015 Apr;33(4):364-76. doi: 10.1038/nbt.3157. Epub 2015 Feb 18.

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