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Items: 26

1.

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.

McDowell IC, Barrera A, D'Ippolito AM, Vockley CM, Hong LK, Leichter SM, Bartelt LC, Majoros WH, Song L, Safi A, Koçak DD, Gersbach CA, Hartemink AJ, Crawford GE, Engelhardt BE, Reddy TE.

Genome Res. 2018 Aug 10. doi: 10.1101/gr.233346.117. [Epub ahead of print]

2.

Statistical tests for detecting variance effects in quantitative trait studies.

Dumitrascu B, Darnell G, Ayroles J, Engelhardt BE.

Bioinformatics. 2018 Jul 6. doi: 10.1093/bioinformatics/bty565. [Epub ahead of print]

PMID:
29982387
3.

Bayesian nonparametric discovery of isoforms and individual specific quantification.

Aguiar D, Cheng LF, Dumitrascu B, Mordelet F, Pai AA, Engelhardt BE.

Nat Commun. 2018 Apr 27;9(1):1681. doi: 10.1038/s41467-018-03402-w.

4.

Expandable factor analysis.

Srivastava S, Engelhardt BE, Dunson DB.

Biometrika. 2017 Sep;104(3):649-663. doi: 10.1093/biomet/asx030. Epub 2017 Jun 16.

PMID:
29430037
5.

Clustering gene expression time series data using an infinite Gaussian process mixture model.

McDowell IC, Manandhar D, Vockley CM, Schmid AK, Reddy TE, Engelhardt BE.

PLoS Comput Biol. 2018 Jan 16;14(1):e1005896. doi: 10.1371/journal.pcbi.1005896. eCollection 2018 Jan.

6.

Genetic effects on gene expression across human tissues.

GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz; Lead analysts:; Laboratory, Data Analysis &Coordinating Center (LDACC):; NIH program management:; Biospecimen collection:; Pathology:; eQTL manuscript working group:, Battle A, Brown CD, Engelhardt BE, Montgomery SB.

Nature. 2017 Oct 11;550(7675):204-213. doi: 10.1038/nature24277. Erratum in: Nature. 2017 Dec 20;:.

7.

Co-expression networks reveal the tissue-specific regulation of transcription and splicing.

Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC; GTEx Consortium, Engelhardt BE, Battle A.

Genome Res. 2017 Nov;27(11):1843-1858. doi: 10.1101/gr.216721.116. Epub 2017 Oct 11.

8.

Detecting differential growth of microbial populations with Gaussian process regression.

Tonner PD, Darnell CL, Engelhardt BE, Schmid AK.

Genome Res. 2017 Feb;27(2):320-333. doi: 10.1101/gr.210286.116. Epub 2016 Nov 18.

9.

Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering.

Gao C, McDowell IC, Zhao S, Brown CD, Engelhardt BE.

PLoS Comput Biol. 2016 Jul 28;12(7):e1004791. doi: 10.1371/journal.pcbi.1004791. eCollection 2016 Jul.

10.

Diving deeper to predict noncoding sequence function.

Engelhardt BE, Brown CD.

Nat Methods. 2015 Oct;12(10):925-6. doi: 10.1038/nmeth.3604. No abstract available.

PMID:
26418766
11.

Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium.

van den Berg SM, de Moor MH, Verweij KJ, Krueger RF, Luciano M, Arias Vasquez A, Matteson LK, Derringer J, Esko T, Amin N, Gordon SD, Hansell NK, Hart AB, Seppälä I, Huffman JE, Konte B, Lahti J, Lee M, Miller M, Nutile T, Tanaka T, Teumer A, Viktorin A, Wedenoja J, Abdellaoui A, Abecasis GR, Adkins DE, Agrawal A, Allik J, Appel K, Bigdeli TB, Busonero F, Campbell H, Costa PT, Smith GD, Davies G, de Wit H, Ding J, Engelhardt BE, Eriksson JG, Fedko IO, Ferrucci L, Franke B, Giegling I, Grucza R, Hartmann AM, Heath AC, Heinonen K, Henders AK, Homuth G, Hottenga JJ, Iacono WG, Janzing J, Jokela M, Karlsson R, Kemp JP, Kirkpatrick MG, Latvala A, Lehtimäki T, Liewald DC, Madden PA, Magri C, Magnusson PK, Marten J, Maschio A, Mbarek H, Medland SE, Mihailov E, Milaneschi Y, Montgomery GW, Nauck M, Nivard MG, Ouwens KG, Palotie A, Pettersson E, Polasek O, Qian Y, Pulkki-Råback L, Raitakari OT, Realo A, Rose RJ, Ruggiero D, Schmidt CO, Slutske WS, Sorice R, Starr JM, St Pourcain B, Sutin AR, Timpson NJ, Trochet H, Vermeulen S, Vuoksimaa E, Widen E, Wouda J, Wright MJ, Zgaga L; Generation Scotland, Porteous D, Minelli A, Palmer AA, Rujescu D, Ciullo M, Hayward C, Rudan I, Metspalu A, Kaprio J, Deary IJ, Räikkönen K, Wilson JF, Keltikangas-Järvinen L, Bierut LJ, Hettema JM, Grabe HJ, Penninx BW, van Duijn CM, Evans DM, Schlessinger D, Pedersen NL, Terracciano A, McGue M, Martin NG, Boomsma DI.

Behav Genet. 2016 Mar;46(2):170-82. doi: 10.1007/s10519-015-9735-5. Epub 2015 Sep 11.

12.

Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure.

Mimno D, Blei DM, Engelhardt BE.

Proc Natl Acad Sci U S A. 2015 Jun 30;112(26):E3441-50. doi: 10.1073/pnas.1412301112. Epub 2015 Jun 12.

13.

Meta-analysis of Genome-wide Association Studies for Neuroticism, and the Polygenic Association With Major Depressive Disorder.

Genetics of Personality Consortium, de Moor MH, van den Berg SM, Verweij KJ, Krueger RF, Luciano M, Arias Vasquez A, Matteson LK, Derringer J, Esko T, Amin N, Gordon SD, Hansell NK, Hart AB, Seppälä I, Huffman JE, Konte B, Lahti J, Lee M, Miller M, Nutile T, Tanaka T, Teumer A, Viktorin A, Wedenoja J, Abecasis GR, Adkins DE, Agrawal A, Allik J, Appel K, Bigdeli TB, Busonero F, Campbell H, Costa PT, Davey Smith G, Davies G, de Wit H, Ding J, Engelhardt BE, Eriksson JG, Fedko IO, Ferrucci L, Franke B, Giegling I, Grucza R, Hartmann AM, Heath AC, Heinonen K, Henders AK, Homuth G, Hottenga JJ, Iacono WG, Janzing J, Jokela M, Karlsson R, Kemp JP, Kirkpatrick MG, Latvala A, Lehtimäki T, Liewald DC, Madden PA, Magri C, Magnusson PK, Marten J, Maschio A, Medland SE, Mihailov E, Milaneschi Y, Montgomery GW, Nauck M, Ouwens KG, Palotie A, Pettersson E, Polasek O, Qian Y, Pulkki-Råback L, Raitakari OT, Realo A, Rose RJ, Ruggiero D, Schmidt CO, Slutske WS, Sorice R, Starr JM, St Pourcain B, Sutin AR, Timpson NJ, Trochet H, Vermeulen S, Vuoksimaa E, Widen E, Wouda J, Wright MJ, Zgaga L, Porteous D, Minelli A, Palmer AA, Rujescu D, Ciullo M, Hayward C, Rudan I, Metspalu A, Kaprio J, Deary IJ, Räikkönen K, Wilson JF, Keltikangas-Järvinen L, Bierut LJ, Hettema JM, Grabe HJ, van Duijn CM, Evans DM, Schlessinger D, Pedersen NL, Terracciano A, McGue M, Penninx BW, Martin NG, Boomsma DI.

JAMA Psychiatry. 2015 Jul;72(7):642-50. doi: 10.1001/jamapsychiatry.2015.0554.

14.

Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements.

Zhang W, Spector TD, Deloukas P, Bell JT, Engelhardt BE.

Genome Biol. 2015 Jan 24;16:14. doi: 10.1186/s13059-015-0581-9.

15.

Mangravite et al. reply.

Mangravite LM, Engelhardt BE, Stephens M, Krauss RM.

Nature. 2014 Sep 18;513(7518):E3. doi: 10.1038/nature13630. No abstract available.

PMID:
25230670
16.

Genetic variation associated with euphorigenic effects of d-amphetamine is associated with diminished risk for schizophrenia and attention deficit hyperactivity disorder.

Hart AB, Gamazon ER, Engelhardt BE, Sklar P, Kähler AK, Hultman CM, Sullivan PF, Neale BM, Faraone SV; Psychiatric Genomics Consortium: ADHD Subgroup, de Wit H, Cox NJ, Palmer AA.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):5968-73. doi: 10.1073/pnas.1318810111. Epub 2014 Apr 7.

17.

A statin-dependent QTL for GATM expression is associated with statin-induced myopathy.

Mangravite LM, Engelhardt BE, Medina MW, Smith JD, Brown CD, Chasman DI, Mecham BH, Howie B, Shim H, Naidoo D, Feng Q, Rieder MJ, Chen YD, Rotter JI, Ridker PM, Hopewell JC, Parish S, Armitage J, Collins R, Wilke RA, Nickerson DA, Stephens M, Krauss RM.

Nature. 2013 Oct 17;502(7471):377-80. doi: 10.1038/nature12508. Epub 2013 Aug 28.

18.

Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs.

Brown CD, Mangravite LM, Engelhardt BE.

PLoS Genet. 2013;9(8):e1003649. doi: 10.1371/journal.pgen.1003649. Epub 2013 Aug 1.

19.

Stability selection for regression-based models of transcription factor-DNA binding specificity.

Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gordân R.

Bioinformatics. 2013 Jul 1;29(13):i117-25. doi: 10.1093/bioinformatics/btt221.

20.

Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the Iα subfamily.

Muratore KE, Engelhardt BE, Srouji JR, Jordan MI, Brenner SE, Kirsch JF.

Proteins. 2013 Sep;81(9):1593-609. doi: 10.1002/prot.24318. Epub 2013 Jun 17.

21.

Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).

Hart AB, Engelhardt BE, Wardle MC, Sokoloff G, Stephens M, de Wit H, Palmer AA.

PLoS One. 2012;7(8):e42646. doi: 10.1371/journal.pone.0042646. Epub 2012 Aug 28.

22.

Genome-scale phylogenetic function annotation of large and diverse protein families.

Engelhardt BE, Jordan MI, Srouji JR, Brenner SE.

Genome Res. 2011 Nov;21(11):1969-80. doi: 10.1101/gr.104687.109. Epub 2011 Jul 22.

23.

Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis.

Engelhardt BE, Stephens M.

PLoS Genet. 2010 Sep 16;6(9):e1001117. doi: 10.1371/journal.pgen.1001117.

24.

Understanding mechanisms underlying human gene expression variation with RNA sequencing.

Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK.

Nature. 2010 Apr 1;464(7289):768-72. doi: 10.1038/nature08872. Epub 2010 Mar 10.

25.

Phylogenetic molecular function annotation.

Engelhardt BE, Jordan MI, Repo ST, Brenner SE.

J Phys Conf Ser. 2009;180(1):12024.

26.

Protein molecular function prediction by Bayesian phylogenomics.

Engelhardt BE, Jordan MI, Muratore KE, Brenner SE.

PLoS Comput Biol. 2005 Oct;1(5):e45. Epub 2005 Oct 7.

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