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Suicidal ideation among adults with a recent sexual assault: Prescription opioid use and prior sexual assault.

Gilmore AK, Hahn CK, Jaffe AE, Walsh K, Moreland AD, Ward-Ciesielski EF.

Addict Behav. 2018 May 31;85:120-124. doi: 10.1016/j.addbeh.2018.05.028. [Epub ahead of print]


Convergence of placenta biology and genetic risk for schizophrenia.

Ursini G, Punzi G, Chen Q, Marenco S, Robinson JF, Porcelli A, Hamilton EG, Mitjans M, Maddalena G, Begemann M, Seidel J, Yanamori H, Jaffe AE, Berman KF, Egan MF, Straub RE, Colantuoni C, Blasi G, Hashimoto R, Rujescu D, Ehrenreich H, Bertolino A, Weinberger DR.

Nat Med. 2018 Jun;24(6):792-801. doi: 10.1038/s41591-018-0021-y. Epub 2018 May 28.


A Bayesian Framework for Multiple Trait Colo-calization from Summary Association Statistics.

Giambartolomei C, Zhenli Liu J, Zhang W, Hauberg M, Shi H, Boocock J, Pickrell J, Jaffe AE; CommonMind Consortium, Pasaniuc B, Roussos P.

Bioinformatics. 2018 Mar 19. doi: 10.1093/bioinformatics/bty147. [Epub ahead of print]


Student engagement and comfort during a web-based personalized feedback intervention for alcohol and sexual assault.

Jaffe AE, Bountress KE, Metzger IW, Maples-Keller JL, Pinsky HT, George WH, Gilmore AK.

Addict Behav. 2018 Jul;82:23-27. doi: 10.1016/j.addbeh.2018.02.020. Epub 2018 Feb 14.


Characterizing Sexual Violence in Intimate Relationships: An Examination of Blame Attributions and Rape Acknowledgment.

Jaffe AE, Steel AL, DiLillo D, Messman-Moore TL, Gratz KL.

J Interpers Violence. 2017 Aug 1:886260517726972. doi: 10.1177/0886260517726972. [Epub ahead of print]


recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.

Collado-Torres L, Nellore A, Jaffe AE.

F1000Res. 2017 Aug 24;6:1558. doi: 10.12688/f1000research.12223.1. eCollection 2017.


qSVA framework for RNA quality correction in differential expression analysis.

Jaffe AE, Tao R, Norris AL, Kealhofer M, Nellore A, Shin JH, Kim D, Jia Y, Hyde TM, Kleinman JE, Straub RE, Leek JT, Weinberger DR.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7130-7135. doi: 10.1073/pnas.1617384114. Epub 2017 Jun 20.


Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder.

Rutten BPF, Vermetten E, Vinkers CH, Ursini G, Daskalakis NP, Pishva E, de Nijs L, Houtepen LC, Eijssen L, Jaffe AE, Kenis G, Viechtbauer W, van den Hove D, Schraut KG, Lesch KP, Kleinman JE, Hyde TM, Weinberger DR, Schalkwyk L, Lunnon K, Mill J, Cohen H, Yehuda R, Baker DG, Maihofer AX, Nievergelt CM, Geuze E, Boks MPM.

Mol Psychiatry. 2018 May;23(5):1145-1156. doi: 10.1038/mp.2017.120. Epub 2017 Jun 20.


DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age.

Kozlenkov A, Jaffe AE, Timashpolsky A, Apontes P, Rudchenko S, Barbu M, Byne W, Hurd YL, Horvath S, Dracheva S.

Genes (Basel). 2017 May 30;8(6). pii: E152. doi: 10.3390/genes8060152.


Victim Alcohol Intoxication During a Sexual Assault: Relations With Subsequent PTSD Symptoms.

Jaffe AE, Steel AL, DiLillo D, Hoffman L, Gratz KL, Messman-Moore TL.

Violence Vict. 2017 Aug 1;32(4):642-657. doi: 10.1891/0886-6708.VV-D-16-00045. Epub 2017 May 17.


Altered expression of histamine signaling genes in autism spectrum disorder.

Wright C, Shin JH, Rajpurohit A, Deep-Soboslay A, Collado-Torres L, Brandon NJ, Hyde TM, Kleinman JE, Jaffe AE, Cross AJ, Weinberger DR.

Transl Psychiatry. 2017 May 9;7(5):e1126. doi: 10.1038/tp.2017.87.


Investigating the neuroimmunogenic architecture of schizophrenia.

Birnbaum R, Jaffe AE, Chen Q, Shin JH; BrainSeq Consortium, Kleinman JE, Hyde TM, Weinberger DR.

Mol Psychiatry. 2018 May;23(5):1251-1260. doi: 10.1038/mp.2017.89. Epub 2017 May 9.


GAD1 alternative transcripts and DNA methylation in human prefrontal cortex and hippocampus in brain development, schizophrenia.

Tao R, Davis KN, Li C, Shin JH, Gao Y, Jaffe AE, Gondré-Lewis MC, Weinberger DR, Kleinman JE, Hyde TM.

Mol Psychiatry. 2017 May 9. doi: 10.1038/mp.2017.105. [Epub ahead of print]


Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network.

McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM; Brain Somatic Mosaicism Network.

Science. 2017 Apr 28;356(6336). pii: eaal1641. doi: 10.1126/science.aal1641. Epub 2017 Apr 27. Review.


Reproducible RNA-seq analysis using recount2.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT.

Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. No abstract available.


The Occurrence and Traumatic Impact of Sexual Revictimization in Newlywed Couples.

DiLillo D, Jaffe AE, Watkins LE, Peugh J, Kras A, Campbell C.

Couple Family Psychol. 2016 Dec;5(4):212-225. doi: 10.1037/cfp0000067. Epub 2016 Oct 10.


The schizophrenia- and autism-associated gene, transcription factor 4 regulates the columnar distribution of layer 2/3 prefrontal pyramidal neurons in an activity-dependent manner.

Page SC, Hamersky GR, Gallo RA, Rannals MD, Calcaterra NE, Campbell MN, Mayfield B, Briley A, Phan BN, Jaffe AE, Maher BJ.

Mol Psychiatry. 2018 Feb;23(2):304-315. doi: 10.1038/mp.2017.37. Epub 2017 Mar 14.


Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Zheng SC, Beck S, Jaffe AE, Koestler DC, Hansen KD, Houseman AE, Irizarry RA, Teschendorff AE.

Nat Methods. 2017 Feb 28;14(3):216-217. doi: 10.1038/nmeth.4187. No abstract available.


Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA III, Karbhari N, Hansen KD, Langmead B, Leek JT.

Genome Biol. 2016 Dec 30;17(1):266. doi: 10.1186/s13059-016-1118-6.


Genetic risk mechanisms of posttraumatic stress disorder in the human brain.

Bharadwaj RA, Jaffe AE, Chen Q, Deep-Soboslay A, Goldman AL, Mighdoll MI, Cotoia JA, Brandtjen AC, Shin J, Hyde TM, Mattay VS, Weinberger DR, Kleinman JE.

J Neurosci Res. 2018 Jan;96(1):21-30. doi: 10.1002/jnr.23957. Epub 2016 Oct 24.


Flexible expressed region analysis for RNA-seq with derfinder.

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE.

Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29.


Genetic and epigenetic analysis of schizophrenia in blood-a no-brainer?

Jaffe AE, Kleinman JE.

Genome Med. 2016 Sep 21;8(1):96.


Rail-RNA: scalable analysis of RNA-seq splicing and coverage.

Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B.

Bioinformatics. 2017 Dec 15;33(24):4033-4040. doi: 10.1093/bioinformatics/btw575.


Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis.

Jaffe AE, Hyde T, Kleinman J, Weinberger DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C.

BMC Bioinformatics. 2016 Aug 10;17:302. doi: 10.1186/s12859-016-1152-0. No abstract available.


Associations Between Family History of Substance Use, Childhood Trauma, and Age of First Drug Use in Persons With Methamphetamine Dependence.

Svingen L, Dykstra RE, Simpson JL, Jaffe AE, Bevins RA, Carlo G, DiLillo D, Grant KM.

J Addict Med. 2016 Jul-Aug;10(4):269-73. doi: 10.1097/ADM.0000000000000233.


Assessment of genetic risk for distribution of total interstitial white matter neurons in dorsolateral prefrontal cortex: role in schizophrenia.

McFadden WC, Jaffe AE, Ye T, Paltán-Ortiz JD, Hyde TM, Kleinman JE.

Schizophr Res. 2016 Oct;176(2-3):141-143. doi: 10.1016/j.schres.2016.04.007. Epub 2016 May 27. No abstract available.


A human-specific AS3MT isoform and BORCS7 are molecular risk factors in the 10q24.32 schizophrenia-associated locus.

Li M, Jaffe AE, Straub RE, Tao R, Shin JH, Wang Y, Chen Q, Li C, Jia Y, Ohi K, Maher BJ, Brandon NJ, Cross A, Chenoweth JG, Hoeppner DJ, Wei H, Hyde TM, McKay R, Kleinman JE, Weinberger DR.

Nat Med. 2016 Jun;22(6):649-56. doi: 10.1038/nm.4096. Epub 2016 May 9.


C1q/TNF-Related Protein-9 (CTRP9) Levels Are Associated With Obesity and Decrease Following Weight Loss Surgery.

Wolf RM, Steele KE, Peterson LA, Zeng X, Jaffe AE, Schweitzer MA, Magnuson TH, Wong GW.

J Clin Endocrinol Metab. 2016 May;101(5):2211-7. doi: 10.1210/jc.2016-1027. Epub 2016 Mar 16.


Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1.

Rannals MD, Hamersky GR, Page SC, Campbell MN, Briley A, Gallo RA, Phan BN, Hyde TM, Kleinman JE, Shin JH, Jaffe AE, Weinberger DR, Maher BJ.

Neuron. 2016 Apr 6;90(1):43-55. doi: 10.1016/j.neuron.2016.02.021. Epub 2016 Mar 10.


Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age.

Ivanov NA, Tao R, Chenoweth JG, Brandtjen A, Mighdoll MI, Genova JD, McKay RD, Jia Y, Weinberger DR, Kleinman JE, Hyde TM, Jaffe AE.

PLoS Genet. 2016 Feb 25;12(2):e1005819. doi: 10.1371/journal.pgen.1005819. eCollection 2016 Feb.


Schizophrenia-Associated hERG channel Kv11.1-3.1 Exhibits a Unique Trafficking Deficit that is Rescued Through Proteasome Inhibition for High Throughput Screening.

Calcaterra NE, Hoeppner DJ, Wei H, Jaffe AE, Maher BJ, Barrow JC.

Sci Rep. 2016 Feb 16;6:19976. doi: 10.1038/srep19976.


Alcohol Expectancies, Posttraumatic Stress Disorder, and Alcohol Use in College Students With a History of Childhood Trauma.

Tuliao AP, Jaffe AE, McChargue DE.

J Dual Diagn. 2016;12(1):4-14. doi: 10.1080/15504263.2016.1146382.


Postmortem human brain genomics in neuropsychiatric disorders--how far can we go?

Jaffe AE.

Curr Opin Neurobiol. 2016 Feb;36:107-11. doi: 10.1016/j.conb.2015.11.002. Epub 2015 Dec 10. Review.


Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex.

Jaffe AE, Gao Y, Deep-Soboslay A, Tao R, Hyde TM, Weinberger DR, Kleinman JE.

Nat Neurosci. 2016 Jan;19(1):40-7. doi: 10.1038/nn.4181. Epub 2015 Nov 30.


The PsychENCODE project.

PsychENCODE Consortium, Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FC, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CC, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N.

Nat Neurosci. 2015 Dec;18(12):1707-12. doi: 10.1038/nn.4156. Review. No abstract available.


Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis.

Jaffe AE, Hyde T, Kleinman J, Weinbergern DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C.

BMC Bioinformatics. 2015 Nov 6;16:372. doi: 10.1186/s12859-015-0808-5. Erratum in: BMC Bioinformatics. 2016;17:302.


Relationship between self-reported physical health problems and sleep disturbances among trauma survivors: a brief report.

Miller KE, Jaffe AE, Davis JL, Pruiksma KE, Rhudy JL.

Sleep Health. 2015 Sep;1(3):166-168. doi: 10.1016/j.sleh.2015.05.002. Epub 2015 Jul 20.


Differential DNA methylation identified in the blood and retina of AMD patients.

Oliver VF, Jaffe AE, Song J, Wang G, Zhang P, Branham KE, Swaroop A, Eberhart CG, Zack DJ, Qian J, Merbs SL.

Epigenetics. 2015;10(8):698-707. doi: 10.1080/15592294.2015.1060388.


Does it hurt to ask? A meta-analysis of participant reactions to trauma research.

Jaffe AE, DiLillo D, Hoffman L, Haikalis M, Dykstra RE.

Clin Psychol Rev. 2015 Aug;40:40-56. doi: 10.1016/j.cpr.2015.05.004. Epub 2015 May 22. Review.


Polyester: simulating RNA-seq datasets with differential transcript expression.

Frazee AC, Jaffe AE, Langmead B, Leek JT.

Bioinformatics. 2015 Sep 1;31(17):2778-84. doi: 10.1093/bioinformatics/btv272. Epub 2015 Apr 28.


Prenatal mercury concentration is associated with changes in DNA methylation at TCEANC2 in newborns.

Bakulski KM, Lee H, Feinberg JI, Wells EM, Brown S, Herbstman JB, Witter FR, Halden RU, Caldwell K, Mortensen ME, Jaffe AE, Moye J Jr, Caulfield LE, Pan Y, Goldman LR, Feinberg AP, Fallin MD.

Int J Epidemiol. 2015 Aug;44(4):1249-62. doi: 10.1093/ije/dyv032. Epub 2015 Apr 22.


Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort.

Feinberg JI, Bakulski KM, Jaffe AE, Tryggvadottir R, Brown SC, Goldman LR, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Fallin MD, Feinberg AP.

Int J Epidemiol. 2015 Aug;44(4):1199-210. doi: 10.1093/ije/dyv028. Epub 2015 Apr 14.


Ballgown bridges the gap between transcriptome assembly and expression analysis.

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT.

Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172. No abstract available.


DNA methylation age of blood predicts all-cause mortality in later life.

Marioni RE, Shah S, McRae AF, Chen BH, Colicino E, Harris SE, Gibson J, Henders AK, Redmond P, Cox SR, Pattie A, Corley J, Murphy L, Martin NG, Montgomery GW, Feinberg AP, Fallin MD, Multhaup ML, Jaffe AE, Joehanes R, Schwartz J, Just AC, Lunetta KL, Murabito JM, Starr JM, Horvath S, Baccarelli AA, Levy D, Visscher PM, Wray NR, Deary IJ.

Genome Biol. 2015 Jan 30;16:25. doi: 10.1186/s13059-015-0584-6.


Investigation of the prenatal expression patterns of 108 schizophrenia-associated genetic loci.

Birnbaum R, Jaffe AE, Chen Q, Hyde TM, Kleinman JE, Weinberger DR.

Biol Psychiatry. 2015 Jun 1;77(11):e43-51. doi: 10.1016/j.biopsych.2014.10.008. Epub 2014 Oct 22. No abstract available.


Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes.

Multhaup ML, Seldin MM, Jaffe AE, Lei X, Kirchner H, Mondal P, Li Y, Rodriguez V, Drong A, Hussain M, Lindgren C, McCarthy M, Näslund E, Zierath JR, Wong GW, Feinberg AP.

Cell Metab. 2015 Jan 6;21(1):138-49. doi: 10.1016/j.cmet.2014.12.014.


regionReport: Interactive reports for region-level and feature-level genomic analyses.

Collado-Torres L, Jaffe AE, Leek JT.

Version 2. F1000Res. 2015 May 1 [revised 2016 Jan 1];4:105. doi: 10.12688/f1000research.6379.2. eCollection 2015.


Developmental regulation of human cortex transcription and its clinical relevance at single base resolution.

Jaffe AE, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, Gao Y, Jia Y, Maher BJ, Hyde TM, Kleinman JE, Weinberger DR.

Nat Neurosci. 2015 Jan;18(1):154-161. doi: 10.1038/nn.3898. Epub 2014 Dec 15.


Genetic neuropathology of obsessive psychiatric syndromes.

Jaffe AE, Deep-Soboslay A, Tao R, Hauptman DT, Kaye WH, Arango V, Weinberger DR, Hyde TM, Kleinman JE.

Transl Psychiatry. 2014 Sep 2;4:e432. doi: 10.1038/tp.2014.68.


Expression of ZNF804A in human brain and alterations in schizophrenia, bipolar disorder, and major depressive disorder: a novel transcript fetally regulated by the psychosis risk variant rs1344706.

Tao R, Cousijn H, Jaffe AE, Burnet PW, Edwards F, Eastwood SL, Shin JH, Lane TA, Walker MA, Maher BJ, Weinberger DR, Harrison PJ, Hyde TM, Kleinman JE.

JAMA Psychiatry. 2014 Oct;71(10):1112-20. doi: 10.1001/jamapsychiatry.2014.1079.

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