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Recounting the FANTOM CAGEAssociated Transcriptome.

Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Pereira Lobo FP, Yip CW, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon CC, de Hoon MJ, Shin JW, Carninci P, Jaffe AE, Leek JT, Favorov A, Franco GR, Langmead B, Marchionni L.

Genome Res. 2020 Feb 20. pii: gr.254656.119. doi: 10.1101/gr.254656.119. [Epub ahead of print]


A myelin-related transcriptomic profile is shared by Pitt-Hopkins syndrome models and human autism spectrum disorder.

Phan BN, Bohlen JF, Davis BA, Ye Z, Chen HY, Mayfield B, Sripathy SR, Cerceo Page S, Campbell MN, Smith HL, Gallop D, Kim H, Thaxton CL, Simon JM, Burke EE, Shin JH, Kennedy AJ, Sweatt JD, Philpot BD, Jaffe AE, Maher BJ.

Nat Neurosci. 2020 Feb 3. doi: 10.1038/s41593-019-0578-x. [Epub ahead of print]


Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs.

Burke EE, Chenoweth JG, Shin JH, Collado-Torres L, Kim SK, Micali N, Wang Y, Colantuoni C, Straub RE, Hoeppner DJ, Chen HY, Sellers A, Shibbani K, Hamersky GR, Diaz Bustamante M, Phan BN, Ulrich WS, Valencia C, Jaishankar A, Price AJ, Rajpurohit A, Semick SA, Bürli RW, Barrow JC, Hiler DJ, Page SC, Martinowich K, Hyde TM, Kleinman JE, Berman KF, Apud JA, Cross AJ, Brandon NJ, Weinberger DR, Maher BJ, McKay RDG, Jaffe AE.

Nat Commun. 2020 Jan 23;11(1):462. doi: 10.1038/s41467-019-14266-z.


TrkB Signaling Influences Gene Expression in Cortistatin-Expressing Interneurons.

Maynard KR, Kardian A, Hill JL, Mai Y, Barry B, Hallock HL, Jaffe AE, Martinowich K.

eNeuro. 2020 Feb 10;7(1). pii: ENEURO.0310-19.2019. doi: 10.1523/ENEURO.0310-19.2019. Print 2020 Jan/Feb.


Acute Stress Symptoms After Forcible and Substance-Involved Rapes.

Jaffe AE, Hahn CK, Gilmore AK.

Psychol Women Q. 2019 Dec;43(4):485-493. doi: 10.1177/0361684319845099. Epub 2019 May 7.


Program Evaluation of an Integrated Behavioral Health Clinic in an Outpatient Women's Health Clinic: Challenges and Considerations.

Carroll AJ, Jaffe AE, Stanton K, Guille C, Lazenby GB, Soper DE, Gilmore AK, Holland-Carter L.

J Clin Psychol Med Settings. 2019 Dec 19. doi: 10.1007/s10880-019-09684-6. [Epub ahead of print]


Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation.

Price AJ, Hwang T, Tao R, Burke EE, Rajpurohit A, Shin JH, Hyde TM, Kleinman JE, Jaffe AE, Weinberger DR.

Genome Res. 2020 Jan;30(1):1-11. doi: 10.1101/gr.250217.119. Epub 2019 Dec 18.


Post-Sexual Assault Mental Health: A Randomized Clinical Trial of a Video-Based Intervention.

Gilmore AK, Walsh K, Frazier P, Meredith L, Ledray L, Davis J, Acierno R, Ruggiero KJ, Kilpatrick DG, Jaffe AE, Resnick HS.

J Interpers Violence. 2019 Nov 9:886260519884674. doi: 10.1177/0886260519884674. [Epub ahead of print]


African-American and Caucasian participation in postmortem human brain donation for neuropsychiatric research.

Deep-Soboslay A, Mighdoll MI, Jaffe AE, Thomas SB, Herman MM, Sirovatka J, King JP, Fowler DR, Zulauf D, DiAngelo C, Hyde TM, Kleinman JE.

PLoS One. 2019 Oct 23;14(10):e0222565. doi: 10.1371/journal.pone.0222565. eCollection 2019.


Prospective Risk for Incapacitated Rape among Sexual Minority Women: Hookups and Drinking.

Jaffe AE, Blayney JA, Lewis MA, Kaysen D.

J Sex Res. 2019 Sep 26:1-12. doi: 10.1080/00224499.2019.1661949. [Epub ahead of print]


Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation.

Price AJ, Collado-Torres L, Ivanov NA, Xia W, Burke EE, Shin JH, Tao R, Ma L, Jia Y, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE.

Genome Biol. 2019 Sep 26;20(1):196. doi: 10.1186/s13059-019-1805-1.


Are trauma memories state-dependent? Intrusive memories following alcohol-involved sexual assault.

Jaffe AE, Blayney JA, Bedard-Gilligan M, Kaysen D.

Eur J Psychotraumatol. 2019 Jul 11;10(1):1634939. doi: 10.1080/20008198.2019.1634939. eCollection 2019.


Spatial transcriptomics: putting genome-wide expression on the map.

Maynard KR, Jaffe AE, Martinowich K.

Neuropsychopharmacology. 2020 Jan;45(1):232-233. doi: 10.1038/s41386-019-0484-7. No abstract available.


Observing Alcohol Myopia in the Context of a Trauma Film Paradigm: Differential Recall of Central and Peripheral Details.

Jaffe AE, Harris CM, DiLillo D.

Alcohol Clin Exp Res. 2019 Oct;43(10):2203-2211. doi: 10.1111/acer.14156. Epub 2019 Aug 19.


Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods.

Wright C, Rajpurohit A, Burke EE, Williams C, Collado-Torres L, Kimos M, Brandon NJ, Cross AJ, Jaffe AE, Weinberger DR, Shin JH.

BMC Genomics. 2019 Jun 21;20(1):513. doi: 10.1186/s12864-019-5870-3.


Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq.

Gådin JR, Buil A, Colantuoni C, Jaffe AE, Nielsen J, Shin JH, Hyde TM, Kleinman JE; BrainSeq Consortium, Plath N, Eriksson P, Brunak S, Didriksen M, Weinberger DR, Folkersen L.

PLoS One. 2019 Jun 17;14(6):e0217765. doi: 10.1371/journal.pone.0217765. eCollection 2019.


Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia.

Collado-Torres L, Burke EE, Peterson A, Shin J, Straub RE, Rajpurohit A, Semick SA, Ulrich WS; BrainSeq Consortium, Price AJ, Valencia C, Tao R, Deep-Soboslay A, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE.

Neuron. 2019 Jul 17;103(2):203-216.e8. doi: 10.1016/j.neuron.2019.05.013. Epub 2019 Jun 4.


Prefrontal Coexpression of Schizophrenia Risk Genes Is Associated With Treatment Response in Patients.

Pergola G, Di Carlo P, Jaffe AE, Papalino M, Chen Q, Hyde TM, Kleinman JE, Shin JH, Rampino A, Blasi G, Weinberger DR, Bertolino A.

Biol Psychiatry. 2019 Jul 1;86(1):45-55. doi: 10.1016/j.biopsych.2019.03.981. Epub 2019 Apr 3.


Addressing confounding artifacts in reconstruction of gene co-expression networks.

Parsana P, Ruberman C, Jaffe AE, Schatz MC, Battle A, Leek JT.

Genome Biol. 2019 May 16;20(1):94. doi: 10.1186/s13059-019-1700-9.


Risk for Revictimization Following Interpersonal and Noninterpersonal Trauma: Clarifying the Role of Posttraumatic Stress Symptoms and Trauma-Related Cognitions.

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

J Trauma Stress. 2019 Feb;32(1):42-55. doi: 10.1002/jts.22372. Epub 2019 Feb 12.


Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer's disease.

Semick SA, Bharadwaj RA, Collado-Torres L, Tao R, Shin JH, Deep-Soboslay A, Weiss JR, Weinberger DR, Hyde TM, Kleinman JE, Jaffe AE, Mattay VS.

Acta Neuropathol. 2019 Apr;137(4):557-569. doi: 10.1007/s00401-019-01966-5. Epub 2019 Feb 2.


Schizophrenia risk variants influence multiple classes of transcripts of sorting nexin 19 (SNX19).

Ma L, Semick SA, Chen Q, Li C, Tao R, Price AJ, Shin JH, Jia Y; BrainSeq Consortium, Brandon NJ, Cross AJ, Hyde TM, Kleinman JE, Jaffe AE, Weinberger DR, Straub RE.

Mol Psychiatry. 2019 Jan 11. doi: 10.1038/s41380-018-0293-0. [Epub ahead of print]


Association of a Noncoding RNA Postmortem With Suicide by Violent Means and In Vivo With Aggressive Phenotypes.

Punzi G, Ursini G, Viscanti G, Radulescu E, Shin JH, Quarto T, Catanesi R, Blasi G, Jaffe AE, Deep-Soboslay A, Hyde TM, Kleinman JE, Bertolino A, Weinberger DR.

Biol Psychiatry. 2019 Mar 1;85(5):417-424. doi: 10.1016/j.biopsych.2018.11.002. Epub 2018 Nov 16.


Comprehensive functional genomic resource and integrative model for the human brain.

Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, Yan C, Rhie SK, Manakongtreecheep K, Zhou H, Nathan A, Peters M, Mattei E, Fitzgerald D, Brunetti T, Moore J, Jiang Y, Girdhar K, Hoffman GE, Kalayci S, Gümüş ZH, Crawford GE; PsychENCODE Consortium, Roussos P, Akbarian S, Jaffe AE, White KP, Weng Z, Sestan N, Geschwind DH, Knowles JA, Gerstein MB.

Science. 2018 Dec 14;362(6420). pii: eaat8464. doi: 10.1126/science.aat8464.


Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.

Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE; PsychENCODE Consortium, Peters MA, Gerstein M, Liu C, Iakoucheva LM, Pinto D, Geschwind DH.

Science. 2018 Dec 14;362(6420). pii: eaat8127. doi: 10.1126/science.aat8127.


Cytokine, Chemokine, and Cytokine Receptor Changes Are Associated With Metabolic Improvements After Bariatric Surgery.

Wolf RM, Jaffe AE, Steele KE, Schweitzer MA, Magnuson TH, Wolfe A, Wong GW.

J Clin Endocrinol Metab. 2019 Mar 1;104(3):947-956. doi: 10.1210/jc.2018-02245.


Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses.

Kuri-Magaña H, Collado-Torres L, Jaffe AE, Valdovinos-Torres H, Ovilla-Muñoz M, Téllez-Sosa J, Bonifaz LC, Martínez-Barnetche J.

Front Immunol. 2018 Nov 21;9:2679. doi: 10.3389/fimmu.2018.02679. eCollection 2018.


Identification and prioritization of gene sets associated with schizophrenia risk by co-expression network analysis in human brain.

Radulescu E, Jaffe AE, Straub RE, Chen Q, Shin JH, Hyde TM, Kleinman JE, Weinberger DR.

Mol Psychiatry. 2018 Nov 26. doi: 10.1038/s41380-018-0304-1. [Epub ahead of print]


Depressive Symptoms Following Recent Sexual Assault: The Role of Drug and Alcohol Use, Acute Stress, and Assault Characteristics.

Dir AL, Hahn C, Jaffe AE, Stanton K, Gilmore AK.

J Interpers Violence. 2018 Oct 24:886260518803605. doi: 10.1177/0886260518803605. [Epub ahead of print]


BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior.

Maynard KR, Hobbs JW, Phan BN, Gupta A, Rajpurohit S, Williams C, Rajpurohit A, Shin JH, Jaffe AE, Martinowich K.

Elife. 2018 Sep 7;7. pii: e33676. doi: 10.7554/eLife.33676.


Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome.

Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Huestis MA, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE, Jaffe AE.

Mol Psychiatry. 2018 Aug 21. doi: 10.1038/s41380-018-0223-1. [Epub ahead of print]


Genetic vulnerability to DUSP22 promoter hypermethylation is involved in the relation between in utero famine exposure and schizophrenia.

Boks MP, Houtepen LC, Xu Z, He Y, Ursini G, Maihofer AX, Rajarajan P, Yu Q, Xu H, Wu Y, Wang S, Shi JP, Hulshoff Pol HE, Strengman E, Rutten BPF, Jaffe AE, Kleinman JE, Baker DG, Hol EM, Akbarian S, Nievergelt CM, De Witte LD, Vinkers CH, Weinberger DR, Yu J, Kahn RS.

NPJ Schizophr. 2018 Aug 21;4(1):16. doi: 10.1038/s41537-018-0058-4.


Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.

Jaffe AE, Straub RE, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A; BrainSeq Consortium, Cross AJ, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR.

Nat Neurosci. 2018 Aug;21(8):1117-1125. doi: 10.1038/s41593-018-0197-y. Epub 2018 Jul 26.


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 Oct;85:120-124. doi: 10.1016/j.addbeh.2018.05.028. Epub 2018 May 31.


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 colocalization 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 Aug 1;34(15):2538-2545. doi: 10.1093/bioinformatics/bty147.


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. 2018 Jun;23(6):1496-1505. doi: 10.1038/mp.2017.105. Epub 2017 May 9.


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.

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