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Battle, Alexis

Associate Professor
Biomedical Engineering
Personal Website

Clark Hall
(410) 516-4253
ajbattle@jhu.edu

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About

Education
  • Ph.D. 2013, Stanford
  • Master of Science 2013, Stanford
  • Bachelor of Science 2003, Stanford
Presentations
  • "RNA-Seq: Analysis Methods", GTEx Community Meeting.  Boston, MA.  June 17, 2014
  • "Regulatory variation from RNA to protein", Biology of Genomes.  CSHL.  May 6, 2014
  • Big Data in Biomedicine.  Stanford University.  May 1, 2014

Publications

Journal Articles
  • Graham Linck EJ, Richmond PA, Tarailo-Graovac M, Engelke U, Kluijtmans LAJ, Coene KLM, Wevers RA, Wasserman W, van Karnebeek CDM, Mostafavi S (2020).  metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes.  npj Genomic Medicine.  5(1).
  • Arvanitis M, Tampakakis E, Zhang Y, Wang W, Auton A, Agee M, Aslibekyan S, Bell RK, Bryc K, Clark SK, Elson SL, Fletez-Brant K, Fontanillas P, Furlotte NA, Gandhi PM, Heilbron K, Hicks B, Hinds DA, Huber KE, Jewett EM, Jiang Y, Kleinman A, Lin KH, Litterman NK, McCreight JC, McIntyre MH, McManus KF, Mountain JL, Mozaffari SV, Nandakumar P, Noblin ES, Northover CAM, O’Connell J, Pitts SJ, Poznik GD, Sathirapongsasuti JF, Shastri AJ, Shelton JF, Shringarpure S, Tian C, Tung JY, Tunney RJ, Vacic V, Wang X, Zare AS, Dutta D, Glavaris S, Keramati A, Chatterjee N, Chi NC, Ren B, Post WS, Battle A (2020).  Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure.  Nature Communications.  11(1).
  • Wan YW, Al-Ouran R, Mangleburg CG, Perumal TM, Lee TV, Allison K, Swarup V, Funk CC, Gaiteri C, Allen M, Wang M, Neuner SM, Kaczorowski CC, Philip VM, Howell GR, Martini-Stoica H, Zheng H, Mei H, Zhong X, Kim JW, Dawson VL, Dawson TM, Pao PC, Tsai LH, Haure-Mirande JV, Ehrlich ME, Chakrabarty P, Levites Y, Wang X, Dammer EB, Srivastava G, Mukherjee S, Sieberts SK, Omberg L, Dang KD, Eddy JA, Snyder P, Chae Y, Amberkar S, Wei W, Hide W, Preuss C, Ergun A, Ebert PJ, Airey DC, Mostafavi S, Yu L, Klein HU, Carter GW, Collier DA, Golde TE, Levey AI, Bennett DA, Estrada K, Townsend TM, Zhang B, Schadt E, De Jager PL, Price ND, Ertekin-Taner N, Liu Z, Shulman JM, Mangravite LM, Logsdon BA (2020).  Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.  Cell Reports.  32(2).
  • Coleman JRI, Peyrot WJ, Purves KL, Davis KAS, Rayner C, Choi SW, Hübel C, Gaspar HA, Kan C, Van der Auwera S, Adams MJ, Lyall DM, Choi KW, Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TFM, Bacanu S-A, Bækvad-Hansen M, Beekman ATF, Bigdeli TB, Binder EB, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke T-K, Coleman JRI, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Escott-Price V, Kiadeh FFH, Finucane HK, Foo JC, Forstner AJ, Frank J, Gill M, Goes FS, Gordon SD, Grove J, Hall LS, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga J-J, Hougaard DM, Howard DM, Ising M, Jansen R, Jones I, Jones LA, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Kutalik Z, Li Y, Lind PA, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGr...Hotopf M (2020).  Genome-wide gene-environment analyses of major depressive disorder and reported lifetime traumatic experiences in UK Biobank.  Molecular Psychiatry.  25(7).  1430-1446.
  • Richmond PA, van der Kloet F, Vaz FM, Lin D, Uzozie A, Graham E, Kobor M, Mostafavi S, Moerland PD, Lange PF, van Kampen AHC, Wasserman WW, Engelen M, Kemp S, van Karnebeek CDM (2020).  Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy.  Frontiers in Cell and Developmental Biology.  8.
  • Gatev E, Gladish N, Mostafavi S, Mostafavi S, Mostafavi S, Mostafavi S, Kobor MS (2020).  CoMeBack: DNA methylation array data analysis for co-methylated regions.  Bioinformatics.  36(9).  2675-2683.
  • Schultz KR, Kariminia A, Ng B, Abdossamadi S, Lauener M, Nemecek ER, Wahlstrom JT, Kitko CL, Lewis VA, Schechter T, Jacobsohn DA, Harris AC, Pulsipher MA, Bittencourt H, Choi SW, Caywood EH, Kasow KA, Bhatia M, Oshrine BR, Flower A, Chaudhury S, Coulter D, Chewning JH, Joyce M, Savasan S, Pawlowska AB, Megason GC, Mitchell D, Cheerva AC, Lawitschka A, Azadpour S, Ostroumov E, Subrt P, Halevy A, Mostafavi S, Cuvelier GDE (2020).  Immune profile differences between chronic GVHD and late acute GVHD: results of the ABLE/PBMTC 1202 studies.  Blood.  135(15).  1287-1298.
  • Glanville KP, Coleman JRI, Hanscombe KB, Euesden J, Choi SW, Purves KL, Breen G, Air TM, Andlauer TFM, Baune BT, Binder EB, Blackwood DHR, Boomsma DI, Buttenschøn HN, Colodro-Conde L, Dannlowski U, Direk N, Dunn EC, Forstner AJ, de Geus EJC, Grabe HJ, Hamilton SP, Jones I, Jones LA, Knowles JA, Kutalik Z, Levinson DF, Lewis G, Lind PA, Lucae S, Magnusson PK, McGuffin P, McIntosh AM, Milaneschi Y, Mors O, Mostafavi S, Müller-Myhsok B, Pedersen NL, Penninx BWJH, Potash JB, Preisig M, Ripke S, Shi J, Shyn SI, Smoller JW, Streit F, Sullivan PF, Tiemeier H, Uher R, Van der Auwera S, Weissman MM, Wray NR, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Bacanu S-A, Bækvad-Hansen M, Beekman ATF, Bigdeli TB, Bryois J, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke T-K, Couvy-Duchesne B, Craddock N, Crawford GE, Davies G, Deary IJ, Degenhardt F, Derks EM, Dolan CV, Eley TC, Escott-Price V, Hassan Kiadeh FF, Finucane HK, Foo JC, Frank J, Gaspar...Børglum AD (2020).  Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression.  Biological Psychiatry.  87(5).  419-430.
  • Hammerschlag AR, Byrne EM, Agbessi M, Ahsan H, Alves I, Andiappan A, Arindrarto W, Awadalla P, Battle A, Beutner F, Bonder MJ, Boomsma DI, Christiansen M, Claringbould A, Deelen P, Esko T, Favé M-J, Franke L, Frayling T, Gharib SA, Gibson G, Heijmans BT, Hemani G, Jansen R, Kähönen M, Kalnapenkis A, Kasela S, Kettunen J, Kim Y, Kirsten H, Kovacs P, Krohn K, Kronberg-Guzman J, Kukushkina V, Kutalik Z, Lee B, Lehtimäki T, Loeffler M, Marigorta UM, Mei H, Milani L, Montgomery GW, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Perola M, Pervjakova N, Pierce BL, Powell J, Prokisch H, Psaty BM, Raitakari OT, Ripatti S, Rotzschke O, Rüeger S, Saha A, Scholz M, Schramm K, Seppälä I, Slagboom EP, Stehouwer CDA, Stumvoll M, Sullivan P, ‘t Hoen PAC, Teumer A, Thiery J, Tong L, Tönjes A, van Dongen J, van Iterson M, van Meurs J, Veldink JH, Verlouw J, Visscher PM, Völker U, Võsa U, Westra H-J, Wijmenga C, Yaghootkar H, Yang J, Zeng B, Zhang F, Isaacs A, Pool R, Hottenga JJ, van G...Middeldorp CM (2020).  Refining Attention-Deficit/Hyperactivity Disorder and Autism Spectrum Disorder Genetic Loci by Integrating Summary Data From Genome-wide Association, Gene Expression, and DNA Methylation Studies.  Biological Psychiatry.
  • Tasaki S, Gaiteri C, Mostafavi S, Wang Y (2020).  Deep learning decodes the principles of differential gene expression.  Nature Machine Intelligence.
  • Coleman JRI, Gaspar HA, Bryois J, Byrne EM, Forstner AJ, Holmans PA, de Leeuw CA, Mattheisen M, McQuillin A, Whitehead Pavlides JM, Pers TH, Ripke S, Stahl EA, Steinberg S, Trubetskoy V, Trzaskowski M, Wang Y, Abbott L, Abdellaoui A, Adams MJ, Adolfsson AN, Agerbo E, Akil H, Albani D, Alliey-Rodriguez N, Als TD, Andlauer TFM, Anjorin A, Antilla V, Van der Auwera S, Awasthi S, Bacanu S-A, Badner JA, Bækvad-Hansen M, Barchas JD, Bass N, Bauer M, Beekman ATF, Belliveau R, Bergen SE, Bigdeli TB, Binder EB, Bøen E, Boks M, Boocock J, Budde M, Bunney W, Burmeister M, Buttenschøn HN, Bybjerg-Grauholm J, Byerley W, Cai N, Casas M, Castelao E, Cerrato F, Cervantes P, Chambert K, Charney AW, Chen D, Christensen JH, Churchhouse C, St Clair D, Clarke T-K, Colodro-Conde L, Coryell W, Couvy-Duchesne B, Craig DW, Crawford GE, Cruceanu C, Czerski PM, Dale AM, Davies G, Deary IJ, Degenhardt F, Del-Favero J, DePaulo JR, Derks EM, Direk N, Djurovic S, Dobbyn AL, Dolan CV, Dumont A, Dunn EC, Ele...Breen G (2020).  The Genetics of the Mood Disorder Spectrum: Genome-wide Association Analyses of More Than 185,000 Cases and 439,000 Controls.  Biological Psychiatry.
  • Amare AT, Schubert KO, Hou L, Clark SR, Papiol S, Cearns M, Heilbronner U, Degenhardt F, Tekola-Ayele F, Hsu Y-H, Shekhtman T, Adli M, Akula N, Akiyama K, Ardau R, Arias B, Aubry J-M, Backlund L, Bhattacharjee AK, Bellivier F, Benabarre A, Bengesser S, Biernacka JM, Birner A, Brichant-Petitjean C, Cervantes P, Chen H-C, Chillotti C, Cichon S, Cruceanu C, Czerski PM, Dalkner N, Dayer A, Del Zompo M, DePaulo JR, Étain B, Jamain S, Falkai P, Forstner AJ, Frisen L, Frye MA, Fullerton JM, Gard S, Garnham JS, Goes FS, Grigoroiu-Serbanescu M, Grof P, Hashimoto R, Hauser J, Herms S, Hoffmann P, Hofmann A, Jiménez E, Kahn J-P, Kassem L, Kuo P-H, Kato T, Kelsoe JR, Kittel-Schneider S, Kliwicki S, König B, Kusumi I, Laje G, Landén M, Lavebratt C, Leboyer M, Leckband SG, Tortorella A, Manchia M, Martinsson L, McCarthy MJ, McElroy SL, Colom F, Mitjans M, Mondimore FM, Monteleone P, Nievergelt CM, Nöthen MM, Novák T, O’Donovan C, Ozaki N, Ösby U, Pfennig A, Potash JB, Reif A, Wray NR, R...McMahon FJ (2020).  Association of polygenic score for major depression with response to lithium in patients with bipolar disorder.  Molecular Psychiatry.
  • Lee PH, Anttila V, Won H, Feng Y-CA, Rosenthal J, Zhu Z, Tucker-Drob EM, Nivard MG, Grotzinger AD, Posthuma D, Wang MM-J, Yu D, Stahl EA, Walters RK, Anney RJL, Duncan LE, Ge T, Adolfsson R, Banaschewski T, Belangero S, Cook EH, Coppola G, Derks EM, Hoekstra PJ, Kaprio J, Keski-Rahkonen A, Kirov G, Kranzler HR, Luykx JJ, Rohde LA, Zai CC, Agerbo E, Arranz MJ, Asherson P, Bækvad-Hansen M, Baldursson G, Bellgrove M, Belliveau RA, Buitelaar J, Burton CL, Bybjerg-Grauholm J, Casas M, Cerrato F, Chambert K, Churchhouse C, Cormand B, Crosbie J, Dalsgaard S, Demontis D, Doyle AE, Dumont A, Elia J, Grove J, Gudmundsson OO, Haavik J, Hakonarson H, Hansen CS, Hartman CA, Hawi Z, Hervás A, Hougaard DM, Howrigan DP, Huang H, Kuntsi J, Langley K, Lesch K-P, Leung PWL, Loo SK, Martin J, Martin AR, McGough JJ, Medland SE, Moran JL, Mors O, Mortensen PB, Oades RD, Palmer DS, Pedersen CB, Pedersen MG, Peters T, Poterba T, Poulsen JB, Ramos-Quiroga JA, Reif A, Ribasés M, Rothenberger A, Rov...Smoller JW (2019).  Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders.  Cell.  179(7).  1469-1482.e11.
  • Czamara D, Eraslan G, Page CM, Lahti J, Lahti-Pulkkinen M, Hämäläinen E, Kajantie E, Laivuori H, Villa PM, Reynolds RM, Nystad W, Håberg SE, London SJ, O’Donnell KJ, Garg E, Meaney MJ, Entringer S, Wadhwa PD, Buss C, Jones MJ, Lin DTS, MacIsaac JL, Kobor MS, Koen N, Zar HJ, Koenen KC, Dalvie S, Stein DJ, Kondofersky I, Müller NS, Theis FJ, Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TFM, Bacanu S-A, Bækvad-Hansen M, Beekman ATF, Bigdeli TB, Blackwood DHR, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke T-K, Coleman JRI, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Escott-Price V, Kiadeh FFH, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Goes FS, Gordon SD, Grove J, Hall LS, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga J-J, Hougaard DM...Binder EB (2019).  Integrated analysis of environmental and genetic influences on cord blood DNA methylation in new-borns.  Nature Communications.  10(1).
  • Porcu E, Rüeger S, Lepik K, Agbessi M, Ahsan H, Alves I, Andiappan A, Arindrarto W, Awadalla P, Battle A, Beutner F, Jan Bonder M, Boomsma D, Christiansen M, Claringbould A, Deelen P, Esko T, Favé M-J, Franke L, Frayling T, Gharib SA, Gibson G, Heijmans BT, Hemani G, Jansen R, Kähönen M, Kalnapenkis A, Kasela S, Kettunen J, Kim Y, Kirsten H, Kovacs P, Krohn K, Kronberg-Guzman J, Kukushkina V, Lee B, Lehtimäki T, Loeffler M, Marigorta UM, Mei H, Milani L, Montgomery GW, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Perola M, Pervjakova N, Pierce BL, Powell J, Prokisch H, Psaty BM, Raitakari OT, Ripatti S, Rotzschke O, Saha A, Scholz M, Schramm K, Seppälä I, Slagboom EP, Stehouwer CDA, Stumvoll M, Sullivan P, ’t Hoen PAC, Teumer A, Thiery J, Tong L, Tönjes A, van Dongen J, van Iterson M, van Meurs J, Veldink JH, Verlouw J, Visscher PM, Völker U, Võsa U, Westra H-J, Wijmenga C, Yaghootkar H, Yang J, Zeng B, Zhang F, Beekman M, Boomsma DI, Bot J, Deelen J, Franke L, Hofman B...Kutalik Z (2019).  Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits.  Nature Communications.  10(1).
  • Ronsley R, Kariminia A, Ng B, Mostafavi S, Reid G, Subrt P, Hijiya N, Schultz KR (2019).  The TLR9 agonist (GNKG168) induces a unique immune activation pattern in vivo in children with minimal residual disease positive acute leukemia: Results of the TACL T2009-008 phase I study.  Pediatric Hematology and Oncology.  36(8).  468-481.
  • Graham EJ, Vermeulen M, Vardarajan B, Bennett D, De Jager P, Pearse RV, Young-Pearse TL, Mostafavi S (2019).  Somatic mosaicism of sex chromosomes in the blood and brain.  Brain Research.  1721.
  • van Karnebeek CDM, Beumer D, Pawliuk C, Goez H, Mostafavi S, Andrews G, Steele R, Siden H (2019).  A novel classification system for research reporting in rare and progressive genetic conditions.  Developmental Medicine and Child Neurology.  61(10).  1208-1213.
  • Ng B, Casazza W, Patrick E, Tasaki S, Novakovsky G, Felsky D, Ma Y, Bennett DA, Gaiteri C, De Jager PL, Mostafavi S (2019).  Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain.  American Journal of Human Genetics.  105(3).  562-572.
  • Gaiteri C, Dawe R, Mostafavi S, Blizinsky KD, Tasaki S, Komashko V, Yu L, Wang Y, Schneider JA, Arfanakis K, De Jager PL, Bennett DA (2019).  Gene expression and DNA methylation are extensively coordinated with MRI-based brain microstructural characteristics.  Brain Imaging and Behavior.  13(4).  963-972.
  • Yuan V, Price EM, Del Gobbo G, Mostafavi S, Cox B, Binder AM, Michels KB, Marsit C, Robinson WP (2019).  Accurate ethnicity prediction from placental DNA methylation data.  Epigenetics and Chromatin.  12(1).
  • Frésard L, Smail C, Ferraro NM, Teran NA, Li X, Smith KS, Bonner D, Kernohan KD, Marwaha S, Zappala Z, Balliu B, Davis JR, Liu B, Prybol CJ, Kohler JN, Zastrow DB, Reuter CM, Fisk DG, Grove ME, Davidson JM, Hartley T, Joshi R, Strober BJ, Utiramerur S, Adams DR, Aday A, Alejandro ME, Allard P, Ashley EA, Azamian MS, Bacino CA, Baker E, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bellen HJ, Bernstein JA, Berry GT, Bican A, Bick DP, Birch CL, Boone BE, Bostwick BL, Briere LC, Brokamp E, Brown DM, Brush M, Burke EA, Burrage LC, Butte MJ, Chen S, Clark GD, Coakley TR, Cogan JD, Colley HA, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Davidson JM, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Dries AM, Duncan L, Eckstein DJ, Emrick LT, Eng CM, Enns GM, Eskin A, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldma...Montgomery SB (2019).  Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.  Nature Medicine.  25(6).  911-919.
  • Parsana P, Ruberman C, Jaffe AE, Schatz MC, Battle A, Leek JT (2019).  Addressing confounding artifacts in reconstruction of gene co-expression networks.  Genome Biology.  20(1).
  • Grove J, Ripke S, Als TD, Mattheisen M, Walters RK, Won H, Pallesen J, Agerbo E, Andreassen OA, Anney R, Awashti S, Belliveau R, Bettella F, Buxbaum JD, Bybjerg-Grauholm J, Bækvad-Hansen M, Cerrato F, Chambert K, Christensen JH, Churchhouse C, Dellenvall K, Demontis D, De Rubeis S, Devlin B, Djurovic S, Dumont AL, Goldstein JI, Hansen CS, Hauberg ME, Hollegaard MV, Hope S, Howrigan DP, Huang H, Hultman CM, Klei L, Maller J, Martin J, Martin AR, Moran JL, Nyegaard M, Nærland T, Palmer DS, Palotie A, Pedersen CB, Pedersen MG, dPoterba T, Poulsen JB, Pourcain BS, Qvist P, Rehnström K, Reichenberg A, Reichert J, Robinson EB, Roeder K, Roussos P, Saemundsen E, Sandin S, Satterstrom FK, Davey Smith G, Stefansson H, Steinberg S, Stevens CR, Sullivan PF, Turley P, Walters GB, Xu X, Wray NR, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Air TM, Andlauer TFM, Bacanu S-A, Beekman ATF, Bigdeli TB, Binder EB, Blackwood DHR, Bryois J, Buttenschøn HN, Cai N, Castelao E, Clarke T-K, Co...Børglum AD (2019).  Identification of common genetic risk variants for autism spectrum disorder.  Nature Genetics.  51(3).  431-444.
  • Yoshida H, Lareau CA, Ramirez RN, Rose SA, Maier B, Wroblewska A, Desland F, Chudnovskiy A, Mortha A, Dominguez C, Tellier J, Kim E, Dwyer D, Shinton S, Nabekura T, Qi YL, Yu B, Robinette M, Kim KW, Wagers A, Rhoads A, Nutt SL, Brown BD, Mostafavi S, Buenrostro JD, Benoist C (2019).  The cis-Regulatory Atlas of the Mouse Immune System.  Cell.  176(4).  897-912.e20.
  • Karlsson Linnér R, Biroli P, Kong E, Meddens SFW, Wedow R, Fontana MA, Lebreton M, Tino SP, Abdellaoui A, Hammerschlag AR, Nivard MG, Okbay A, Rietveld CA, Timshel PN, Trzaskowski M, Vlaming R, Zünd CL, Bao Y, Buzdugan L, Caplin AH, Chen C-Y, Eibich P, Fontanillas P, Gonzalez JR, Joshi PK, Karhunen V, Kleinman A, Levin RZ, Lill CM, Meddens GA, Muntané G, Sanchez-Roige S, Rooij FJ, Taskesen E, Wu Y, Zhang F, Agee M, Alipanahi B, Bell RK, Bryc K, Elson SL, Furlotte NA, Huber KE, Litterman NK, McCreight JC, McIntyre MH, Mountain JL, Northover CAM, Pitts SJ, Sathirapongsasuti JF, Sazonova OV, Shelton JF, Shringarpure S, Tian C, Tung JY, Vacic V, Wilson CH, Agbessi M, Ahsan H, Alves I, Andiappan A, Awadalla P, Battle A, Beutner F, Jan Bonder M, Boomsma DI, Christiansen M, Claringbould A, Deelen P, Esko T, Favé M-J, Franke L, Frayling T, Gharib SA, Gibson G, Heijmans B, Hemani G, Jansen R, Kähönen M, Kalnapenkis A, Kasela S, Kettunen J, Kim Y, Kirsten H, Kovacs P, Krohn K, Kronbe...Wagner GG (2019).  Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences.  Nature Genetics.  51(2).  245-257.
  • Timmers PR, Mounier N, Lall K, Fischer K, Ning Z, Feng X, Bretherick AD, Clark DW, Agbessi M, Ahsan H, Alves I, Andiappan A, Awadalla P, Battle A, Bonder MJ, Boomsma D, Christiansen M, Claringbould A, Deelen P, van Dongen J, Esko T, Favé M, Franke L, Frayling T, Gharib SA, Gibson G, Hemani G, Jansen R, Kalnapenkis A, Kasela S, Kettunen J, Kim Y, Kirsten H, Kovacs P, Krohn K, Kronberg-Guzman J, Kukushkina V, Kutalik Z, Kähönen M, Lee B, Lehtimäki T, Loeffler M, Marigorta U, Metspalu A, van Meurs J, Milani L, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Perola M, Pervjakova N, Pierce B, Powell J, Prokisch H, Psaty BM, Raitakari O, Ring S, Ripatti S, Rotzschke O, Ruëger S, Saha A, Scholz M, Schramm K, Seppälä I, Stumvoll M, Sullivan P, Teumer A, Thiery J, Tong L, Tönjes A, Verlouw J, Visscher PM, Võsa U, Völker U, Yaghootkar H, Yang J, Zeng B, Völker U, Shen X, Esko T, Kutalik Z, Wilson JF, Joshi PK (2019).  Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances.  eLife.  8.
  • Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, Gilad Y (2019).  Dynamic genetic regulation of gene expression during cellular differentiation.  Science.  364(6447).  1287-1290.
  • Saha A, Battle A (2019).  False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors [version 2; peer review: 3 approved].  F1000Research.  7.
  • Wheeler HE, Ploch S, Barbeira AN, Bonazzola R, Andaleon A, Fotuhi Siahpirani A, Saha A, Battle A, Roy S, Im HK (2019).  Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits.  Genetic Epidemiology.  43(6).  596-608.
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  • Knowles DA, Davis JR, Edgington H, Raj A, Favé MJ, Zhu X, Potash JB, Weissman MM, Shi J, Levinson DF, Awadalla P, Mostafavi S, Montgomery SB, Battle A (2017).  Allele-specific expression reveals interactions between genetic variation and environment.  Nature Methods.  14(7).  699-702.
  • Parsana P, Amend SR, Hernandez J, Pienta KJ, Battle A (2017).  Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration.  BMC Cancer.  17(1).
  • Del Bel KL, Ragotte RJ, Saferali A, Lee S, Vercauteren SM, Mostafavi SA, Schreiber RA, Prendiville JS, Phang MS, Halparin J, Au N, Dean JM, Priatel JJ, Jewels E, Junker AK, Rogers PC, Seear M, McKinnon ML, Turvey SE (2017).  JAK1 gain-of-function causes an autosomal dominant immune dysregulatory and hypereosinophilic syndrome.  Journal of Allergy and Clinical Immunology.  139(6).  2016-2020.e5.
  • Pala M, Zappala Z, Marongiu M, Li X, Davis JR, Cusano R, Crobu F, Kukurba KR, Gloudemans MJ, Reinier F, Berutti R, Piras MG, Mulas A, Zoledziewska M, Marongiu M, Sorokin EP, Hess GT, Smith KS, Busonero F, Maschio A, Steri M, Sidore C, Sanna S, Fiorillo E, Bassik MC, Sawcer SJ, Battle A, Novembre J, Jones C, Angius A, Abecasis GR, Schlessinger D, Cucca F, Montgomery SB (2017).  Population- and individual-specific regulatory variation in Sardinia.  Nature Genetics.  49(5).  700-707.
  • Chiang C, Scott AJ, Davis JR, Tsang EK, Li X, Kim Y, Hadzic T, Damani FN, Ganel L, Montgomery SB, Battle A, Conrad DF, Hall IM (2017).  The impact of structural variation on human gene expression.  Nature Genetics.  49(5).  692-699.
  • Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S, Foley AR, Bolduc V, Waddell LB, Sandaradura SA, O'Grady GL, Estrella E, Reddy HM, Zhao F, Weisburd B, Karczewski KJ, O'Donnell-Luria AH, Birnbaum D, Sarkozy A, Hu Y, Gonorazky H, Claeys K, Joshi H, Bournazos A, Oates EC, Ghaoui R, Davis MR, Laing NG, Topf A, Kang PB, Beggs AH, North KN, Straub V, Dowling JJ, Muntoni F, Clarke NF, Cooper ST, Bönnemann CG, MacArthur DG, Ardlie KG, Getz G, Gelfand ET, Segrè AV, Aguet F, Sullivan TJ, Li X, Nedzel JL, Trowbridge CA, Hadley K, Huang KH, Noble MS, Nguyen DT, Nobel AB, Wright FA, Shabalin AA, Palowitch JJ, Zhou Y-H, Dermitzakis ET, McCarthy MI, Payne AJ, Lappalainen T, Castel S, Kim-Hellmuth S, Mohammadi P, Battle A, Parsana P, Mostafavi S, Brown A, Ongen H, Delaneau O, Panousis N, Howald C, Van De Bunt M, Guigo R, Monlong J, Reverter F, Garrido D, Munoz M, Bogu G, Sodaei R, Papasaikas P, Ndungu AW, Montgomery SB, Li X, Fresard L, Davis JR, Tsang EK, Zappala Z, Abell NS, G...Zaugg JB (2017).  Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.  Science Translational Medicine.  9(386).
  • Ritchie MD, Davis JR, Aschard H, Battle A, Conti D, Du M, Eskin E, Fallin MD, Hsu L, Kraft P, Moore JH, Pierce BL, Bien SA, Blair Thomas DC, Wei P, Montgomery SB (2017).  Incorporation of Biological Knowledge into the Study of Gene-Environment Interactions.  American Journal of Epidemiology.  186(7).  771-777.
  • Clifford RL, Jones MJ, MacIsaac JL, McEwen LM, Goodman SJ, Mostafavi S, Kobor MS, Carlsten C (2017).  Inhalation of diesel exhaust and allergen alters human bronchial epithelium DNA methylation.  Journal of Allergy and Clinical Immunology.  139(1).  112-121.
  • Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, Engelhardt BE, Battle A (2017).  Co-expression networks reveal the tissue-specific regulation of transcription and splicing.  Genome Research.  27(11).  1843-1858.
  • Sharon E, Sibener LV, Battle A, Fraser HB, Christopher Garcia K, Pritchard JK (2016).  Genetic variation in MHC proteins is associated with T cell receptor expression biases.  Nature Genetics.  48(9).  995-1002.
  • Moodley D, Yoshida H, Mostafavi S, Asinovski N, Ortiz-Lopez A, Symanowicz P, Telliez JB, Hegen M, Clark JD, Mathis D, Benoist C (2016).  Network pharmacology of JAK inhibitors.  Proceedings of the National Academy of Sciences of the United States of America.  113(35).  9852-9857.
  • Gaiteri C, Mostafavi S, Honey CJ, De Jager PL, Bennett DA (2016).  Genetic variants in Alzheimer disease-molecular and brain network approaches.  Nature Reviews Neurology.  12(7).  413-427.
  • Dwyer DF, Barrett NA, Austen KF, Kim EY, Brenner MB, Shaw L, Yu B, Goldrath A, Mostafavi S, Regev A, Rhoades A, Moodley D, Yoshida H, Mathis D, Benoist C, Nabekura T, Lam V, Lanier LL, Brown B, Merad M, Cremasco V, Turley S, Monach P, Dustin ML, Li Y, Shinton SA, Hardy RR, Shay T, Qi Y, Sylvia K, Kang J, Fairfax K, Randolph GJ, Robinette ML, Fuchs A, Colonna M (2016).  Expression profiling of constitutive mast cells reveals a unique identity within the immune system.  Nature Immunology.  17(7).  878-887.
  • Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, Awadalla P, Mostafavi S, Battle A, Montgomery SB (2016).  Impact of the X chromosome and sex on regulatory variation.  Genome Research.  26(6).  768-777.
  • Mostafavi S, Yoshida H, Moodley D, Leboité H, Rothamel K, Raj T, Ye CJ, Chevrier N, Zhang SY, Feng T, Lee M, Casanova JL, Clark JD, Hegen M, Telliez JB, Hacohen N, De Jager PL, Regev A, Mathis D, Benoist C (2016).  Parsing the Interferon Transcriptional Network and Its Disease Associations.  Cell.  164(3).  564-578.
  • Davis JR, Fresard L, Knowles DA, Pala M, Bustamante CD, Battle A, Montgomery SB (2016).  An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.  American Journal of Human Genetics.  98(1).  216-224.
  • Yang J, Huang T, Petralia F, Long Q, Zhang B, Argmann C, Zhao Y, Mobbs CV, Schadt EE, Zhu J, Tu Z, Ardlie KG, Deluca DS, Segrè AV, Sullivan TJ, Young TR, Gelfand ET, Trowbridge CA, Maller JB, Tukiainen T, Lek M, Ward LD, Kheradpour P, Iriarte B, Meng Y, Palmer CD, Winckler W, Hirschhorn J, Kellis M, MacArthur DG, Getz G, Shablin AA, Li G, Zhou Y-H, Nobel AB, Rusyn I, Wright FA, Lappalainen T, Ferreira PG, Ongen H, Rivas MA, Battle A, Mostafavi S, Monlong J, Sammeth M, Mele M, Reverter F, Goldman J, Koller D, Guigo R, McCarthy MI, Dermitzakis ET, Gamazon ER, Konkashbaev A, Nicolae DL, Cox NJ, Flutre T, Wen X, Stephens M, Pritchard JK, Lin L, Liu J, Brown A, Mestichelli B, Tidwell D, Lo E, Salvatore M, Shad S, Thomas JA, Lonsdale JT, Choi C, Karasik E, Ramsey K, Moser MT, Foster BA, Gillard BM, Syron J, Fleming J, Magazine H, Hasz R, Walters GD, Bridge JP, Miklos M, Sullivan S, Barker LK, Traino H, Mosavel M, Siminoff LA, Valley DR, Rohrer DC, Jewel S, Branton P, Sobin LH, ...Lockhart NC (2015).  Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases.  Scientific Reports.  5.
  • Ardlie KG, DeLuca DS, Segrè AV, Sullivan TJ, Young TR, Gelfand ET, Trowbridge CA, Maller JB, Tukiainen T, Lek M, Ward LD, Kheradpour P, Iriarte B, Meng Y, Palmer CD, Esko T, Winckler W, Hirschhorn JN, Kellis M, MacArthur DG, Getz G, Shabalin AA, Li G, Zhou Y-H, Nobel AB, Rusyn I, Wright FA, Lappalainen T, Ferreira PG, Ongen H, Rivas MA, Battle A, Mostafavi S, Monlong J, Sammeth M, Melé M, Reverter F, Goldmann JM, Koller D, Guigó R, McCarthy MI, Dermitzakis ET, Gamazon ER, Im HK, Konkashbaev A, Nicolae DL, Cox NJ, Flutre T, Wen X, Stephens M, Pritchard JK, Tu Z, Zhang B, Huang T, Long Q, Lin L, Yang J, Zhu J, Liu J, Brown A, Mestichelli B, Tidwell D, Lo E, Salvatore M, Shad S, Thomas JA, Lonsdale JT, Moser MT, Gillard BM, Karasik E, Ramsey K, Choi C, Foster BA, Syron J, Fleming J, Magazine H, Hasz R, Walters GD, Bridge JP, Miklos M, Sullivan S, Barker LK, Traino HM, Mosavel M, Siminoff LA, Valley DR, Rohrer DC, Jewell SD, Branton PA, Sobin LH, Barcus M, Qi L, McLean J, Hariha...Lockhart (2015).  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans.  Science.  348(6235).  648-660.
  • Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y (2015).  Impact of regulatory variation from RNA to protein.  Science.  347(6222).  664-667.
  • Holm A, Lin L, Faraco J, Mostafavi S, Battle A, Zhu X, Levinson DF, Han F, Gammeltoft S, Jennum P, Mignot E, Kornum BR (2015).  EIF3G is associated with narcolepsy across ethnicities.  European Journal of Human Genetics.  23(11).  1573-1580.
  • Pierson E, Koller D, Battle A, Mostafavi S (2015).  Sharing and Specificity of Co-expression Networks across 35 Human Tissues.  PLoS Computational Biology.  11(5).
  • Carithers LJ, Ardlie K, Barcus M, Branton PA, Britton A, Buia SA, Compton CC, Deluca DS, Peter-Demchok J, Gelfand ET, Guan P, Korzeniewski GE, Lockhart NC, Rabiner CA, Rao AK, Robinson KL, Roche NV, Sawyer SJ, Segrè AV, Shive CE, Smith AM, Sobin LH, Undale AH, Valentino KM, Vaught J, Young TR, Moore HM, Barker L, Basile M, Battle A, Boyer J, Bradbury D, Bridge JP, Brown A, Burges R, Choi C, Colantuoni D, Cox N, Dermitzakis ET, Derr LK, Dinsmore MJ, Erickson K, Fleming J, Flutre T, Foster BA, Gamazon ER, Getz G, Gillard BM, Guigó R, Hambright KW, Hariharan P, Hasz R, Im HK, Jewell S, Karasik E, Kellis M, Kheradpour P, Koester S, Koller D, Konkashbaev A, Lappalainen T, Little R, Liu J, Lo E, Lonsdale JT, Lu C, MacArthur DG, Magazine H, Maller JB, Marcus Y, Mash DC, McCarthy MI, McLean J, Mestichelli B, Miklos M, Monlong J, Mosavel M, Moser MT, Mostafavi S, Nicolae DL, Pritchard J, Qi L, Ramsey K, Rivas MA, Robles BE, Rohrer DC, Salvatore M, Sammeth M, Seleski J, Shad S, Simi...Williams P (2015).  A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project.  Biopreservation and Biobanking.  13(5).  311-317.
  • Holm A, Lin L, Faraco J, Mostafavi S, Battle A, Zhu X, Levinson DF, Han F, Gammeltoft S, Jennum P, others (2015).  EIF3G is associated with narcolepsy across ethnicities.  European Journal of Human Genetics.
  • Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-Ud-Din M, Hintsanen P, Khan SA, Mpindi J-P, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K, Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G, Abbuehl J-P, Allen J, Altman RB, Balcome S, Battle A, Bender A, Berger B, Bernard J, Bhattacharjee M, Bhuvaneshwar K, Bieberich AA, Boehm F, Califano A, Chan C, Chen B, Chen T-H, Choi J, Coelho LP, Cokelaer T, Collins JC, Creighton CJ, Cui J, Dampier W, Davisson VJ, De Baets B, Deshpande R, DiCamillo B, Dundar M, Duren Z, Ertel A, Fan H, Fang H, Gauba R, Gottlieb A, Grau M, Gusev Y, Ha MJ, Han L, Harris M, Henderson N, Hejase HA, Homicsko K, Hou JP, Hwang W, IJzerman AP, Karacali B, Keles S, Kendziorski C, Kim J, Kim M, Kim Y, Knowles DA, Koller D, Lee J, Lee JK, Lenselink EB, Li B, Li B, Li J, Liang H, Ma J, Madhavan S, Mooney S, Myers CL, Newton MA, Overington JP, Pal R, Peng J, Pestell R, Prill RJ, Qiu P, R...Van Westen GJP (2014).  A community effort to assess and improve drug sensitivity prediction algorithms.  Nature Biotechnology.  32(12).  1202-1212.
  • Mostafavi S, Ortiz-Lopez A, Bogue MA, Hattori K, Pop C, Koller D, Mathis D, Benoist C, Blair DA, Dustin ML, Shinton SA, Hardy RR, Shay T, Regev A, Cohen N, Brennan P, Brenner M, Kim F, Rao TN, Wagers A, Heng T, Ericson J, Rothamel K, Kreslavsky T, Fletcher A, Elpek K, Bellemare-Pelletier A, Malhotra D, Turley S, Miller J, Brown B, Merad M, Gautier EL, Jakubzick C, Randolph GJ, Monach P, Best AJ, Knell J, Goldrath A, Jojic V, Laidlaw D, Collins J, Gazit R, Rossi DJ, Malhotra N, Sylvia K, Kang J, Bezman NA, Sun JC, Min-Oo G, Kim CC, Lanier LL (2014).  Variation and genetic control of gene expression in primary immunocytes across inbred mouse strains.  Journal of Immunology.  193(9).  4485-4496.
  • Cho H, Davis J, Li X, Smith KS, Battle A, Montgomery SB (2014).  High-resolution transcriptome analysis with long-read RNA sequencing.  PLoS ONE.  9(9).
  • Davies MN, Krause L, Bell JT, Gao F, Ward KJ, Wu H, Lu H, Liu Y, Tsai PC, Collier DA, Murphy T, Dempster E, Mill J, Battle A, Mostafavi S, Zhu X, Henders A, Byrne E, Wray NR, Martin NG, Spector TD, Wang J (2014).  Hypermethylation in the ZBTB20 gene is associated with major depressive disorder.  Genome Biology.  15(4).
  • Nance T, Smith KS, Anaya V, Richardson R, Ho L, Pala M, Mostafavi S, Battle A, Feghali-Bostwick C, Rosen G, Montgomery SB (2014).  Transcriptome analysis reveals differential splicing events in IPF lung tissue.  PLoS ONE.  9(3).
  • Cho H, Davis J, Li X, Smith KS, Battle A, Montgomery SB (2014).  High-resolution transcriptome analysis with long-read RNA sequencing.  PloS one.  9(9).  e108095.
  • Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y (2014).  Impact of regulatory variation from RNA to protein.  Science.  1260793.
  • Battle A, Montgomery S (2014).  Determining causality and consequence of expression quantitative trait loci.  Human genetics.  133(6).  727-735.
  • Nance T, Smith K, Anaya V, Richardson R, Ho L, Pala M, Mostafavi S, Battle A, Feghali-Bostwick C, Rosen G, others (2014).  Transcriptome analysis reveals differential splicing events in IPF lung tissue..  PloS one.  9(5).  e97550-e97550.
  • Li X, Battle A, Karczewski KJ, Zappala Z, Knowles DA, Smith KS, Kukurba KR, Wu E, Simon N, Montgomery SB (2014).  Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants.  The American Journal of Human Genetics.  95(3).  245-256.
  • Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, others (2014).  Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.  Genome research.  24(1).  14-24.
  • Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D (2014).  Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.  Genome Research.  24(1).  14-24.
  • Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL (2014).  Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.  Science.  344(6183).  519-523.
  • Nance T, Smith KS, Anaya V, Richardson R, Ho L, Pala M, Mostafavi S, Battle A, Feghali-Bostwick C, Rosen G, Montgomery SB (2014).  Transcriptome analysis reveals differential splicing events in IPF lung tissue.  PloS one.  9(5).  e97550.
  • Battle A, Montgomery SB (2014).  Determining causality and consequence of expression quantitative trait loci.  Human Genetics.  133(6).  727-735.
  • Li X, Battle A, Karczewski KJ, Zappala Z, Knowles DA, Smith KS, Kukurba KR, Wu E, Simon N, Montgomery SB (2014).  Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants.  American Journal of Human Genetics.  95(3).  245-256.
  • Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, Mccormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, Mackinnon DF, Notes L, Schweizer B, Furman D, Montgomery SB, Urban AE, Koller D, Levinson DF (2014).  Type I interferon signaling genes in recurrent major depression: Increased expression detected by whole-blood RNA sequencing.  Molecular Psychiatry.  19(12).  1267-1274.
  • Mostafavi S, Battle A, Zhu X, Urban AE, Levinson D, Montgomery SB, Koller D (2013).  Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge.  PLoS ONE.  8(7).
  • Mostafavi S, Battle A, Zhu X, Potash J, Weissman M, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, others (2013).  Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing.  Molecular psychiatry.
  • Mostafavi S, Battle A, Zhu X, Urban AE, Levinson D, Montgomery SB, Koller D (2013).  Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge.  PloS one.  8(7).  e68141.
  • Mostafavi S, Goldenberg A, Morris Q (2012).  Labeling Nodes Using Three Degrees of Propagation.  PLoS ONE.  7(12).
  • Mostafavi S, Amiri A (2012).  Extending fuzzy c-means to clustering data streams.  ICEE 2012 - 20th Iranian Conference on Electrical Engineering.  726-729.
  • Benoist C, Lanier L, Merad M, Mathis D, Ericson J, Painter M, Davis S, Laplace C, Hyatt G, Paik H, Rothamel K, Cruse R, Doran G, Heng T, Asinovski N, Ortiz-Lopes A, Ergun A, Gray D, Wakamatsu E, Hill J, Mingueneau M, Cipolletta D, Yoshida H, Cohen N, Kim E, Brennan P, Lynch L, Brenner M, Costello J, Collins JJ, Blair D, Dustin M, Knell J, Yang E, Best A, Shaw L, Doedens A, Goldrath A, Shinton S, Zhou Y, Hardy R, Jojic V, Mostafavi S, Koller D, Jianu R, Laidlaw D, Bezman N, Sun J, Zhu Y, Hendricks D, Kamimura Y, Min-Oo G, Morvan M, Kamimura Y, Nabekura T, Lam V, Kim C, Greter M, Helft J, Chow A, Bogunovic M, Mortha A, Price J, Hashimoto D, Miller J, Sathe P, Chudnovskiy A, Lavin Y, Idoyaga J, Gautier E, Jakubzick C, D'Angelo J, Randolph G, Shay T, Regev A, Gazit R, Rossi D, Kreslawsky T, von Bohmer H, Bellemare-Pelletier A, Elpek K, Spelv L, Fletcher A, Malhotra D, Cremasco V, Turley S, Kim F, Nageswara Rao T, Wagers A (2012).  Consortium biology in immunology: The perspective from the Immunological Genome Project.  Nature Reviews Immunology.  12(10).  734-740.
  • Mostafavi S, Morris Q (2012).  Combining many interaction networks to predict gene function and analyze gene lists.  Proteomics.  12(10).  1687-1696.
  • Ahmad S, Battle A, Malkani Z, Kamvar SD (2011).  The jabberwocky programming environment for structured social computing.  UIST'11 - Proceedings of the 24th Annual ACM Symposium on User Interface Software and Technology.  53-63.
  • Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD (2011).  Unsupervised detection of genes of influence in lung cancer using biological networks.  Bioinformatics.  27(22).  3166-3172.
  • Mostafavi S, Goldenberg A, Morris Q (2011).  Predicting node characteristics from molecular networks.  Methods in Molecular Biology.  781.  399-414.
  • Mostafavi SM, Hamadani E, Kuehn R, Tafazolli R (2011).  Delay minimisation in multipath routing using intelligent traffic distribution policies.  IET Communications.  5(10).  1405-1412.
  • Schimmer BP, Tsao J, Cordova M, Mostafavi S, Morris Q, Scheys JO (2011).  Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells.  Molecular and Cellular Endocrinology.  336(1-2).  85-91.
  • Mostafavi SM, Hamadani E, Tafazzoli R (2010).  Maximum delay minimization in multipath routing.  CNSR 2010 - Proceedings of the 8th Annual Conference on Communication Networks and Services Research.  310-314.
  • Mostafavi SM, Hamadani E, Tafazolli R (2010).  Delay minimization in multipath routing.  IWCMC 2010 - Proceedings of the 6th International Wireless Communications and Mobile Computing Conference.  711-715.
  • Knott S, Mostafavi S, Mousavi P (2010).  A neural network based modeling and validation approach for identifying gene regulatory networks.  Neurocomputing.  73(13-15).  2419-2429.
  • Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q (2010).  The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function.  Nucleic Acids Research.  38(SUPPL. 2).
  • Battle A, Jonikas MC, Walter P, Weissman JS, Koller D (2010).  Automated identification of pathways from quantitative genetic interaction data.  Molecular Systems Biology.  6.
  • Mostafavi S, Morris Q (2010).  Fast integration of heterogeneous data sources for predicting gene function with limited annotation.  Bioinformatics.  26(14).  1759-1765.
  • Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JLY, Toufighi K, Mostafavi S, Prinz J, St. Onge RP, Vandersluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, Luis BJS, Shuteriqi E, Tong AHY, Van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C (2010).  The genetic landscape of a cell.  Science.  327(5964).  425-431.
  • Battle A, Jonikas MC, Walter P, Weissman JS, Koller D (2010).  Automated identification of pathways from quantitative genetic interaction data.  Molecular systems biology.  6(1).
  • Mostafavi S, Morris Q (2009).  Using the Gene Ontology hierarchy when predicting gene function.  Proceedings of the 25th Conference on Uncertainty in Artificial Intelligence, UAI 2009.  419-427.
  • Hanzo L, Mostafavi SM, Tafazolli R (2008).  Connectivity-related properties of mobile nodes obeying the random walk and random waypoint mobility models.  IEEE Vehicular Technology Conference.  133-137.
  • Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP (2008).  A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.  Genome Biology.  9(SUPPL. 1).
  • Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q (2008).  GeneMANIA: A real-time multiple association network integration algorithm for predicting gene function.  Genome Biology.  9(SUPPL. 1).
  • Kühn R, Mostafavi SM (2008).  Optimal routing policy.  IEEE Communications Letters.  12(3).  222-224.
  • Battle A, Chechik G, Koller D (2007).  Temporal and cross-subject probabilistic models for fMRI prediction tasks.  Advances in Neural Information Processing Systems.  121-128.
  • Lee H, Battle A, Raina R, Ng AY (2007).  Efficient sparse coding algorithms.  Advances in Neural Information Processing Systems.  801-808.
  • Otaegui D, Mostafavi S, Bernard CCA, De Munain AL, Mousavi P, Oksenberg JR, Baranzini SE (2007).  Increased transcriptional activity of milk-related genes following the active phase of experimental autoimmune encephalomyelitis and multiple sclerosis.  Journal of Immunology.  179(6).  4074-4082.
  • Raina R, Battle A, Lee H, Packer B, Ng AY (2007).  Self-taught learning: Transfer learning from unlabeled data.  ACM International Conference Proceeding Series.  227.  759-766.
  • Mostafavi S, Baranzini S, Oksernberg J, Mousavi P (2006).  Predictive modeling of therapy response in multiple sclerosis using gene expression data.  Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings.  5519-5522.
  • Mostafavi S, Baranzini S, Oksenberg J, Mousavi P (2006).  A fast multivariate feature-selection/classification approach for prediction of therapy response in multiple sclerosis.  Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06.  312-319.
  • Knott S, Mostafavi S, Mousavi P (2006).  A neural network based approach for inference and verification of transcriptional regulatory interactions.  Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings.  5838-5841.
  • Battle A, Segal E, Koller D (2005).  Probabilistic discovery of overlapping cellular processes and their regulation.  Journal of Computational Biology.  12(7).  909-927.
  • Battle A, Segal E, Koller D (2005).  Probabilistic discovery of overlapping cellular processes and their regulation.  Journal of Computational Biology.  12(7).  909-927.
  • Battle A, Segal E, Koller D (2004).  Probabilistic discovery of overlapping cellular processes and their regulation.  Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB.  8.  167-176.
  • Segal E, Battle A, Koller D (2003).  Decomposing gene expression into cellular processes..  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.  89-100.
  • Lemon O, Gruenstein A, Gullett R, Battle A, Hiatt L, Peters S (2003).  Generation of collaborative spoken dialogue contributions in dynamic task environments.  Proceedings of the AAAI Spring Symposium on Natural Language Generation in Spoken and Written Dialogue.
  • Segal E, Battle A, Koller D (2003).  Decomposing gene expression into cellular processes.  Proceedings of the Pacific Symposium on Biocomputing.  8.  89-100.
Conference Proceedings
  • Ahmad S, Battle A, Malkani Z, Kamvar S (2011).  The jabberwocky programming environment for structured social computing.  Proceedings of the 24th annual ACM symposium on User interface software and technology.  53-64.
  • Raina R, Battle A, Lee H, Packer B, Ng AY (2007).  Self-taught learning: transfer learning from unlabeled data.  Proceedings of the 24th international conference on Machine learning.  759-766.
  • Lee H, Battle A, Raina R, Ng AY (2006).  Efficient sparse coding algorithms.  Advances in neural information processing systems.  801-808.
  • Lemon O, Gruenstein A, Battle A, Peters S (2002).  Multi-tasking and collaborative activities in dialogue systems.  Proceedings of the 3rd SIGdial workshop on Discourse and dialogue-Volume 2.  113-124.
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