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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
  • 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.
  • 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).
  • 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.
  • 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.
  • 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.
  • Klein HU, McCabe C, Gjoneska E, Sullivan SE, Kaskow BJ, Tang A, Smith RV, Xu J, Pfenning AR, Bernstein BE, Meissner A, Schneider JA, Mostafavi S, Tsai LH, Young-Pearse TL, Bennett DA, De Jager PL (2019).  Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains.  Nature Neuroscience.  22(1).  37-46.
  • Knerich V, Jones AA, Seyedin S, Siu C, Dinh L, Mostafavi S, Barr AM, Panenka WJ, Thornton AE, Honer WG, Rutherford AR (2019).  Social and structural factors associated with substance use within the support network of adults living in precarious housing in a socially marginalized neighborhood of Vancouver, Canada.  PLoS ONE.  14(9).
  • Barbeira AN, Dickinson SP, Bonazzola R, Zheng J, Wheeler HE, Torres JM, Torstenson ES, Shah KP, Garcia T, Edwards TL, Stahl EA, Huckins LM, Aguet F, Ardlie KG, Cummings BB, Gelfand ET, Getz G, Hadley K, Handsaker RE, Huang KH, Kashin S, Karczewski KJ, Lek M, Li X, MacArthur DG, Nedzel JL, Nguyen DT, Noble MS, Segrè AV, Trowbridge CA, Tukiainen T, Abell NS, Balliu B, Barshir R, Basha O, Battle A, Bogu GK, Brown A, Brown CD, Castel SE, Chen LS, Chiang C, Conrad DF, Damani FN, Davis JR, Delaneau O, Dermitzakis ET, Engelhardt BE, Eskin E, Ferreira PG, Frésard L, Gamazon ER, Garrido-Martín D, Gewirtz ADH, Gliner G, Gloudemans MJ, Guigo R, Hall IM, Han B, He Y, Hormozdiari F, Howald C, Jo B, Kang EY, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy MI, McDowell IC, Mohammadi P, Monlong J, Montgomery SB, Muñoz-Aguirre M, Ndungu AW, Nobel AB, Oliva M, Ongen H, Palowitch JJ, Panousis N, Papasaikas P, Park Y, Parsana P, Payne AJ, Peterson CB, Quan J, Reverter F...Im HK (2018).  Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics.  Nature Communications.  9(1).
  • Qi T, Wu Y, Zeng J, Zhang F, Xue A, Jiang L, Zhu Z, Kemper K, Yengo L, Zheng Z, Agbessi M, Ahsan H, Alves I, Andiappan A, Awadalla P, Battle A, Beutner F, Jan Bonder M, Boomsma D, Christiansen M, Claringbould A, Deelen P, Esko T, Favé MJ, Franke L, Frayling T, Gharib S, Gibson G, 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, Metspalu A, Milani L, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Perola M, Pervjakova N, Pierce B, Powell J, Prokisch H, Psaty B, 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, Van Dongen J, Van Meurs J, Verlouw J, Völker U, Võsa U, Yaghootkar H, Zeng B, Marioni RE, Montgomery GW, Deary IJ, Wray NR, Visscher PM, McRae AF, Yang J (2018).  Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood.  Nature Communications.  9(1).
  • Raj T, Li YI, Wong G, Humphrey J, Wang M, Ramdhani S, Wang YC, Ng B, Gupta I, Haroutunian V, Schadt EE, Young-Pearse T, Mostafavi S, Zhang B, Sklar P, Bennett DA, De Jager PL (2018).  Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility.  Nature Genetics.  50(11).  1584-1592.
  • Tasaki S, Gaiteri C, Mostafavi S, De Jager PL, Bennett DA (2018).  The molecular and neuropathological consequences of genetic risk for Alzheimer's dementia.  Frontiers in Neuroscience.  12(OCT).
  • Tasaki S, Gaiteri C, Mostafavi S, Yu L, Wang Y, De Jager PL, Bennett DA (2018).  Multi-omic directed networks describe features of gene regulation in aged brains and expand the set of genes driving cognitive decline.  Frontiers in Genetics.  9(AUG).
  • De Jager PL, Ma Y, McCabe C, Xu J, Vardarajan BN, Felsky D, Klein HU, White CC, Peters MA, Lodgson B, Nejad P, Tang A, Mangravite LM, Yu L, Gaiteri C, Mostafavi S, Schneider JA, Bennett DA (2018).  Data descriptor: A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research.  Scientific Data.  5.
  • Felsky D, Patrick E, Schneider JA, Mostafavi S, Gaiteri C, Patsopoulos N, Bennett DA, De Jager PL (2018).  Polygenic analysis of inflammatory disease variants and effects on microglia in the aging brain.  Molecular Neurodegeneration.  13(1).
  • Peyrot WJ, Van der Auwera S, Milaneschi Y, Dolan CV, Madden PAF, Sullivan PF, Strohmaier J, Ripke S, Rietschel M, Nivard MG, Mullins N, Montgomery GW, Henders AK, Heat AC, Fisher HL, Dunn EC, Byrne EM, Air TA, Wray NR, Mattheisen M, Trzaskowski M, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TFM, Bacanu S-A, Bækvad-Hansen M, Beekman ATF, Bigdeli TB, Binder EB, 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, Eley TC, Escott-Price V, Farnush, Kiadeh FH, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Goes FS, Gordon SD, Grove J, Hall LS, Hansen CS, Hansen TF, Herms S, Hicki IB, Hoffmann P, Homuth G, Horn C, Hottenga J-J, Hougaard DM, Ising M, Jansen R, Jorgenson E, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Li Y, Lind PA, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, ...Nelson EN (2018).  Does Childhood Trauma Moderate Polygenic Risk for Depression? A Meta-analysis of 5765 Subjects From the Psychiatric Genomics Consortium.  Biological Psychiatry.  84(2).  138-147.
  • Yu L, Petyuk VA, Gaiteri C, Mostafavi S, Young-Pearse T, Shah RC, Buchman AS, Schneider JA, Piehowski PD, Sontag RL, Fillmore TL, Shi T, Smith RD, De Jager PL, Bennett DA (2018).  Targeted brain proteomics uncover multiple pathways to Alzheimer's dementia.  Annals of Neurology.  84(1).  78-88.
  • Mostafavi S, Gaiteri C, Sullivan SE, White CC, Tasaki S, Xu J, Taga M, Klein HU, Patrick E, Komashko V, McCabe C, Smith R, Bradshaw EM, Root DE, Regev A, Yu L, Chibnik LB, Schneider JA, Young-Pearse TL, Bennett DA, De Jager PL (2018).  A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease.  Nature Neuroscience.  21(6).  811-819.
  • Graham E, Lee J, Price M, Tarailo-Graovac M, Matthews A, Engelke U, Tang J, Kluijtmans LAJ, Wevers RA, Wasserman WW, van Karnebeek CDM, Mostafavi S (2018).  Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review.  Journal of Inherited Metabolic Disease.  41(3).  435-445.
  • Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu S-A, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke T-K, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, DIrek N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CSø, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga J-J, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medl...Sullivan PF (2018).  Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.  Nature Genetics.  50(5).  668-681.
  • Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ (2018).  Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.  Nature Biotechnology.  36(1).  89-94.
  • Ioannidis NM, Davis JR, DeGorter MK, Larson NB, McDonnell SK, French AJ, Battle AJ, Hastie TJ, Thibodeau SN, Montgomery SB, Bustamante CD, Sieh W, Whittemore AS (2017).  FIRE: Functional inference of genetic variants that regulate gene expression.  Bioinformatics.  33(24).  3895-3901.
  • Milaneschi Y, Lamers F, Peyrot WJ, Baune BT, Breen G, Dehghan A, Forstner AJ, Grabe HJ, Homuth G, Kan C, Lewis C, Mullins N, Nauck M, Pistis G, Preisig M, Rivera M, Rietschel M, Streit F, Strohmaier J, Teumer A, Van Der Auwera S, Wray NR, Boomsma DI, Penninx BWJH, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TFM, Bacanu S-A, Bakvad-Hansen M, Beekman ATF, Bigdeli TB, Binder EB, Blackwood DHR, Bryois J, Buttenschon 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, Frank J, Gaspar HA, Gill M, Goes FS, Gordon SD, Grove J, Hall LS, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Horn C, Hottenga J-J, Hougaard DM, Ising M, Jansen R, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutal...Sullivan PF (2017).  Genetic association of major depression with a typical features and obesity-related immunometabolic dysregulations.  JAMA Psychiatry.  74(12).  1214-1225.
  • Rietschel L, Streit F, Zhu G, McAloney K, Frank J, Couvy-Duchesne B, Witt SH, Binz TM, Bolton JL, Hayward C, Direk N, Anderson A, Huffman J, Wilson JF, Campbell H, Rudan I, Wright A, Hastie N, Wild SH, Velders FP, Hofman A, Uitterlinden AG, Lahti J, Räikkönen K, Kajantie E, Widen E, Palotie A, Eriksson JG, Kaakinen M, Järvelin M-R, Timpson NJ, Davey Smith G, Ring SM, Evans DM, St Pourcain B, Tanaka T, Milaneschi Y, Bandinelli S, Ferrucci L, Van Der Harst P, Rosmalen JG, Bakker SJ, Verweij N, Dullaart RP, Mahajan A, Lindgren CM, Morris A, Lind L, Ingelsson E, Anderson LN, Pennell CE, Lye SJ, Matthews SG, Eriksson J, Mellstrom D, Ohlsson C, Price JF, Strachan MW, Reynolds RM, Tiemeier H, Ripke S, Mattheisen M, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TF, Bacanu S-A, Bækvad-Hansen M, Beekman AT, Bennett DA, Berger K, Bigdeli TB, Bybjerg-Grauholm J, Byrne EM, Cai N, Castelao E, Clarke T-K, Coleman JR, Consortium C, Craddock N, Dannlowski U, Davies G, Davies G, De Ge...Rietschel M (2017).  Hair Cortisol in Twins: Heritability and Genetic Overlap with Psychological Variables and Stress-System Genes.  Scientific Reports.  7(1).
  • Kariminia A, Ivison S, Ng B, Rozmus J, Sung S, Varshney A, Aljurf M, Lachance S, Walker I, Toze C, Lipton J, Lee SJ, Szer J, Doocey R, Lewis I, Smith C, Chaudhri N, Levings MK, Broady R, Devins G, Szwajcer D, Foley R, Mostafavi S, Pavletic S, Wall DA, Couban S, Panzarella T, Schultz KR (2017).  CD56 bright natural killer regulatory cells in filgrastim primed donor blood or marrow products regulate chronic graft-versus-host disease: The Canadian blood and marrow transplant group randomized 0601 study results.  Haematologica.  102(11).  1936-1946.
  • Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD, Aguet F, Ardlie KG, Cummings BB, Gelfand ET, Getz G, Hadley K, Handsaker RE, Huang KH, Kashin S, Karczewski KJ, Lek M, Li X, MacArthur DG, Nedzel JL, Nguyen DT, Noble MS, Segrè AV, Trowbridge CA, Tukiainen T, Abell NS, Balliu B, Barshir R, Basha O, Bogu GK, Brown A, Brown CD, Castel SE, Chen LS, Conrad DF, Cox NJ, Delaneau O, Dermitzakis ET, Engelhardt BE, Eskin E, Ferreira PG, Frésard L, Gamazon ER, Garrido-Martín D, Gewirtz ADH, Gliner G, Gloudemans MJ, Guigo R, Hall IM, Han B, He Y, Hormozdiari F, Howald C, Im HK, Jo B, Kang EY, Kim-Hellmuth S, Lappalainen T, Li G, Liu B, Mangul S, McCarthy MI, McDowell IC, Mohammadi P, Monlong J, Muñoz-Aguirre M, Ndungu AW, Nicolae DL, Nobel AB, Oliva M, Ongen H, Palowitch JJ, Panousis N, Papasaikas P, Park Y, Parsana P, Payne AJ, Peterson CB, Quan J, Reverter F, Sabatti C, Saha A, Sammeth M, Shabalin ...Montgomery SB (2017).  The impact of rare variation on gene expression across tissues.  Nature.  550(7675).  239-243.
  • Tukiainen T, Villani A-C, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A, Gelfand ET, Getz G, Hadley K, Handsaker RE, Huang KH, Kashin S, Lek M, Li X, Nedzel JL, Nguyen DT, Noble MS, Segrè AV, Trowbridge CA, Abell NS, Balliu B, Barshir R, Basha O, Battle A, Bogu GK, Brown A, Brown CD, Chen LS, Chiang C, Conrad DF, Cox NJ, Damani FN, Davis JR, Delaneau O, Dermitzakis ET, Engelhardt BE, Eskin E, Ferreira PG, Frésard L, Gamazon ER, Garrido-Martín D, Gewirtz ADH, Gliner G, Gloudemans MJ, Guigo R, Hall IM, Han B, He Y, Hormozdiari F, Howald C, Im HK, Jo B, Kang EY, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy MI, McDowell IC, Mohammadi P, Monlong J, Montgomery SB, Muñoz-Aguirre M, Ndungu AW, Nicolae DL, Nobel AB, Oliva M, Ongen H, Palowitch JJ, Panousis N, Papasaikas P, Park Y, Parsana P, Payne AJ, Peterson CB, Quan J, Reverter F, Sabatti C, Saha A, Sam...MacArthur DG (2017).  Landscape of X chromosome inactivation across human tissues.  Nature.  550(7675).  244-248.
  • Aguet F, Brown AA, Castel SE, Davis JR, He Y, Jo B, Mohammadi P, Park Y, Parsana P, Segrè AV, Strober BJ, Zappala Z, Cummings BB, Gelfand ET, Hadley K, Huang KH, Lek M, Li X, Nedzel JL, Nguyen DY, Noble MS, Sullivan TJ, Tukiainen T, MacArthur DG, Getz G, Addington A, Guan P, Koester S, Little AR, Lockhart NC, Moore HM, Rao A, Struewing JP, Volpi S, Brigham LE, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber WF, Lonsdale JT, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas JA, Walters G, Washington M, Wheeler J, Bridge J, Foster BA, Gillard BM, Karasik E, Kumar R, Miklos M, Moser MT, Jewell SD, Montroy RG, Rohrer DC, Valley D, Mash DC, Davis DA, Sobin L, Barcus ME, Branton PA, Abell NS, Balliu B, Delaneau O, Frésard L, Gamazon ER, Garrido-Martín D, Gewirtz ADH, Gliner G, Gloudemans MJ, Han B, He AZ, Hormozdiari F, Li X, Liu B, Kang EY, McDowell IC, Ongen H, Palowitch JJ, Peterson CB, Quon G, Ripke S, Saha A, Shabalin AA, Shimko TC, Sul JH, Teran NA,...Zhu J (2017).  Genetic effects on gene expression across human tissues.  Nature.  550(7675).  204-213.
  • Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS, Aguet F, Ardlie KG, Cummings BB, Gelfand ET, Getz G, Hadley K, Handsaker RE, Huang KH, Kashin S, Karczewski KJ, Lek M, Li X, MacArthur DG, Nedzel JL, Nguyen DT, Noble MS, Segrè AV, Trowbridge CA, Tukiainen T, Abell NS, Balliu B, Barshir R, Basha O, Battle A, Bogu GK, Brown A, Brown CD, Castel SE, Chen LS, Chiang C, Conrad DF, Cox NJ, Damani FN, Davis JR, Delaneau O, Dermitzakis ET, Engelhardt BE, Eskin E, Ferreira PG, Frésard L, Gamazon ER, Garrido-Martín D, Gewirtz ADH, Gliner G, Gloudemans MJ, Guigo R, Hall IM, Han B, He Y, Hormozdiari F, Howald C, Im HK, Jo B, Kang EY, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy MI, McDowell IC, Mohammadi P, Monlong J, Montgomery SB, Muñoz-Aguirre M, Ndungu AW, Nicolae DL, Nobel AB, Oliva M, Ongen H, Palowitch JJ, Panousis...Li JB (2017).  Dynamic landscape and regulation of RNA editing in mammals.  Nature.  550(7675).  249-254.
  • Ng B, White CC, Klein HU, Sieberts SK, McCabe C, Patrick E, Xu J, Yu L, Gaiteri C, Bennett DA, Mostafavi S, De Jager PL (2017).  An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome.  Nature Neuroscience.  20(10).  1418-1426.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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, 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).
  • 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.
  • 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.
  • 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.
  • Battle A, Montgomery SB (2014).  Determining causality and consequence of expression quantitative trait loci.  Human Genetics.  133(6).  727-735.
  • 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, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y (2014).  Impact of regulatory variation from RNA to protein.  Science.  1260793.
  • 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.
  • Battle A, Montgomery S (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.  The American Journal of Human Genetics.  95(3).  245-256.
  • 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.
  • 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).
  • 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).
  • 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.
  • Segal E, Battle A, Koller D (2003).  Decomposing gene expression into cellular processes.  Proceedings of the Pacific Symposium on Biocomputing.  8.  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.
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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