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
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
  • 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).
  • 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).
  • 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.
  • 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.
  • 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).
  • 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, 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).
  • 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, Montgomery S (2014).  Determining causality and consequence of expression quantitative trait loci.  Human genetics.  133(6).  727-735.
  • 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.
  • 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.
  • 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).
  • Battle A, Segal E, Koller D (2005).  Probabilistic discovery of overlapping cellular processes and their regulation.  Journal of Computational Biology.  12(7).  909-927.
  • 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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