Bader, Joel S.

Biomedical EngineeringBME Profile

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Johns Hopkins scholars, leaders celebrate faculty research awards

September 4, 2015

Scholars from across Johns Hopkins University’s 10 divisions gathered last night at the George Peabody Library to celebrate 60 innovative research projects that are being supported by the inaugural Catalyst and Discovery awards. Thirty-seven early career scholars (five of them from WSE) received Catalyst Awards and 23 cross-divisional faculty teams, which included 14 WSE faculty […]

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  • Ph.D. 1991, Univ of California Berkeley
  • 2010 - Present:  Deputy Editor, PLoS Computational Biology
  • 2010 - 2010:  Co-Chair, ISMB
  • 2009 - 2009:  Area Co-Chair, ISMB
  • 2008 - 2008:  Area Co-Chair, ISMB
  • 2008 - Present:  Joint, SOM Biomedical Engineering
  • 2007 - 2007:  Vice Chair, Gordon
  • 2007 - 2007:  Area Chair, ISMB
  • 2006 - 2006:  Area Chair, ISMB
Research Areas
  • Bioinformatics
  • Bioinformatics and Computational Biology
  • Biotechnology
  • Computational Biology
  • Genetics
  • Genomics
  • Proteomics
  • Synthetic Biology
  • Systems Biology
  • 2009:  2008-2009 Awards:Kleberg Foundation (PI Bader) Translational Systems Biology for Human Disease Genetics Develop methods to identify disease-causing genetics variants NIH R24 (PI Friedmann)
  • 2009:  Integrative Genetic Analysis of Autism BrainsRole: Co-I Nominated - Whiting School of Engineering Excellence in Teaching Award
  • 2008:  Johns Hopkins Ion Channel Screening Center (Roadmap Center)Role: Director - Computational Core Simons Foundation Autism Research Institute (PI Dan Arking)
  • 2008:  Lesch Nyhan Disease: A Model for Complex Genetic - Proteomics - and Metabolomic PathwaysRole: Co-I.NIH U54 MH084691 (PI M.Li)
  • 2006:  NSF Career Award
  • 2003:  Whitaker Biomedical Engineering Foundation New Faculty
  • 1986:  Tau Beta PI
  • 1986:  NSF Pre-Doctoral research Fellowship
  • 1986:  Phi Beta Kappa


Journal Articles
  • van Setten J, Brody JA, Jamshidi Y, Swenson BR, Butler AM, Campbell H, Del Greco FM, Evans DS, Gibson Q, Gudbjartsson DF, Kerr KF, Krijthe BP, Lyytikäinen L-P, Müller C, Müller-Nurasyid M, Nolte IM, Padmanabhan S, Ritchie MD, Robino A, Smith AV, Steri M, Tanaka T, Teumer A, Trompet S, Ulivi S, Verweij N, Yin X, Arnar DO, Asselbergs FW, Bader JS, Barnard J, Bis J, Blankenberg S, Boerwinkle E, Bradford Y, Buckley BM, Chung MK, Crawford D, den Hoed M, Denny JC, Dominiczak AF, Ehret GB, Eijgelsheim M, Ellinor PT, Felix SB, Franco OH, Franke L, Harris TB, Holm H, Ilaria G, Iorio A, Kähönen M, Kolcic I, Kors JA, Lakatta EG, Launer LJ, Lin H, Lin HJ, Loos RJF, Lubitz SA, Macfarlane PW, Magnani JW, Leach IM, Meitinger T, Mitchell BD, Munzel T, Papanicolaou GJ, Peters A, Pfeufer A, Pramstaller PP, Raitakari OT, Rotter JI, Rudan I, Samani NJ, Schlessinger D, Silva Aldana CT, Sinner MF, Smith JD, Snieder H, Soliman EZ, Spector TD, Stott DJ, Strauch K, Tarasov KV, Thorsteinsdottir ...Sotoodehnia N (2018).  PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity.  Nature Communications.  9(1).
  • Shen MJ, Wu Y, Yang K, Li Y, Xu H, Zhang H, Li BZ, Li X, Xiao WH, Zhou X, Mitchell LA, Bader JS, Yuan Y, Boeke JD (2018).  Heterozygous diploid and interspecies SCRaMbLEing.  Nature Communications.  9(1).
  • Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Kain DB, Keegan S, Saul R, Colantonio S, Zhang H, Pauli-Behn F, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, De Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S (2018).  A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors.  Nature Methods.  15(5).  330-338.
  • Matern WM, Rifat D, Bader JS, Karakousis PC (2018).  Gene enrichment analysis reveals major regulators of Mycobacterium tuberculosis gene expression in two models of antibiotic tolerance.  Frontiers in Microbiology.  9(APR).
  • Matern WM, Bader JS, Karakousis PC (2018).  Data descriptor: Genome analysis of mycobacterium avium subspecies hominissuis strain 109.  Scientific Data.  5.
  • Weiner DJ, Wigdor EM, Ripke S, Walters RK, Kosmicki JA, Grove J, Samocha KE, Goldstein JI, Okbay A, Bybjerg-Grauholm J, Werge T, Hougaard DM, Taylor J, Skuse D, Devlin B, Anney R, Sanders SJ, Bishop S, Mortensen PB, Børglum AD, Smith GD, Daly MJ, Robinson EB, Bækvad-Hansen M, Dumont A, Hansen C, Hansen TF, Howrigan D, Mattheisen M, Moran J, Mors O, Nordentoft M, Nørgaard-Pedersen B, Poterba T, Poulsen J, Stevens C, Anttila V, Holmans P, Huang H, Klei L, Lee PH, Medland SE, Neale B, Weiss LA, Zwaigenbaum L, Yu TW, Wittemeyer K, Willsey AJ, Wijsman EM, Wassink TH, Waltes R, Walsh CA, Wallace S, Vorstman JAS, Vieland VJ, Vicente AM, Van Engeland H, Tsang K, Thompson AP, Szatmari P, Svantesson O, Steinberg S, Stefansson K, Stefansson H, State MW, Soorya L, Silagadze T, Scherer SW, Schellenberg GD, Sandin S, Saemundsen E, Rouleau GA, Rogé B, Roeder K, Roberts W, Reichert J, Reichenberg A, Rehnström K, Regan R, Poustka F, Poultney CS, Piven J, Pinto D, Pericak-Vance MA, Pejovic-M...Arking DE (2017).  Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders.  Nature Genetics.  49(7).  978-985.
  • Anney RJL, Ripke S, Anttila V, Grove J, Holmans P, Huang H, Klei L, Lee PH, Medland SE, Neale B, Robinson E, Weiss LA, Zwaigenbaum L, Yu TW, Wittemeyer K, Willsey AJ, Wijsman EM, Werge T, Wassink TH, Waltes R, Walsh CA, Wallace S, Vorstman JAS, Vieland VJ, Vicente AM, Vanengeland H, Tsang K, Thompson AP, Szatmari P, Svantesson O, Steinberg S, Stefansson K, Stefansson H, State MW, Soorya L, Silagadze T, Scherer SW, Schellenberg GD, Sandin S, Sanders SJ, Saemundsen E, Rouleau GA, Rogé B, Roeder K, Roberts W, Reichert J, Reichenberg A, Rehnström K, Regan R, Poustka F, Poultney CS, Piven J, Pinto D, Pericak-Vance MA, Pejovic-Milovancevic M, Pedersen MG, Pedersen CB, Paterson AD, Parr JR, Pagnamenta AT, Oliveira G, Nurnberger JI, Nordentoft M, Murtha MT, Mouga S, Mortensen PB, Mors O, Morrow EM, Moreno-De-Luca D, Monaco AP, Minshew N, Merikangas A, McMahon WM, McGrew SG, Mattheisen M, Martsenkovsky I, Martin DM, Mane SM, Magnusson P, Magalhaes T, Maestrini E, Lowe JK, Lord C,...Hakonarson H (2017).  Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia.  Molecular Autism.  8(1).
  • Hudock TA, Foreman TW, Bandyopadhyay N, Gautam US, Veatch AV, LoBato DN, Gentry KM, Golden NA, Cavigli A, Mueller M, Hwang SA, Hunter RL, Alvarez X, Lackner AA, Bader JS, Mehra S, Kaushal D (2017).  Hypoxia sensing and persistence genes are expressed during the intragranulomatous survival of mycobacterium tuberculosis.  American Journal of Respiratory Cell and Molecular Biology.  56(5).  637-647.
  • Yang JP, Anderson AE, McCartney A, Ory X, Ma G, Pappalardo E, Bader J, Elisseeff JH (2017).  Metabolically Active Three-Dimensional Brown Adipose Tissue Engineered from White Adipose-Derived Stem Cells.  Tissue Engineering - Part A.  23(7-8).  253-262.
  • Zhang W, Zhao G, Luo Z, Lin Y, Wang L, Guo Y, Wang A, Jiang S, Jiang Q, Gong J, Wang Y, Hou S, Huang J, Li T, Qin Y, Dong J, Qin Q, Zhang J, Zou X, He X, Zhao L, Xiao Y, Xu M, Cheng E, Huang N, Zhou T, Shen Y, Walker R, Luo Y, Kuang Z, Mitchell LA, Yang K, Richardson SM, Wu Y, Li BZ, Yuan YJ, Yang H, Lin J, Chen GQ, Wu Q, Bader JS, Cai Y, Boeke JD, Dai J (2017).  Engineering the ribosomal DNA in a megabase synthetic chromosome.  Science.  355(6329).
  • Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D, Walker R, Zhao H, Chen S, Liu W, Luo Y, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, Mitchell LA, Luo Z, Fan Y, Zhou B, Wen B, Tan F, Wang Y, Zi J, Xie Z, Li B, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan Y, Wang J, Bader JS, Dai J, Boeke JD, Xu X, Cai Y, Yang H (2017).  Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.  Science.  355(6329).
  • Mitchell LA, Wang A, Stracquadanio G, Kuang Z, Wang X, Yang K, Richardson S, Martin JA, Zhao Y, Walker R, Luo Y, Dai H, Dong K, Tang Z, Yang Y, Cai Y, Heguy A, Ueberheide B, Fenyö D, Dai J, Bader JS, Boeke JD (2017).  Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond.  Science.  355(6329).
  • Wu Y, Li BZ, Zhao M, Mitchell LA, Xie ZX, Lin QH, Wang X, Xiao WH, Wang Y, Zhou X, Liu H, Li X, Ding MZ, Liu D, Zhang L, Liu BL, Wu XL, Li FF, Dong XT, Jia B, Zhang WZ, Jiang GZ, Liu Y, Bai X, Song TQ, Chen Y, Zhou SJ, Zhu RY, Gao F, Kuang Z, Wang X, Shen M, Yang K, Stracquadanio G, Richardson SM, Lin Y, Wang L, Walker R, Luo Y, Ma PS, Yang H, Cai Y, Dai J, Bader JS, Boeke JD, Yuan YJ (2017).  Bug mapping and fitness testing of chemically synthesized chromosome X.  Science.  355(6329).
  • Mercy G, Mozziconacci J, Scolari VF, Yang K, Zhao G, Thierry A, Luo Y, Mitchell LA, Shen M, Shen Y, Walker R, Zhang W, Wu Y, Xie ZX, Luo Z, Cai Y, Dai J, Yang H, Yuan YJ, Boeke JD, Bader JS, Muller H, Koszul R (2017).  3D organization of synthetic and scrambled chromosomes.  Science.  355(6329).
  • Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS, DiCarlo JE, Lee D, Huang CLV, Chandrasegaran S, Cai Y, Boeke JD, Bader JS (2017).  Design of a synthetic yeast genome.  Science.  355(6329).  1040-1044.
  • Xie Z-X, Li B-Z, Mitchell LA, Wu Y, Qi X, Jin Z, Jia B, Wang X, Zeng BX, Liu H-M, Wu X-L, Feng Q, Zhang W-Z, Liu W, Ding M-Z, Li X, Zhao G-R, Qiao J-J, Cheng J-S, Zhao M, Kuang Z, Wang X, Martin JA, Stracquadanio G, Yang K, Bai X, Zhao J, Hu M-L, Lin Q-H, Zhang W-Q, Shen M-H, Chen S, Su W, Wang E-X, Guo R, Zhai F, Guo X-J, Du H-X, Zhu J-Q, Song T-Q, Dai J-J, Li F-F, Jiang G-Z, Han S-L, Liu S-Y, Yu Z-C, Yang X-N, Chen K, Hu C, Li D-S, Jia N, Liu Y, Wang L-T, Wang S, Wei X-T, Fu M-Q, Qu L-M, Xin S-Y, Liu T, Tian K-R, Li X-N, Zhang J-H, Song L-X, Liu J-G, Lv J-F, Xu H, Tao R, Wang Y, Zhang T-T, Deng Y-X, Wang Y-R, Li T, Ye G-X, Xu X-R, Xia Z-B, Zhang W, Yang S-L, Liu Y-L, Ding W-Q, Liu Z-N, Zhu J-Q, Liu N-Z, Walker R, Luo Y, Wang Y, Shen Y, Yang H, Cai Y, Ma P-S, Zhang C-T, Bader JS, Boeke JD, Yuan Y-J (2017).  "Perfect" designer chromosome v and behavior of a ring derivative.  Science.  355(6329).
  • Agmon N, Tang Z, Yang K, Sutter B, Ikushima S, Cai Y, Caravelli K, Martin JA, Sun X, Choi WJ, Zhang A, Stracquadanio G, Hao H, Tu BP, Fenyo D, Bader JS, Boeke JD (2017).  Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae.  Proceedings of the National Academy of Sciences of the United States of America.  114(8).  E1470-E1479.
  • Stracquadanio G, Yang K, Boeke JD, Bader JS (2016).  BioPartsDB: A synthetic biology workflow web-application for education and research.  Bioinformatics.  32(22).  3519-3521.
  • Zhu M, Monroe JG, Suhail Y, Villiers F, Mullen J, Pater D, Hauser F, Jeon BW, Bader JS, Kwak JM, Schroeder JI, Mckay JK, Assmann SM (2016).  Molecular and systems approaches towards drought-tolerant canola crops.  New Phytologist.  210(4).  1169-1189.
  • Pienaar E, Matern WM, Linderman JJ, Bader JS, Kirschner DE (2016).  Multiscale model of Mycobacterium tuberculosis infection maps metabolite and gene perturbations to granuloma sterilization predictions.  Infection and Immunity.  84(5).  1650-1669.
  • Cheung KJ, Padmanaban V, Silvestri V, Schipper K, Cohen JD, Fairchild AN, Gorin MA, Verdone JE, Pienta KJ, Bader JS, Ewald AJ (2016).  Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters.  Proceedings of the National Academy of Sciences of the United States of America.  113(7).  E854-E863.
  • Shen Y, Stracquadanio G, Wang Y, Yang K, Mitchell LA, Xue Y, Cai Y, Chen T, Dymond JS, Kang K, Gong J, Zeng X, Zhang Y, Li Y, Feng Q, Xu X, Wang J, Wang J, Yang H, Boeke JD, Bader JS (2016).  SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes.  Genome Research.  26(1).  36-49.
  • Beachley VZ, Wolf MT, Sadtler K, Manda SS, Jacobs H, Blatchley MR, Bader JS, Pandey A, Pardoll D, Elisseeff JH (2015).  Tissue matrix arrays for high-throughput screening and systems analysis of cell function.  Nature Methods.  12(12).  1197-1204.
  • Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS (2015).  BioPartsBuilder: A synthetic biology tool for combinatorial assembly of biological parts.  Bioinformatics.  32(6).  937-939.
  • Chu LH, Vijay CG, Annex BH, Bader JS, Popel AS (2015).  PADPIN: Protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease.  Physiological Genomics.  47(8).  331-343.
  • Subbian S, Tsenova L, Kim MJ, Wainwright HC, Visser A, Bandyopadhyay N, Bader JS, Karakousis PC, Murrmann GB, Bekker LG, Russell DG, Kaplan G (2015).  Lesion-specific immune response in granulomas of patients with pulmonary tuberculosis: A pilot study.  PLoS ONE.  10(7).
  • Lin Q, Jia B, Mitchell LA, Luo J, Yang K, Zeller KI, Zhang W, Xu Z, Stracquadanio G, Bader JS, Boeke JD, Yuan YJ (2015).  RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in saccharomyces cerevisiae.  ACS Synthetic Biology.  4(3).  213-220.
  • Chuang YM, Bandyopadhyay N, Rifat D, Rubin H, Bader JS, Karakousis PC (2015).  Deficiency of the novel exopolyphosphatase Rv1026/PPX2 leads to metabolic downshift and altered cell wall permeability in Mycobacterium tuberculosis.  mBio.  6(2).
  • Cai Y, Agmon N, Choi WJ, Ubide A, Stracquadanio G, Caravelli K, Hao H, Bader JS, Boeke JD (2015).  Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes.  Proceedings of the National Academy of Sciences of the United States of America.  112(6).  1803-1808.
  • Chu LH, Lee E, Bader JS, Popel AS (2014).  Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.  PLoS ONE.  9(10).
  • Dutta NK, Bandyopadhyay N, Veeramani B, Lamichhane G, Karakousis PC, Bader JS (2014).  Systems biology-based identification of Mycobacterium tuberculosis persistence genes in mouse lungs.  mBio.  5(1).
  • Gupta S, Ellis SE, Ashar FN, Moes A, Bader JS, Zhan J, West AB, Arking DE (2014).  Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism.  Nature Communications.  5.
  • Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CYL, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Henry M, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S (2014).  Total synthesis of a functional designer eukaryotic chromosome.  Science.  344(6179).  55-58.
  • Arking DE, Pulit SL, Crotti L, Van Der Harst P, Munroe PB, Koopmann TT, Sotoodehnia N, Rossin EJ, Morley M, Wang X, Johnson AD, Lundby A, Gudbjartsson DF, Noseworthy PA, Eijgelsheim M, Bradford Y, Tarasov KV, Dörr M, Müller-Nurasyid M, Lahtinen AM, Nolte IM, Smith AV, Bis JC, Isaacs A, Newhouse SJ, Evans DS, Post WS, Waggott D, Lyytikäinen L-P, Hicks AA, Eisele L, Ellinghaus D, Hayward C, Navarro P, Ulivi S, Tanaka T, Tester DJ, Chatel S, Gustafsson S, Kumari M, Morris RW, Naluai AT, Padmanabhan S, Kluttig A, Strohmer B, Panayiotou AG, Torres M, Knoflach M, Hubacek JA, Slowikowski K, Raychaudhuri S, Kumar RD, Harris TB, Launer LJ, Shuldiner AR, Alonso A, Bader JS, Ehret G, Huang H, Kao WHL, Strait JB, Macfarlane PW, Brown M, Caulfield MJ, Samani NJ, Kronenberg F, Willeit J, Smith JG, Greiser KH, Zu Schwabedissen HM, Werdan K, Carella M, Zelante L, Heckbert SR, Psaty BM, Rotter JI, Kolcic I, Polašek O, Wright AF, Griffin M, Daly MJ, Arnar DO, Hólm H, Thorsteinsdottir U, ...Newton-Cheh C (2014).  Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.  Nature Genetics.  46(8).  826-836.
  • Shamir ER, Pappalardo E, Jorgens DM, Coutinho K, Tsai WT, Aziz K, Auer M, Tran PT, Bader JS, Ewald AJ (2014).  Twist1-induced dissemination preserves epithelial identity and requires E-cadherin.  Journal of Cell Biology.  204(5).  839-856.
  • Ellis SE, Gupta S, Ashar FN, Bader JS, West AB, Arking DE (2013).  RNA-Seq optimization with eQTL gold standards.  BMC Genomics.  14(1).
  • Kang TH, Park Y, Bader JS, Friedmann T (2013).  The Housekeeping Gene Hypoxanthine Guanine Phosphoribosyltransferase (HPRT) Regulates Multiple Developmental and Metabolic Pathways of Murine Embryonic Stem Cell Neuronal Differentiation.  PLoS ONE.  8(10).
  • Subbian S, Bandyopadhyay N, Tsenova L, O'Brien P, Khetani V, Kushner NL, Peixoto B, Soteropoulos P, Bader JS, Karakousis PC, Fallows D, Kaplan G (2013).  Early innate immunity determines outcome of Mycobacterium tuberculosis pulmonary infection in rabbits.  Cell Communication and Signaling.  11(1).
  • Suhail Y, Kshitiz, Lee J, Walker M, Kim DH, Brennan MD, Bader JS, Levchenko A (2013).  Modeling Intercellular Transfer of Biomolecules Through Tunneling Nanotubes.  Bulletin of Mathematical Biology.  75(8).  1400-1416.
  • Chanda P, Huang H, Arking DE, Bader JS (2013).  Fast Association Tests for Genes with FAST.  PLoS ONE.  8(7).
  • Subbian S, O'Brien P, Kushner NL, Yang G, Tsenova L, Peixoto B, Bandyopadhyay N, Bader JS, Karakousis PC, Fallows D, Kaplan G (2013).  Molecular immunologic correlates of spontaneous latency in a rabbit model of pulmonary tuberculosis.  Cell Communication and Signaling.  11(1).
  • Karchin R, Ochs MF, Stuart JM, Ideker T, Bader JS (2013).  Identification of aberrant pathway and network activity from high-throughput data.  18th Pacific Symposium on Biocomputing, PSB 2013.
  • Alqadah F, Bader JS, Anand R, Reddy CK (2012).  Query-based biclustering using formal concept analysis.  Proceedings of the 12th SIAM International Conference on Data Mining, SDM 2012.  648-659.
  • Chanda P, Elhaik E, Bader JS (2012).  HapZipper: Sharing HapMap populations just got easier.  Nucleic Acids Research.  40(20).
  • Chu LH, Rivera CG, Popel AS, Bader JS (2012).  Constructing the angiome: A global angiogenesis protein interaction network.  Physiological Genomics.  44(19).  915-924.
  • Chanda P, Yuhki N, Li M, Bader JS, Hartz A, Boerwinkle E, Kao WL, Arking DE (2012).  Comprehensive evaluation of imputation performance in African Americans.  Journal of Human Genetics.  57(7).  411-421.
  • Park Y, Bader JS (2012).  How networks change with time.  Bioinformatics.  28(12).
  • Annaluru N, Muller H, Ramalingam S, Kandavelou K, London V, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S (2012).  Assembling DNA fragments by USER fusion.  Methods in Molecular Biology.  852.  77-95.
  • Muller H, Annaluru N, Schwerzmann JW, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S (2012).  Assembling large DNA segments in yeast.  Methods in Molecular Biology.  852.  133-150.
  • Cooper EM, Müller H, Chandrasegaran S, Bader JS, Boeke JD (2012).  The build-a-genome course.  Methods in Molecular Biology.  852.  273-283.
  • Richardson SM, Liu S, Boeke JD, Bader JS (2012).  Design-a-gene with genedesign.  Methods in Molecular Biology.  852.  235-247.
  • Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD (2012).  Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.  Nature.  482(7384).  251-255.
  • Karchin R, Ochs MF, Stuart JM, Bader JS (2012).  Identification of aberrant pathway and network activity from high-throughput data.  17th Pacific Symposium on Biocomputing, PSB 2012.  1-6.
  • Rivera CG, Rosca EV, Pandey NB, Koskimaki JE, Bader JS, Popel AS (2011).  Novel peptide-specific quantitative structure-activity relationship (QSAR) analysis applied to collagen IV peptides with antiangiogenic activity.  Journal of Medicinal Chemistry.  54(19).  6492-6500.
  • Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD (2011).  Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.  Nature.  477(7365).  471-476.
  • Rivera CG, Mellberg S, Claesson-Welsh L, Bader JS, Popel AS (2011).  Analysis of VEGF-A regulated gene expression in endothelial cells to identify genes linked to angiogenesis.  PLoS ONE.  6(9).
  • Rivera CG, Bader JS, Popel AS (2011).  Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins.  Annals of Biomedical Engineering.  39(8).  2213-2222.
  • Huang H, Chanda P, Alonso A, Bader JS, Arking DE (2011).  Gene-Based tests of association.  PLoS Genetics.  7(7).
  • Park Y, Bader JS (2011).  Resolving the structure of interactomes with hierarchical agglomerative clustering.  BMC Bioinformatics.  12(SUPPL. 1).
  • Bader JS (2011).  Grand network convergence..  Genome biology.  12(6).  306.
  • Zou B, Yu H, Babcock JJ, Chanda P, Bader JS, McManus OB, Li M (2010).  Profiling diverse compounds by flux- and electrophysiology-based primary screens for inhibition of human Ether-à-go-go related gene potassium channels.  Assay and Drug Development Technologies.  8(6).  743-754.
  • Zhong J, Krawczyk SA, Chaerkady R, Huang H, Goel R, Bader JS, Wong GW, Corkey BE, Pandey A (2010).  Temporal profiling of the secretome during adipogenesis in humans.  Journal of Proteome Research.  9(10).  5228-5238.
  • Richardson SM, Olson BS, Dymond JS, Burns R, Chandrasegaran S, Boeke JD, Shehu A, Bader JS (2010).  Automated design of assemblable, modular, synthetic chromosomes.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  6068 LNCS(PART 2).  280-289.
  • Veeramani B, Bader JS (2010).  Predicting functional associations from metabolism using bi-partite network algorithms.  BMC Systems Biology.  4.
  • Singh M, Bader JS (2010).  Editorial.  Bioinformatics.  26(12).
  • Richardson SM, Nunley PW, Yarrington RM, Boeke JD, Bader JS (2010).  GeneDesign 3.0 is an updated synthetic biology toolkit.  Nucleic Acids Research.  38(8).  2603-2606.
  • Lee PA, Dymond JS, Scheifele LZ, Richardson SM, Foelber KJ, Boeke JD, Bader JS (2010).  CLONEQC: Lightweight sequence verification for synthetic biology.  Nucleic Acids Research.  38(8).  2617-2623.
  • Rivera CG, Vakil R, Bader JS (2010).  NeMo: Network module identification in cytoscape.  BMC Bioinformatics.  11(SUPPLL.1).
  • Park Y, Moore C, Bader JS (2010).  Dynamic networks from hierarchical Bayesian graph clustering.  PLoS ONE.  5(1).
  • Huang H, Maertens AM, Hyland EM, Dai J, Norris A, Boeke JD, Bader JS (2009).  HistoneHits: A database for histone mutations and their phenotypes.  Genome Research.  19(4).  674-681.
  • Veeramani B, Bader JS (2009).  Metabolic flux correlations, genetic interactions, and disease.  Journal of Computational Biology.  16(2).  291-302.
  • Huang H, Bader JS (2009).  Precision and recall estimates for two-hybrid screens.  Bioinformatics.  25(3).  372-378.
  • Czar MJ, Anderson JC, Bader JS, Peccoud J (2009).  Gene synthesis demystified.  Trends in Biotechnology.  27(2).  63-72.
  • Kut C, Golkhou V, Bader JS (2009).  Analytical approximations for the amplitude and period of a relaxation oscillator.  BMC Systems Biology.  3.
  • Liu LA, Bader JS (2009).  Structure-based ab initio prediction of transcription factor-binding sites..  Methods in molecular biology (Clifton, N.J.).  541.  23-41.
  • Dymond JS, Scheifele LZ, Richardson S, Lee P, Chandrasegaran S, Bader JS, Boeke JD (2009).  Teaching synthetic biology, bioinformatics and engineering to undergraduates: The interdisciplinary build-a-genome course.  Genetics.  181(1).  13-21.
  • Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS (2008).  Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions.  Genome Research.  18(12).  1991-2004.
  • Dai J, Hyland EM, Yuan DS, Huang H, Bader JS, Boeke JD (2008).  Probing Nucleosome Function: A Highly Versatile Library of Synthetic Histone H3 and H4 Mutants.  Cell.  134(6).  1066-1078.
  • Guha U, Chaerkady R, Marimuthu A, Patterson AS, Kashyap MK, Harsha HC, Sato M, Bader JS, Lash AE, Minna JD, Pandey A, Varmus HE (2008).  Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS.  Proceedings of the National Academy of Sciences of the United States of America.  105(37).  14112-14117.
  • Lin YY, Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD (2008).  A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation.  Genes and Development.  22(15).  2062-2074.
  • Pan X, Yuan D, Ye P, Bader J, Boeke JD (2008).  Response to Dr Stephen Cooper's 'On the use of metaphor to understand, explain, or rationalize redundant genes in yeast'.  FEMS Yeast Research.  8(3).  349-350.
  • Bader JS (2008).  Systems approaches for pharmacogenetics and pharmacogenomics.  Pharmacogenomics.  9(3).  257-262.
  • Huang H, Zhang LV, Roth FP, Bader JS (2007).  Probabilistic paths for protein complex inference.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).  4532 LNBI.  14-28.
  • Angela Liu L, Bader JS (2007).  AB initio prediction of transcription factor binding sites.  Pacific Symposium on Biocomputing 2007, PSB 2007.  484-495.
  • Huang H, Jedynak BM, Bader JS (2007).  Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps.  PLoS Computational Biology.  3(11).  2155-2174.
  • Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-Aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, Rivas JDL, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H (2007).  The minimum information required for reporting a molecular interaction experiment (MIMIx).  Nature Biotechnology.  25(8).  894-898.
  • Stuart LM, Boulais J, Charriere GM, Hennessy EJ, Brunet S, Jutras I, Goyette G, Rondeau C, Letarte S, Huang H, Ye P, Morales F, Kocks C, Bader JS, Desjardins M, Ezekowitz RAB (2007).  A systems biology analysis of the Drosophila phagosome.  Nature.  445(7123).  95-101.
  • Huang H, Jedynak B, Bader J (2007).  Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps.  PLoS computational biology.  3(11).  e214.
  • Angela Liu L, Bader JS (2006).  Decoding transcriptional regulatory interactions.  Physica D: Nonlinear Phenomena.  224(1-2).  174-181.
  • Dorer MS, Kirton D, Bader JS, Isberg RR (2006).  RNA interference analysis of Legionella in Drosophila cells: Exploitation of early secretory apparatus dynamics.  PLoS Pathogens.  2(4).  315-327.
  • Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD (2006).  A DNA integrity network in the yeast Saccharomyces cerevisiae.  Cell.  124(5).  1069-1081.
  • Bader JS, Chant J (2006).  When proteomes collide.  Science.  311(5758).  187-188.
  • Gandhi TKB, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A (2006).  Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets.  Nature Genetics.  38(3).  285-293.
  • Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD (2006).  Global synthetic-lethality analysis and yeast functional profiling.  Trends in Genetics.  22(1).  56-63.
  • Qi Y, Ye P, Bader JS (2005).  Genetic interaction motif finding by expectation maximization - A novel statistical model for inferring gene modules from synthetic lethality.  BMC Bioinformatics.  6.
  • Bader JS (2005).  A disease-centric draft map of the human interactome.  AIChE Annual Meeting, Conference Proceedings.  12441-12448.
  • Ye P, Peyser BD, Spencer FA, Bader JS (2005).  Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.  BMC Bioinformatics.  6.
  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005).  Genome sequencing in microfabricated high-density picolitre reactors.  Nature.  437(7057).  376-380.
  • Ye P, Peyser BD, Pan X, Boeke JD, Spencer FA, Bader JS (2005).  Gene function prediction from congruent synthetic lethal interactions in yeast..  Molecular systems biology.  1.
  • Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS, Hieter P, Spencer F, Boeke JD (2004).  A robust toolkit for functional profiling of the yeast genome.  Molecular Cell.  16(3).  487-496.
  • Iossifov I, Krauthammer M, Friedman C, Hatzivassiloglou V, Bader JS, White KP, Rzhetsky A (2004).  Probabilistic inference of molecular networks from noisy data sources.  Bioinformatics.  20(8).  1205-1213.
  • Bader JS, Chaudhuri A, Rothberg JM, Chant J (2004).  Gaining confidence in high-throughput protein interaction networks.  Nature Biotechnology.  22(1).  78-85.
  • Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM (2003).  A Protein Interaction Map of Drosophila melanogaster.  Science.  302(5651).  1727-1736.
  • Bader JS (2003).  Greedily building protein networks with confidence.  Bioinformatics.  19(15).  1869-1874.
  • Bader JS, Sham P (2002).  Family-based association tests for quantitative traits using pooled DNA.  European Journal of Human Genetics.  10(12).  870-878.
  • Sham P, Bader JS, Craig I, O'Donovan M, Owen M (2002).  DNA pooling: A tool for large-scale association studies.  Nature Reviews Genetics.  3(11).  862-871.
  • Bader JS, Deem MW, Hammond RW, Henck SA, Simpson JW, Rothberg JM (2002).  A Brownian-ratchet DNA pump with applications to single-nucleotide polymorphism genotyping.  Applied Physics A: Materials Science and Processing.  75(2).  275-278.
  • Jawaid A, Bader JS, Purcell S, Cherny SS, Sham P (2002).  Optimal selection strategies for QTL mapping using pooled DNA samples.  European Journal of Human Genetics.  10(2).  125-132.
  • Jawaid A, Bader JS, Purcell S, Cherny SS, Sham P (2002).  Optimal selection strategies for QTL mapping using pooled DNA samples.  European Journal of Human Genetics.  10(2).  125-132.
  • Bader JS (2001).  The relative power of SNPs and haplotype as genetic markers for association tests.  Pharmacogenomics.  2(1).  11-24.
  • Hammond RW, Bader JS, Henck SA, Deem MW, McDermott GA, Bustillo JM, Rothberg JM (2000).  Differential transport of DNA by a rectified Brownian motion device.  Electrophoresis.  21(1).  74-80.
  • Bader JS, Hammond RW, Henck SA, Deem MW, McDermott GA, Bustillo JM, Simpson JW, Mulhern GT, Rothberg JM (1999).  DNA transport by a micromachined Brownian ratchet device.  Proceedings of the National Academy of Sciences of the United States of America.  96(23).  13165-13169.
  • Bader JS, Cortis CM, Berne BJ (1997).  Solvation and reorganization energies in polarizable molecular and continuum solvents.  Journal of Chemical Physics.  106(6).  2372-2387.
  • Deem MW, Bader JS (1996).  A configurational bias Monte Carlo method for linear and cyclic peptides.  Molecular Physics.  87(6).  1245-1260.
  • Bader JS, Berne BJ, Pollak E, Hänggi P (1996).  The energy relaxation of a nonlinear oscillator coupled to a linear bath.  Journal of Chemical Physics.  104(3).  1111-1119.
  • Bader JS, Berne BJ (1996).  Solvation energies and electronic spectra in polar, polarizable media: Simulation tests of dielectric continuum theory.  Journal of Chemical Physics.  104(4).  1293-1308.
  • Rick SW, Stuart SJ, Bader JS, Berne BJ (1995).  Fluctuating Charge Force Fields for Aqueous Solutions.  Studies in Physical and Theoretical Chemistry.  83(C).  31-40.
  • Bader JS, Berne BJ, Pollak E (1995).  Activated rate processes: The reactive flux method for one-dimensional surface diffusion.  The Journal of Chemical Physics.  102(10).  4037-4055.
  • Bader JS, Berne BJ (1995).  The energy-dependent transmission coefficient and the energy distribution of classical particles escaping from a metastable well.  The Journal of Chemical Physics.  102(20).  7953-7965.
  • Rick SW, Stuart SJ, Bader JS, Berne BJ (1995).  Fluctuating charge force fields for aqueous solutions.  Journal of Molecular Liquids.  65-66(C).  31-40.
  • Bader JS, Berne BJ (1994).  Quantum and classical relaxation rates from classical simulations.  The Journal of Chemical Physics.  100(11).  8359-8366.
  • Pollak E, Bader J, Berne BJ, Talkner P (1993).  Theory of correlated hops in surface diffusion.  Physical Review Letters.  70(21).  3299-3302.
  • Bader JS, Chandler D (1992).  Computer simulation study of the mean forces between ferrous and ferric ions in water.  Journal of Physical Chemistry.  96(15).  6423-6427.
  • Bader JS, Kuharski RA, Chandler D (1990).  Role of nuclear tunneling in aqueous ferrous-ferric electron transfer.  The Journal of Chemical Physics.  93(1).  230-236.
  • Bader JS, Chandler D (1989).  Computer simulation of photochemically induced electron transfer.  Chemical Physics Letters.  157(6).  501-504.
  • Kuharski RA, Bader JS, Chandler D, Sprik M, Klein ML, Impey RW (1988).  Molecular model for aqueous ferrous-ferric electron transfer.  The Journal of Chemical Physics.  89(5).  3248-3257.
Book Chapters
  • Park Y, Bader JS (2015).  Dynamic network models of protein complexes.  Systems Genetics: Linking Genotypes and Phenotypes.  191-213.
  • Rivera CG, Chu LH, Bader JS, Popel AS (2012).  Applications of Network Bioinformatics to Cancer Angiogenesis.  Systems Biology in Cancer Research and Drug Discovery.  9789400748194.  229-244.
  • Bressler J, Bader J, Goldberg A (2010).  Alternatives to Conventional Toxicology Testing.  Comprehensive Toxicology, Second Edition.  3.  247-259.
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