Search Publications

Behnke-Parks WM, Vendome J, Honig B, Maliga Z, Moores C, Rosenfeld S.  2011.  Loop L5 acts as a conformational latch in the mitotic kinesin Eg5. J Biol Chem. 286(7):5242-53. Go to Pubmed
Akavia UDavid, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D.  2010.  An integrated approach to uncover drivers of cancer. Cell. 143(6):1005-17. Go to Pubmed
Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, J Smith G, Kovvali S, Kang HMin, Newton-Cheh C, Daly MJ et al.  2011.  Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population. Hum Mol Genet. 20(4):827-39. Go to Pubmed
Roberts RJ, Chang Y-C, Hu Z, Rachlin J, Anton BP, Pokrzywa R, Choi H-P, Faller LL, Guleria J, Housman G et al.  2011.  COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res. 39(Database issue):D11-4. Go to Pubmed
Hoffstrom BG, Kaplan A, Letso R, Schmid RS, Turmel GJ, Lo D, Stockwell BR.  2010.  Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins. Nat Chem Biol. 6(12):900-6. Go to Pubmed
Cheung YHim, Watkinson J, Anastassiou D.  2011.  Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC. Hum Genet. 129(2):161-76. Go to Pubmed
Kim H, Watkinson J, Varadan V, Anastassiou D.  2010.  Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1. BMC Med Genomics. 3:51. Go to Pubmed
Yang X, Lee Y, Huang Y, Chen JL, Xing RH, Lussier YA.  2010.  Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. BMC Bioinformatics. 11 Suppl 9:S11. Go to Pubmed
Dai H, Murphy C, Kaiser G.  2010.  CONFU: Configuration Fuzzing Testing Framework for Software Vulnerability Detection. Int J Secur Softw Eng. 1(3):41-55. Go to Pubmed
Mugler A, Ziv E, Nemenman I, Wiggins CH.  2009.  Quantifying evolvability in small biological networks. IET Syst Biol. 3(5):379-87. Go to Pubmed
Gamazon ER, Im H-K, Duan S, Lussier YA, Cox NJ, M Dolan E, Zhang W.  2010.  Exprtarget: an integrative approach to predicting human microRNA targets. PLoS One. 5(10):e13534. Go to Pubmed
Plata G, Gottesman ME, Vitkup D.  2010.  The rate of the molecular clock and the cost of gratuitous protein synthesis. Genome Biol. 11(9):R98. Go to Pubmed
Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ et al.  2010.  Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell. 143(2):212-24. Go to Pubmed
Wu Y, Jin X, Harrison O, Shapiro L, Honig B, Ben-Shaul A.  2010.  Cooperativity between trans and cis interactions in cadherin-mediated junction formation. Proc Natl Acad Sci U S A. 107(41):17592-7. Go to Pubmed
Mugler A, Walczak AM, Wiggins C.  2010.  Information-optimal transcriptional response to oscillatory driving. Phys Rev Lett. 105(5):058101. Go to Pubmed
Lee E, Bussemaker HJ.  2010.  Identifying the genetic determinants of transcription factor activity. Mol Syst Biol. 6:412. Go to Pubmed
Khiabanian H, Holmes AB, Kelly BJ, Gururaj M, Hripcsak G, Rabadan R.  2010.  Signs of the 2009 influenza pandemic in the New York-Presbyterian Hospital electronic health records. PLoS One. 5(9) Go to Pubmed
de Hoon MJL, Eichenberger P, Vitkup D.  2010.  Hierarchical evolution of the bacterial sporulation network. Curr Biol. 20(17):R735-45. Go to Pubmed
Laframboise T, Dewal N, Wilkins K, Pe'er I, Freedman ML.  2010.  Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis. PLoS Genet. 6(9):e1001086. Go to Pubmed
Plata G, Hsiao T-L, Olszewski KL, Llinás M, Vitkup D.  2010.  Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol Syst Biol. 6:408. Go to Pubmed
Wombacher R, Heidbreder M, van de Linde S, Sheetz MP, Heilemann M, Cornish VW, Sauer M.  2010.  Live-cell super-resolution imaging with trimethoprim conjugates. Nat Methods. 7(9):717-9. Go to Pubmed
Love J, Mancia F, Shapiro L, Punta M, Rost B, Girvin M, Wang D-N, Zhou M, Hunt J, Szyperski T et al.  2010.  The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins. J Struct Funct Genomics. 11(3):191-9. Go to Pubmed
Koehnke J, Katsamba PS, Ahlsen G, Bahna F, Vendome J, Honig B, Shapiro L, Jin X.  2010.  Splice form dependence of beta-neurexin/neuroligin binding interactions. Neuron. 67(1):61-74. Go to Pubmed
Atzmon G, Hao L, Pe'er I, Velez C, Pearlman A, Palamara PFrancesco, Morrow B, Friedman E, Oddoux C, Burns E et al.  2010.  Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry. Am J Hum Genet. 86(6):850-9. Go to Pubmed
Zhang QCliff, Petrey D, Norel R, Honig B.  2010.  Protein interface conservation across structure space. Proc Natl Acad Sci U S A. 107(24):10896-901. Go to Pubmed
Lefebvre C, Rajbhandari P, Alvarez M, Bandaru P, Lim WKeat, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska B et al.  2010.  A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol. 6:377. Go to Pubmed
Norel R, Petrey D, Honig B.  2010.  PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Res. 38(Web Server issue):W550-4. Go to Pubmed
Floratos A, Smith K, Ji Z, Watkinson J, Califano A.  2010.  geWorkbench: an open source platform for integrative genomics. Bioinformatics. 26(14):1779-80. Go to Pubmed
Khiabanian H, Van Vlierberghe P, Palomero T, Ferrando AA, Rabadan R.  2010.  ParMap, an algorithm for the identification of small genomic insertions and deletions in nextgen sequencing data. BMC Res Notes. 3:147. Go to Pubmed
Cadeiras M, von Bayern M, Sinha A, Shahzad K, Latif F, Lim WKeat, Grenett H, Tabak E, Klingler T, Califano A et al.  2011.  Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation. J Cell Mol Med. 15(4):949-56. Go to Pubmed
Pantazatos SP, Li J, Pavlidis P, Lussier YA.  2009.  Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. Cancer Inform. 8:75-94. Go to Pubmed
Lussier YA, Butte AJ, Hunter L.  2010.  Current methodologies for translational bioinformatics. J Biomed Inform. 43(3):355-7. Go to Pubmed
Li X, Panea C, Wiggins C, Reinke V, Leslie C.  2010.  Learning "graph-mer" motifs that predict gene expression trajectories in development. PLoS Comput Biol. 6(4):e1000761. Go to Pubmed
Yang X, Huang Y, Crowson M, Li J, Maitland ML, Lussier Y.  2010.  Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data. J Biomed Inform. 43(3):376-84. Go to Pubmed
Raj A, Wiggins CH.  2010.  An information-theoretic derivation of min-cut-based clustering. IEEE Trans Pattern Anal Mach Intell. 32(6):988-95. Go to Pubmed
Chastanet A, Vitkup D, Yuan G-C, Norman TM, Liu JS, Losick RM.  2010.  Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis. Proc Natl Acad Sci U S A. 107(18):8486-91. Go to Pubmed
Sanchez-Garcia F, Akavia UDavid, Mozes E, Pe'er D.  2010.  JISTIC: identification of significant targets in cancer. BMC Bioinformatics. 11:189. Go to Pubmed
Lee H, Li Z, Silkov A, Fischer M, Petrey D, Honig B, Murray D.  2010.  High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. J Struct Funct Genomics. 11(1):51-9. Go to Pubmed
Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen MW et al.  2010.  Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol. 6(4):e1000730. Go to Pubmed
Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z.  2010.  Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat Struct Mol Biol. 17(4):423-9. Go to Pubmed
Zhou X, Sumazin P, Rajbhandari P, Califano A.  2010.  A systems biology approach to transcription factor binding site prediction. PLoS One. 5(3):e9878. Go to Pubmed
Chen J, Sam L, Huang Y, Lee Y, Li J, Liu Y, H Xing R, Lussier Y.  2010.  Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures. J Biomed Inform. 43(3):385-96. Go to Pubmed
Yao L, Evans JA, Rzhetsky A.  2010.  Novel opportunities for computational biology and sociology in drug discovery. Trends Biotechnol. 28(4):161-70. Go to Pubmed
Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS.  2010.  Origins of specificity in protein-DNA recognition. Annu Rev Biochem. 79:233-69. Go to Pubmed
West SM, Rohs R, Mann RS, Honig B.  2010.  Electrostatic interactions between arginines and the minor groove in the nucleosome. J Biomol Struct Dyn. 27(6):861-6. Go to Pubmed
Van Vlierberghe P, Palomero T, Khiabanian H, Van der Meulen J, Castillo-Martin M, Van Roy N, De Moerloose B, Philippé J, González-García S, Toribio ML et al.  2010.  PHF6 mutations in T-cell acute lymphoblastic leukemia. Nat Genet. 42(4):338-42. Go to Pubmed
Lu X-J, Olson WK, Bussemaker H.  2010.  The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. Nucleic Acids Res. 38(14):4868-76. Go to Pubmed
Ciatto C, Bahna F, Zampieri N, VanSteenhouse HC, Katsamba PS, Ahlsen G, Harrison O, Brasch J, Jin X, Posy S et al.  2010.  T-cadherin structures reveal a novel adhesive binding mechanism. Nat Struct Mol Biol. 17(3):339-47. Go to Pubmed
Harrison O, Bahna F, Katsamba PS, Jin X, Brasch J, Vendome J, Ahlsen G, Carroll K, Price SR, Honig B et al.  2010.  Two-step adhesive binding by classical cadherins. Nat Struct Mol Biol. 17(3):348-57. Go to Pubmed
Bu D-xiu, Rai V, Shen X, Rosario R, Lu Y, D'Agati V, Yan SFang, Friedman R, Nuglozeh E, Schmidt AMarie.  2010.  Activation of the ROCK1 branch of the transforming growth factor-beta pathway contributes to RAGE-dependent acceleration of atherosclerosis in diabetic ApoE-null mice. Circ Res. 106(6):1040-51. Go to Pubmed
Zhu J, Cheng L, Fang Q, Z Zhou H, Honig B.  2010.  Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement. J Mol Biol. 397(3):835-51. Go to Pubmed
van Batenburg MF, Li H, J Polman A, Lachize S, Datson NA, Bussemaker H, Meijer OC.  2010.  Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene. PLoS One. 5(1):e8839. Go to Pubmed
Klein U, Lia M, Crespo M, Siegel R, Shen Q, Mo T, Ambesi-Impiombato A, Califano A, Migliazza A, Bhagat G et al.  2010.  The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell. 17(1):28-40. Go to Pubmed
Alvarez M, Sumazin P, Rajbhandari P, Califano A.  2009.  Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biol. 10(12):R143. Go to Pubmed
Carro MStella, Lim WKeat, Alvarez M, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H et al.  2010.  The transcriptional network for mesenchymal transformation of brain tumours. Nature. 463(7279):318-25. Go to Pubmed
Khiabanian H, Trifonov V, Rabadan R.  2009.  Reassortment patterns in Swine influenza viruses. PLoS Curr. 1:RRN1008. Go to Pubmed
Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim W-K, Kitagawa Y, Schneider C, Alvarez MJ, Califano A et al.  2010.  Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood. 115(5):975-84. Go to Pubmed
Hsiao T-L, Revelles O, Chen L, Sauer U, Vitkup D.  2010.  Automatic policing of biochemical annotations using genomic correlations. Nat Chem Biol. 6(1):34-40. Go to Pubmed
Singarapu KKumar, Mills JL, Xiao R, Acton T, Punta M, Fischer M, Honig B, Rost B, Montelione G, Szyperski T.  2010.  Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175. Proteins. 78(3):779-84. Go to Pubmed
Effraim PR, Wang J, Englander MT, Avins J, Leyh TS, Gonzalez RL, Cornish VW.  2009.  Natural amino acids do not require their native tRNAs for efficient selection by the ribosome. Nat Chem Biol. 5(12):947-53. Go to Pubmed
Mugler A, Walczak AM, Wiggins CH.  2009.  Spectral solutions to stochastic models of gene expression with bursts and regulation. Phys Rev E Stat Nonlin Soft Matter Phys. 80(4 Pt 1):041921. Go to Pubmed
Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A.  2009.  Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol. 5(11):e1000559. Go to Pubmed
Chen B-J, Causton HC, Mancenido D, Goddard NL, Perlstein EO, Pe'er D.  2009.  Harnessing gene expression to identify the genetic basis of drug resistance. Mol Syst Biol. 5:310. Go to Pubmed
Rohs R, West SM, Sosinsky A, Liu P, Mann RS, Honig B.  2009.  The role of DNA shape in protein-DNA recognition. Nature. 461(7268):1248-53. Go to Pubmed
Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, Pe'er I.  2010.  European admixture on the Micronesian island of Kosrae: lessons from complete genetic information. Eur J Hum Genet. 18(3):309-16. Go to Pubmed
Khiabanian H, Trifonov V, Rabadan R.  2009.  Reassortment patterns in Swine influenza viruses. PLoS One. 4(10):e7366. Go to Pubmed
Petrey D, Fischer M, Honig B.  2009.  Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci U S A. 106(41):17377-82. Go to Pubmed
Wang K, Saito M, Bisikirska B, Alvarez M, Lim WKeat, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin A et al.  2009.  Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol. 27(9):829-39. Go to Pubmed
Khiabanian H, Farrell GM, St George K, Rabadan R.  2009.  Differences in patient age distribution between influenza A subtypes. PLoS One. 4(8):e6832. Go to Pubmed
Zhao X, Arca DD', Lim WKeat, Brahmachary M, Carro MStella, Ludwig T, Cardo CCordon, Guillemot F, Aldape K, Califano A et al.  2009.  The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell. 17(2):210-21. Go to Pubmed
Katsamba PS, Carroll K, Ahlsen G, Bahna F, Vendome J, Posy S, Rajebhosale M, Price SR, Jessell T, Ben-Shaul A et al.  2009.  Linking molecular affinity and cellular specificity in cadherin-mediated adhesion. Proc Natl Acad Sci U S A. 106(28):11594-9. Go to Pubmed
Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A et al.  2009.  BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A. 106(27):11294-9. Go to Pubmed
Daly AK, Donaldson PT, Bhatnagar P, Shen Y, Pe'er I, Floratos A, Daly MJ, Goldstein DB, John S, Nelson MR et al.  2009.  HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat Genet. 41(7):816-9. Go to Pubmed
Trifonov V, Khiabanian H, Rabadan R.  2009.  Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus. N Engl J Med. 361(2):115-9. Go to Pubmed
Khan AA, Betel D, Miller ML, Sander C, Leslie C, Marks DS.  2009.  Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol. 27(6):549-55. Go to Pubmed
Prabhu S, Pe'er I.  2009.  Overlapping pools for high-throughput targeted resequencing. Genome Res. 19(7):1254-61. Go to Pubmed
Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, Kitagawa Y, Mandelbaum J, Haddad J, Chen C-Z, Califano A et al.  2009.  Identification of the human mature B cell miRNome. Immunity. 30(5):744-52. Go to Pubmed
Trifonov V, Khiabanian H, Greenbaum B, Rabadan R.  2009.  The origin of the recent swine influenza A(H1N1) virus infecting humans. Euro Surveill. 14(17) Go to Pubmed
Compagno M, Lim WKeat, Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M, Scandurra M, Califano A et al.  2009.  Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature. 459(7247):717-21. Go to Pubmed
Rohs R, West SM, Liu P, Honig B.  2009.  Nuance in the double-helix and its role in protein-DNA recognition. Curr Opin Struct Biol. 19(2):171-7. Go to Pubmed
Walczak AM, Mugler A, Wiggins C.  2009.  A stochastic spectral analysis of transcriptional regulatory cascades. Proc Natl Acad Sci U S A. 106(16):6529-34. Go to Pubmed
Waltz D, Buchanan BG.  2009.  Computer science. Automating science. Science. 324(5923):43-4. Go to Pubmed
Petrey D, Honig B.  2009.  Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol. 19(3):363-8. Go to Pubmed
Nimrod G, Szilágyi A, Leslie C, Ben-Tal N.  2009.  Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. J Mol Biol. 387(4):1040-53. Go to Pubmed
Litvin O, Causton HC, Chen B-J, Pe'er D.  2009.  Modularity and interactions in the genetics of gene expression. Proc Natl Acad Sci U S A. 106(16):6441-6. Go to Pubmed
Lim WKeat, Lyashenko E, Califano A.  2009.  Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput. :504-15. Go to Pubmed
Wang K, Alvarez M, Bisikirska B, Linding R, Basso K, Dalla-Favera R, Califano A.  2009.  Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput. :264-75. Go to Pubmed
Sam LT, Mendonça EA, Li J, Blake J, Friedman C, Lussier Y.  2009.  PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinformatics. 10 Suppl 2:S8. Go to Pubmed
Liu Y, Sam L, Li J, Lussier Y.  2009.  Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays. BMC Bioinformatics. 10 Suppl 2:S11. Go to Pubmed
Lowe JK, Maller JB, Pe'er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, J Smith G, Ji W et al.  2009.  Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. PLoS Genet. 5(2):e1000365. Go to Pubmed
Sachs K, Itani S, Carlisle J, Nolan GP, Pe'er D, Lauffenburger DA.  2009.  Learning signaling network structures with sparsely distributed data. J Comput Biol. 16(2):201-12. Go to Pubmed
Lee S-I, Dudley AM, Drubin D, Silver PA, Krogan N, Pe'er D, Koller D.  2009.  Learning a prior on regulatory potential from eQTL data. PLoS Genet. 5(1):e1000358. Go to Pubmed
Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T et al.  2009.  Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer. Science. 323(5918):1218-22. Go to Pubmed
Meyer NJ, Huang Y, Singleton PA, Sammani S, Moitra J, Evenoski C, Husain AN, Mitra S, Moreno-Vinasco L, Jacobson JR et al.  2009.  GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling. FASEB J. 23(5):1325-37. Go to Pubmed
Margolin AA, Palomero T, Sumazin P, Califano A, Ferrando AA, Stolovitzky G.  2009.  ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc Natl Acad Sci U S A. 106(1):244-9. Go to Pubmed
Shen Y, Sarin S, Liu Y, Hobert O, Pe'er I.  2008.  Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS One. 3(12):e4012. Go to Pubmed
Wang T, Moreno-Vinasco L, Huang Y, Lang GD, Linares JD, Goonewardena SN, Grabavoy A, Samet JM, Geyh AS, Breysse PN et al.  2008.  Murine lung responses to ambient particulate matter: genomic analysis and influence on airway hyperresponsiveness. Environ Health Perspect. 116(11):1500-8. Go to Pubmed
Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C.  2008.  A predictive model of the oxygen and heme regulatory network in yeast. PLoS Comput Biol. 4(11):e1000224. Go to Pubmed
Melvin I, Weston J, Leslie C, Noble WStafford.  2009.  RANKPROP: a web server for protein remote homology detection. Bioinformatics. 25(1):121-2. Go to Pubmed
Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow J, Friedman JM, Pe'er I.  2009.  Whole population, genome-wide mapping of hidden relatedness. Genome Res. 19(2):318-26. Go to Pubmed

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