Student Publications

2008

Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED. Integration of relational and hierarchical network information for protein function prediction. BMC Bioinformatics 9(1):350 (2008).

Nariai N, Kasif S. Context specific protein function prediction. Genome Inform 18:173-82 (2007).

2007

Cheng, A.C.; Coleman, R.G.; Smyth, K.T.; Cao, Q.; Soulard, P.; Caffrey, D.R.; Salzberg, A.C.; Huang, E.S. (2007). "Structure-based maximal affinity model predicts small-molecule druggability."  Nature Biotechnology 25(1):71-75.  [Abstract]

Dwyer D, Kohanski M, Hayete B, Collins JJ. (2007) "Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli." Mol Syst. Biol. Mar 13, 3:91. [Article]

Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, et al. (2007) "Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles." PLoS Biol 5(1): e8. [Abstract]

Hayete B, Gardner TS, Collins JJ. (2007) "Size Matters: network inference tackles the genome scale." Mol Syst Biol. 3:77. Epub Feb 13. [Article]

Landon MR, Lancia DR Jr, Yu J, Thiel SC, Vajda S. (2007) "Identification of Hot Spots within Druggable Binding Regions by Computational Solvent Mapping of Proteins." J Med Chem. Feb 17; [Epub ahead of print]. [Absract]

Liu D*, Brockman JM*, Dass B, Hutchins LN, Singh P, McCarrey J, MacDonald C, Graber JH. (2007). "Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis." Nucleic Acids Research Jan 12; 35(1): 234-246. [Abstract]

Mak D, Benson G (2007) "All Hits All The Time: Parameter Free Calculation of Seed Sensitivity." APBC 327-340. [Full Text]

Nariai N, Kolaczyk ED, Kasif S. (2007). "Probabilistic protein function prediction from heterogeneous genome-wide data." PLoS ONE, Mar 28;2:e337. [Abstract]

Pierce B, Weng Z (Accepted) "ZRANK: Reranking Protein Docking Predictions with an Optimized Energy Function." Proteins.

Pierce B, Phillips AT, Weng Z (2007) "Structure Prediction of Protein Complexes." In Xu Y, Xu D & Liang J. (Eds.), Computational Methods for Protein Structure Prediction and Modeling Volume 2: Structure Prediction. (pp. 109-134). New York: Springer.

Ryan JF, Mazza ME, Pang K, Matus DQ, Baxevanis AD, Martindale MQ, Finnerty JR. (2007) “Pre-Bilaterian Origins of the Hox Cluster and the Hox Code: Evidence from the Sea Anemone, Nematostella vectensis.” PLoS ONE Jan 24;2:e153. [Abstract]

Spira A, Beane JE, Shah V, Steiling K, Liu G, Schembri F, Gilman S, Dumas YM, Calner P, Sebastiani P, Sridhar S, Beamis J, Lamb C, Anderson T, Gerry N, Keane J, Lenburg ME, Brody JS. (2007)   "Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer."  Nat Med. Mar;13(3):361-6. [Abstract]

Sullivan JC, Ryan JF, Mullikin JC, Finnerty JR. (2007) “Conserved and novel Wnt clusters in the basal eumetazoan Nematostella vectensis.” Dev Genes Evol. Mar;217(3):235-9. [Abstract]

Tobin JE, Cui J, Wilk JB, Latourelle JC, Laramie JM, McKee AC, Guttman M, Karamohamed S, Destefano AL, Myers RH. (2007). "Sepiapterin reductase expression is increased in Parkinson's disease brain tissue." Brain Res. Mar 30;1139:42-7. [Abstract]

2006

Beane, J., A. Kadar, A. Spira. (2006). "Diagnostic and prognostic impact of high-throughput genomic and proteomic technologies." Henry's Clinical Diagnosis and Management by Laboratory Methods. 21st edition. Saunders/Elsevier, Philadelphia.

Blower, P.E., K.P. Cross, G.S. Eichler, et al. (2006). “Comparison of methods for sequential screening of large compound sets.”  Comb Chem High Throughput Screen 9(2):115-22. [Abstract]

Burroughs AM, Allen KN, Dunaway-Mariano D, Aravind L.  (2006).  “Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes.”  J. Molecular Biology.  Sep 1;361(5):1003-34. [Abstract]

Chung TP, Laramie JM, Meyer DJ, Downey T, Tam LH, Ding H, Buchman TG, Karl I, Stormo GD, Hotchkiss RS, Cobb JP. (2006). "Molecular diagnostics in sepsis: from bedside to bench." J Am Coll Surg. Nov;203(5):585-598.

Clodfelter KH, Waxman DJ, Vajda S. (2006) “Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450.” Biochemistry, Aug 8;45(31):9393-407. [Full Text]

Clodfelter KH, Holloway MG, Hodor P, Park SH, Ray WJ, Waxman DJ. (2006) “Sex-Dependent Liver Gene Expression Is Extensive and Largely Dependent upon Signal Tranducer and Activator of Transcription 5b (STAT5b): STAT5b-Dependent Activation of Male Genes and Repression of Female genes Revealed by Microarray Analysis.” Mol Endocrinol 20, 1333–1351. [Full Text]

Coleman R.G.; Salzberg, A.C.; Cheng A.C. (2006) "Structure-based identification of binding sites using a free energy model."  J. Chem. Inf. Model 46(6):2631-2637. [Abstract]

Demidov, V.V., N.V. Dokholyan, C. Witte-Hoffman, P. Chalasani, et al. (2006). "Fast complementation of split fluorescent protein triggered by DNA hybridization." PNAS 103(7):2052-2056. [Abstract]

Driscoll ME, Gardner TS (2006) "Identification and control of gene networks in living organisms via supervised and unsupervised learning." Journal of Process Control 16:303-311. [Full Text]

Evsikov, A.V., Graber, J.H., Brockman, J.M., Singh, P., et al. (2006) "Cracking the egg: development dynamics and molecular transitions from the fully grown oocyte to embryo." Genes and Development Oct 1; 20(19) [Abstract]

Gustafson AM, Snitkin ES, Parker SC, et. al. (2006). "Towards the identification of essential genes using targeted genome sequencing and comparative analysis." BMC Genomics. Oct 19; 7:265. [Article]

Iyer LM, Burroughs AM, Aravind L. (2006).  “The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism.”  Bioinformatics Feb 1; 22(3):257-63. [Abstract]

Iyer LM, Burroughs AM, Aravind L. (2006).  “The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.”  Genome Biology.  Jul 19;7(7):R60. [Abstract]

Jothi, R. Cherukuri, PF., Tasneem, A., Przytycka, TM. (2006) “Co-evolutionary analysis of domains in interacting proteins reveals insights inot domain-domain interactions mediating protein-protein interactions.” J Mol Biol. Sep 29; 362(4): 861-75. [Abstract]

Kozakov D, Brenke R, Comeau SR, Vajda S. (2006) "PIPER: An FFT-based protein docking program with pairwise potentials" Proteins. Aug 24. [Article]

Kim NK, Tharakaraman K, Spouge JL. (2006) "Adding sequence context to a Markov background model improves the identification of regulatory elements." Bioinformatics Dec 1;22(23):2870-5. Epub Oct 26. [Abstract]

Landon, M.R., D.R. Lancia, Jr., K.H. Clodfelter, S. Vajda. (2006). "Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns." J Mol Graph Model 24(6):426-33. [Article]

Landon MR, Schaus SE. (2006) "JEDA: Joint entropy diversity analysis. An information-theoretic method for choosing diverse and representative subsets from combinatorial libraries." Mol Divers. Aug;10(3):333-9. Epub 2006 Sep 21. [Abstract]

Laramie, J.M., et al. (2006). “Evidence for a gene influencing heart rate on chromosome 5p13-14 in a meta-analysis of genome-wide scans from the NHLBI Family Blood Pressure Program.” BMC Med Genet 7:17. [Abstract]

Lee, Soohyun & Simon Kasif. (2006) "The complete genome sequence of a dog: a perspective." BioEssays v.28. p569-573. [Abstract]

Mak, D., Gelfand, Y., Benson, G. (2006) "Indel seeds for homology search." Bioinformatics Jul. 15; 22(14):e341-9. [Abstract]

McDunn, J.E., T.P. Chung, J.M. Laramie, et al (2006). “Physiologic genomics.” Surgery 139(2):133-9. [Abstract]

Meng Y., et.al. (2006).  ″Association of the Angiotensin-converting Enzyme Gene with Alzheimer Disease in an Israeli-Arab Community.” Am J Hum Genet. May;78(5):871-7. Epub Mar 16. [Abstract]

Nusbaum, C., et al…S. Parker (2006). "DNA Sequence and Analysis of Human Chromosome 8."  Nature 439:331-335. [Abstract]

Ryan, J.F., et al. (2006). "The cnidarian-bilaterian ancestor possesed at least 56 homeoboxes. Evidence from the starlet sea anemone, Nematostella vectensis." Genome Biology 7(7):R64.

Snitkin ES, Gustafson AM, Mellor J, Wu J, et. al. (2006). "Comparative assessment of performance and genome dependence among phylogenetic profiling methods." BMC Bioinformatics. Sep 27; 7:420. [Article]

Sullivan J.C., J.F. Ryan, et al. (2006).  “StellaBase: The Nematostella vectensis Genomics Database.” Nucleic Acids Research, Jan 1;34(Database issue):D495-9. [Abstract]

Tharakaraman, K., Marino-Ramirez, L., Sheetlin, S.L., Landsman, D., Spouge, J.L. (2006) "Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements." BMC Bioinformatics." Sep 8;7:408. [Abstract]

Wade, C.M. and E.K. Karlsson, et al. (2006). “The Dog Genome: Sequence, Evolution and Haplotype Structure.” In The Dog and Its Genome (ed. EA Ostrander, U Giger, K Lindblad-Toh), pp. 179-208. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Wu, J., Z. Hu, C. DeLisi. (2006). "Gene annotation and network inference by phylogenetic profiling." BMC Bioinformatics 7:80. [Abstract]

Wu, J., J.C. Mellor, C. DeLisi. (2005). "Deciphering protein network organization using phylogenetic profile groups." Genome Inform Ser Workshop Genome Inform 16(1):142-9. [Abstract]

2005

Bernstein, B. E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D.K., Huebert, D.J., McMahon, S., Karlsson, E.K., Kulbokas, E.J., 3rd, Gingeras, T.R., Schreiber, S.L., Lander, E.S. (2005). "Genomic maps and comparative analysis of histone modifications in human and mouse." Cell 120(2): 169-81. [Abstract]

Bhutkar, A. (2005). "Synthetic biology: Navigating the challenges ahead." J. Biolaw & Business 8(2). [Abstract]

Brockman, J. M., Singh, P., Liu, D., Quinlan, S., Salisbury, J., Graber, J.H. (2005). "Pacdb: Polya cleavage site and 3'-utr database." Bioinformatics 21(18): 3691-3. [Abstract]

Burroughs, A.M. (2005). “The medical examination in United States immigration applications: the potential use of genetic testing leads to heightened privacy concerns.” J. Biolaw & Business 8(2):22-32. [Abstract]

Comeau, S. R. and C. J. Camacho (2005). "Predicting oligomeric assemblies: N-mers a primer." J Struct Biol 150(3): 233-44. [Abstract]

Comeau, S. R., S. Vajda, et al. (2005). "Performance of the first protein docking server cluspro in capri rounds 3-5." Proteins 60(2): 239-44. [Abstract]

Dilley, W.G., S. Kalyanaraman, S. Verma, J.P. Cobb, J.M. Laramie, T.C. Lairmore. (2005). "Global gene expression in neuroendocrine tumors from patients with the MENI syndrome." Mol Cancer 4(1):9. [Abstract]

Favaretto, P., A. Bhutkar, et al. (2005). "Constraining ribosomal rna conformational space." Nucleic Acids Res 33(16): 5106-11. [Abstract]

Gardner, T. S., Faith, J.J. (2005). "Reverse-engineering transcription control networks." Physics of Life Reviews 2:65-88.

Hu, Z., J. Mellor, et al. (2005). "Visant: Data-integrating visual framework for biological networks and modules." Nucleic Acids Res 33(Web Server issue): W352-7. [Abstract]

Kozakov, D., K. H. Clodfelter, S. Vajda, C.J. Camacho (2005). "Optimal clustering for detecting near-native conformations in protein docking." Biophys J 89(2): 867-75. [Abstract]

Lake, A.C., Y. Sun, J.L. Li, et. al. (2005). "Expressions, regulation, and triglyceride hydrolase activity of Adiponutrin family members." J. Lipid Res 46(11):2477-87. [Abstract]

Landon, M.R. (2005). "Ethics and policy perspectives on personalized medicine in the post-genomic era." J Biolaw Bus 8(3):28-36. [Abstract]

Lee, S., I. Kohane, S. Kasif (2005). "Genes involved in complex adaptive processes tend to have highly conserved upstream regions." BMC Genomics 6:168. [Abstract]

Lindblad-Toh, K., C.M. Wade, T.S. Mikkelsen, E.K. Karlsson et al. (2005). “Genome sequence, comparative analysis and haplotype structure of the domestic dog.” Nature 438(7069):803-19. [Abstract]

Ma, Q., Y. Yu, Y. Meng, et al. (2005).  ″Genome-wide linkage analysis for alcohol dependence: a comparison between single-nucleotide polymorphism and microsatellite marker assays.” BMC Genetics, 6(Suppl 1):S8. [Abstract]

Marchler-Bauer, A., J.B. Anderson, P.F. Cherukuri, et al. (2005). "Cdd: A conserved domain database for protein classification." Nucleic Acids Res 1(33): D192-6. [Abstract]

Meng, Y., Q. Ma, Y. Yu , et.al (2005). ″Multifactor-dimensionality reduction versus family-based association tests in detecting susceptibility loci in discordant sib-pair studies.” BMC Genetics, 6(Suppl 1):S146. [Abstract]

Mintseris, J. and Z. Weng (2005). "Structure, function, and evolution of transient and obligate protein-protein interactions." Proc Natl Acad Sci U S A 102(31): 10930-5. [Abstract]

Mintseris, J., K. Wiehe, et al. (2005). "Protein-protein docking benchmark 2.0: An update." Proteins 60(2): 214-6. [Abstract]

Pierce, B., W. Tong, et al. (2005). "M-zdock: A grid-based approach for cn symmetric multimer docking." Bioinformatics 21(8): 1472-8. [Abstract]

Rachlin, J., C. Ding, et al. (2005). "Computational tradeoffs in multiplex pcr assay design for snp genotyping." BMC Genomics 6: 102. [Abstract]

Rachlin, J., C. Ding, et al. (2005). "Muplex: Multi-objective multiplex pcr assay design." Nucleic Acids Res 33(Web Server issue): W544-7. [Abstract]

Raina, S. Z., Faith, J.J., Seligmann, H., Disotell, T., Stewart, C-B., Pollock, D.D. (2005). "Evolution of base substitution gradients in primate mitochondrial genomes." Genome Research 15(5): 665-73. [Abstract]

Sato, C., A. Morgan, A.E. Lang, S. Salehi-Rad, T. Kawarai, Y. Meng, et al. (2005).  “Analysis of the glucocerebrosidase gene in Parkinson's disease.” Mov. Disord. Mar;20(3):367-70. [Abstract]

Seong, I.S., E. Ivanova, J.M. Lee, Y.S. Choo, E. Fossale, M. Anderson, J.F. Gusella, J.M. Laramie, et al. (2005). “HD CAG repeat implicates a dominant property of huntingtin in mitochondrial energy metabolism.” Hum Mol Genet 14(19):2871-80. [Abstract]

Shah, V., S. Sridhar, J. Beane, J.S. Brody, A. Spira. (2005). "Siege: Smoking induced epithelial gene expression database." Nucleic Acids Res 33(Database issue): D573-9. [Abstract]

Shakhnovich, B. E. (2005). "Improving the precision of the structure-function relationship by considering phylogenetic context." PLoS Comput Biol 1(1): e9. [Abstract]

Shakhnovich, B. E., E. Deeds, et al. (2005). "Protein structure and evolutionary history determine sequence space topology." Genome Res 15(3): 385-92. [Abstract]

Sheu, S. H., T. Kaya, et al. (2005). "Exploring the binding site structure of the ppar gamma ligand-binding domain by computational solvent mapping." Biochemistry 44(4): 1193-209. [Abstract]

Sheu, S. H., D. R. Lancia, Jr., K.H. Clodfelter, M.R. Landon, S. Vajda (2005). "Precise: A database of predicted and consensus interaction sites in enzymes." Nucleic Acids Res 33(Database issue): D206-11. [Abstract]

Tharakaraman, K., L. Marino-Ramirez, S. Sheetlin, D. Landsman, J. L. Spouge "Alignments anchored on genomic landmarks can aid in the identification of regulatory elements"(2005) Bioinformatics 21 Suppl 1: i440-i448. [Abstract]
(AWARD FOR BEST PAPER AT ISMB 2005 CONFERENCE)

Thomas, R., A. Scott, C.F. Langford, S.P. Fosmire, C.M. Jubala, T.D. Lorentzen, C. Hitte, E.K. Karlsson, et al. (2005).  “M. Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors.” Genome Res  15(12):1831-7. [Abstract]

Vinson, J. P., Jaffe, D.B., O'Neill, K., Karlsson, E.K., Stange-Thomann, N., Anderson, S., Mesirov, J.P., Satoh, N,. Satou, Y., Nusbaum, C., Birren, B., Galagan, J.E., Lander, E.S. (2005). "Assembly of polymorphic genomes: Algorithms and application to ciona savignyi." Genome Res 15(8): 1127-35. [Abstract]

Wiehe, K., B. Pierce, et al. (2005). "Zdock and rdock performance in capri rounds 3, 4, and 5." Proteins 60(2): 207-13. [Abstract]

Wu, C. J. and S. Kasif (2005). "Gems: A web server for biclustering analysis of expression data." Nucleic Acids Res 33(Web Server issue): W596-9. [Abstract]

Young, D.W., J. Pratap, A. Javed, B. Weiner, et al. "SWI/SNF chromatin remodeling complex is obligatory for BMP2-induced, RUNx2-dependent skeletal gene expression that controls osteoblast differentiation." J Cell Biochem 94(4):720-30. [Abstract]

Yu, L., P. M. Haverty, et al. (2005). "Genetic and pharmacological inactivation of adenosine a2a receptor reveals an egr-2-mediated transcriptional regulatory network in the mouse striatum." Physiol Genomics 23(1): 89-102. [Abstract]

Yu, Y., Y. Meng, Q. Ma, et al (2005).  ″Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves.” BMC Genetics, 6(Suppl 1):S15. [Abstract]

Yu, Y., et al. (2005). "Multiple QTLs influencing triglyceride and HDL and total cholesterol levels identified in families with atherogenic dyslipidemia." J Lipid Research 46(10):2202-13. [Abstract]

Zheng, Y., R. J. Roberts, et al. (2005). "Characterization of two new aminopeptidases in escherichia coli." J Bacteriol 187(11): 3671-7. [Abstract]

Zheng, Y., B.P. Anton, R.J. Roberts, S. Kasif (2005). “Phylogenetic detection of conserved gene clusters in microbial genomes.” BMC Bioinformatics 6:243. [Abstract]

Zhu, J. and Z. Weng (2005). "Fast: A novel protein structure alignment algorithm." Proteins 58(3): 618-27. [Abstract]

2004

Beane, J. (2004). "A look behind the scenes: bioterrorism, smallpox, and public health policy. Journal of Biolaw and Business 7:40-53. [Abstract]

Comeau, S. R., D. W. Gatchell, et al. (2004). "Cluspro: A fully automated algorithm for protein-protein docking." Nucleic Acids Res 32(Web Server issue): W96-9. [Abstract]

Comeau, S. R., D. W. Gatchell, et al. (2004). "Cluspro: An automated docking and discrimination method for the prediction of protein complexes." Bioinformatics 20(1): 45-50. [Abstract]

Dasu, M.R., J.P. Cobb, J.M. Laramie, et al. (2004). "Gene expression profiles of livers from thermally injured rats." Gene 327(1):51-60. [Abstract]

Ding, C. and C. R. Cantor (2004). "Quantitative analysis of nucleic acids--the last few years of progress." J Biochem Mol Biol 37(1): 1-10. [Abstract]

Ding, C., R. W. Chiu, et al. (2004). "MS analysis of single-nucleotide differences in circulating nucleic acids: Application to noninvasive prenatal diagnosis." Proc Natl Acad Sci U S A 101(29): 10762-7. [Abstract]

Ding, C., E. Maier, et al. (2004). "Simultaneous quantitative and allele-specific expression analysis with real competitive pcr." BMC Genet 5(1): 8. [Abstract]

Feezor, R., Baker, HV, Mindrinos, M, Hayden, D, Tannahill, CL, Brownstein, BH, Fay, A,  MacMillan, SK, Laramie, JM, Xiao, W, Moldawer, LL, Cobb, JP, Miller-Graziano, CL, Maier, RV, Schoenfeld, D, Davis, RW, Tompkins, RG (2004). "Whole blood and leukocyte rna isolation for gene expression analyses." Physiological Genomics 19(3):247-54. [Abstract]

Frith, M. C., Y. Fu, et al. (2004). "Detection of functional DNA motifs via statistical over-representation." Nucleic Acids Res 32(4): 1372-81. [Abstract]

Frith, M. C., A. S. Halees, et al. (2004). "Site2genome: Locating short DNA sequences in whole genomes." Bioinformatics 20(9): 1468-9. [Abstract]

Frith, M. C., U. Hansen, et al. (2004). "Finding functional sequence elements by multiple local alignment." Nucleic Acids Res 32(1): 189-200. [Abstract]

Fu, Y., M. C. Frith, et al. (2004). "Motifviz: An analysis and visualization tool for motif discovery." Nucleic Acids Res 32(Web Server issue): W420-3. [Abstract]

Halees, A. S. and Z. Weng (2004). "PromoSer: Improvements to the algorithm, visualization and accessibility." Nucleic Acids Res 32(Web Server issue): W191-4. [Abstract]

Haverty, P. M., M. C. Frith, et al. (2004). "Carrie web service: Automated transcriptional regulatory network inference and interactive analysis." Nucleic Acids Res 32(Web Server issue): W213-6. [Abstract]

Haverty, P. M., U. Hansen, et al. (2004). "Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification." Nucleic Acids Res 32(1): 179-88. [Abstract]

Haverty, P. M. and Z. Weng (2004). "Cisml: An xml-based format for sequence motif detection software." Bioinformatics 20(11): 1815-7. [Abstract]

Hoffman, A., Awad, T., Spira, A., Palma, J., Webster, T., Wright, G., Buckley, J., Davis, R., Hubbell, E., Jones, W., Tibshirani, R., Tompkins, R., Triche, T., Xiao, W., West, M., Warrington, J. (2004). "Expression profiling - best practices for data generation and interpretation in clinical trials." Nature Reviews Genetics 5: 229-37. [Abstract]

Hu, Z., Y. Fu, et al. (2004). "Seqvista: A new module of integrated computational tools for studying transcriptional regulation." Nucleic Acids Res 32(Web Server issue): W235-41. [Abstract]

Hu, Z., J. Mellor, et al. (2004). "Visant: An online visualization and analysis tool for biological interaction data." BMC Bioinformatics 5: 17. [Abstract]

Karaoz, U., T. M. Murali, et al. (2004). "Whole-genome annotation by using evidence integration in functional-linkage networks." Proc Natl Acad Sci U S A 101(9): 2888-93. [Abstract]

Leyfer, D., A. Bond, et al. (2004). "Cis-element clustering correlates with dose-dependent pro- and antisignaling effects of il18." Genes Immun 5(5): 354-62. [Abstract]

Liu, J., Farmer, S.R. (2004). "Regulating the balance between peroxisome proliferator-activated receptor ? And ?-catenin signaling during adipogenesis." J. Biol. Chem. 279: 45020-27.

Logan, B., Karaoz, U., Moreno, P., Weng, Z., Kasif, S. (2004). "Protein seer: A web server for protein homology detection." EMBS 2004 (26th Annual International Conference, IEEE Engineering in Medicine and Biology Society).

Mellor, J. C., J. Wu, et al. (2004). "Constructing networks with correlation maximization methods." Genome Inform Ser Workshop Genome Inform 15(1): 149-59. [Abstract]

Mintseris, J. and Z. Weng (2004). "Optimizing protein representations with information theory." Genome Inform Ser Workshop Genome Inform 15(1): 160-9. [Abstract]

Prasad, J. C., S. Vajda, and Camacho, C.J. (2004). "Consensus alignment server for reliable comparative modeling with distant templates." Nucleic Acids Res 32(Web Server issue): W50-4. [Abstract]

Rajamani, D., S. Thiel, et al. (2004). "Anchor residues in protein-protein interactions." Proc Natl Acad Sci U S A 101(31): 11287-92. [Abstract]

Shakhnovich, B. E., J. M. Harvey, et al. (2004). "Elisa: A unified, multidimensional view of the protein domain universe." Genome Inform Ser Workshop Genome Inform 15(1): 213-20. [Abstract]

Shakhnovich, B. E. and J. Max Harvey (2004). "Quantifying structure-function uncertainty: A graph theoretical exploration into the origins and limitations of protein annotation." J Mol Biol 337(4): 933-49. [Abstract]

Shakhnovich, B. E., T. E. Reddy, et al. (2004). "Comparisons of predicted genetic modules: Identification of co-expressed genes through module gene flow." Genome Inform Ser Workshop Genome Inform 15(1): 221-8. [Abstract]

Spira, A., J. Beane, F. Schembri, G. Liu, X. Yang, C. Ding, S. Gilman, C. Cantor, J.S. Brody (2004). "Noninvasive method for obtaining rna from buccal mucosa epithelial cells for gene expression profiling." Biotechniques 36(3): 484-87.[Abstract]

Spira, A., J. Beane, V. Pinto-Plata, A. Kadar, G. Liu, V. Shah, B. Celli, J.S. Brody (2004). "Gene expression profiling of human lung tissue from smokers with severe emphysema." Am J Respir Cell Mol Biol. Dec;31(6):601-10. Epub 2004 Sep 16. [Abstract]

Spira, A., J. Beane, V. Shah, G. Liu, F. Schembri, X. Yang, J. Palma, J.S. Brody (2004). "Effects of cigarette smoke on the human airway epithelial cell transcriptome." PNAS USA 101(27): 10143-8. [Abstract]

Spira, A., F. Schembri, J. Beane, V. Shah, G. Liu, J.S. Brody (2004). "Impact of cigarette smoke on the normal airway transcriptome." Chest 125(5 Suppl):115S. [Abstract]

Tullai, J. W., Schaffer, M.E., Mullenbrock, S., Kasif, S., Cooper, G.M (2004). "Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and mek/erk signaling pathways." J. Biol. Chem. 279(19): 20167-77. [Abstract]

Wizorek, J.J., C.M. Coopersmith, J.M. Laramie, et al. (2004). "Sequence makes a difference: paradoxical effects of stress in vivo." Shock 22(3):229-33. [Abstract]

Wu, C. J., Y. Fu, et al. (2004). "Gene expression module discovery using gibbs sampling." Genome Inform Ser Workshop Genome Inform 15(1): 239-48. [Abstract]

Yanai, I. (2004). "The integrated world of functional genomics." Genome Biol 4(301). [Abstract]

Yu, L., M. C. Frith, et al. (2004). "Characterization of genomic organization of the adenosine a2a receptor gene by molecular and bioinformatics analyses." Brain Res 1000(1-2): 156-73. [Abstract]

Zheng, Y., R. J. Roberts, et al. (2004). "Identification of genes with fast-evolving regions in microbial genomes." Nucleic Acids Res 32(21): 6347-57. [Abstract]

Zheng, Y., R. J. Roberts, et al. (2004). "Segmentally variable genes: A new perspective on adaptation." PLoS Biol 2(4): E81. [Abstract]

2003

Bhanot, G., Lousoun, y., Zhu, J., DeLisi, C. (2003). "The importance of thermodynamic equilibrium for high throughput gene expression arrays." Biophysical J 84(1):124-35. [Abstract]

Blake, W. J., K. A. M, et al. (2003). "Noise in eukaryotic gene expression." Nature 422(6932): 633-7. [Abstract]

Chen, R., L. Li, et al. (2003). "Zdock: An initial-stage protein-docking algorithm." Proteins 52(1): 80-7. [Abstract]

Chen, R., J. Mintseris, et al. (2003). "A protein-protein docking benchmark." Proteins 52(1): 88-91.

Chen, R., W. Tong, et al. (2003). "Zdock predictions for the capri challenge." Proteins 52(1): 68-73. [Abstract]

Chen, R. and Z. Weng (2003). "A novel shape complementarity scoring function for protein-protein docking." Proteins 51(3): 397-408.

Ding, C. and C. R. Cantor (2003). "Direct molecular haplotyping of long-range genomic DNA with m1-pcr." Proc Natl Acad Sci U S A 100(13): 7449-53. [Abstract]

Ding, C. and C. R. Cantor (2003). "A high-throughput gene expression analysis technique using competitive pcr and matrix-assisted laser desorption ionization time-of-flight ms." Proc Natl Acad Sci U S A 100(6): 3059-64. [Abstract]

Frith, M. C., M. C. Li, et al. (2003). "Cluster-buster: Finding dense clusters of motifs in DNA sequences." Nucleic Acids Res 31(13): 3666-8. [Abstract]

Gardner, T. S., D. di Bernardo, D. Lorenz, et al. (2003). "Inferring genetic networks and identifying compound mode of action via expression profiling." Science 301(5629): 102-5. [Abstract]

Halees, A. S., D. Leyfer, et al. (2003). "Promoser: A large-scale mammalian promoter and transcription start site identification service." Nucleic Acids Res 31(13): 3554-9. [Abstract]

Hu, Z., M. Frith, et al. (2003). "Seqvista: A graphical tool for sequence feature visualization and comparison." BMC Bioinformatics 4: 1. [Abstract]

Isaacs, F. J., J. Hasty, et al. (2003). "Prediction and measurement of an autoregulatory genetic module." Proc Natl Acad Sci U S A 100(13): 7714-9. [Abstract]

Kaern, M., W. J. Blake, et al. (2003). "The engineering of gene regulatory networks." Annu Rev Biomed Eng 5: 179-206.

Kortvelyesi, T., Dennis, S., Silberstein, M., Brown III, L., and Vajda, S. (2003). "Algorithms for computational solvent mapping of proteins." Proteins 15;51(3):340-51. [Abstract]

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Letovsky, S. and S. Kasif (2003). "Predicting protein function from protein/protein interaction data: A probabilistic approach." Bioinformatics 19 Suppl 1: i197-204. [Abstract]

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Li, L., R. Chen, et al. (2003). "Rdock: Refinement of rigid-body protein docking predictions." Proteins 53(3): 693-707. [Abstract]

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Mintseris, J. and Z. Weng (2003). "Atomic contact vectors in protein-protein recognition." Proteins 53(3): 629-39. [Abstract]

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Powell, C. A., Spira, A., Derti, A., DeLisi, C., Borczuk, A., Busch, S., Sahasrabudhe, S., Chen, Y., Sugarbaker, D., Bueno, R., Richards, W.G., Brody, J.S. (2003). "Gene expression in lung adenocarcinomas of smokers and non smokers." Am J Respiratory Cell and  Mol Biol. Aug;29(2):157-62. [Abstract]

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Spira, A., J.D. Carroll, G. Liu, Z. Aziz, V. Shah, H. Kornfeld, J. Keane (2003). "Apoptosis genes in human alveolar macrophages infected with virulent or attenuated Mycobacterium tuberculosis: a pivotal role for tumor necrosis factor." Am J Respir Cell Mol Biol 29(5):545-51. [Abstract]

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Zhang, L., V. Pavlovic, et al. (2003). "Human-mouse gene identification by comparative evidence integration and evolutionary analysis." Genome Res 13(6A): 1190-202.

2002

Betley, J. N., Frith, M.C., Graber, J.H., Choo, S., Deshler, J.O. (2002). "A ubiquitous and conserved signal for RNA localization in chordates." Current Biology 12(20): 1756. [Abstract]

Blake, W. (2002). "Ethical and legal issues in the use of criminal DNA databases and possible implications for gene-based rehabilitation." J BioLaw & Business, Special Informatics Supplement: 42-8.

Chen, R. and Z. Weng (2002). "Docking unbound proteins using shape complementarity, desolvation, and electrostatics." Proteins 47(3): 281-94.

Chung, T.P., J.M. Laramie, M. Province, J.P. Cobb. (2002). "Functional genomics of critical illness and injury." Crit Care Med 30(1 Supp):S51-S57.

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Cobb, J.P., J.M. Laramie, et al. (2002). "Sepsis gene expression profiling: murine splenic compared with hepatic responses determined by using complementary DNA microarrays. Crit Care Med 30(12):2711-21.

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Haverty, P. M., Z. Weng, et al. (2002). "Hugeindex: A database with visualization tools for high-density oligonucleotide array data from normal human tissues." Nucleic Acids Res 30(1): 214-7. [Abstract]

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Yanai, I. and C. DeLisi (2002). "The society of genes: Networks of functional links between genes from comparative genomics." Genome Biol 3(11): research0064. [Abstract]

Yanai, I., J. C. Mellor, et al. (2002). "Identifying functional links between genes using conserved chromosomal proximity." Trends Genet 18(4): 176-9. [Abstract]

Yanai, I., Y. I. Wolf, et al. (2002). "Evolution of gene fusions: Horizontal transfer versus independent events." Genome Biol 3(5): research0024. [Abstract]

Zheng, Y., R. J. Roberts, et al. (2002). "Genomic functional annotation using co-evolution profiles of gene clusters." Genome Biol 3(11): research0060. [Abstract]

Zheng, Y., J. D. Szustakowski, et al. (2002). "Computational identification of operons in microbial genomes." Genome Res 12(8): 1221-30. [Abstract]

2001

Aach, J., Bulyk, M.L., Church, G.M., Comander, J., Derti, A., Shendure, J. (2001). "Computational comparison of two draft sequences of the human genome." Nature 409(6822): 856-859. [Abstract]

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Yanai, I. (2001). "New patents: The law of DNA worship." J. Biolaw & Business 4(2).

Yanai, I., A. Derti, et al. (2001). "Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes." Proc Natl Acad Sci U S A 98(14): 7940-5. [Abstract]

2000

Yanai, I., Camacho, C., and DeLisi, C. (2000). "Predictions of gene family distributions in microbial genomes:  Evolution by gene duplication and modification." Physical Review of Letters 2641. [Abstract]