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Student Publications

Journal articles published by CBB students

  • Ma K., Reza F., Saaem I., Tian J. Versatile surface functionalization of cyclic olefin copolymer (COC) with sputtered SiO2 thin film for potential BioMEMS applications. Journal of Materials Chemistry. 2009. RSC Link
  • Wasson T, Hartemink AJ, 2009, "An ensemble model of competitive multi-factor binding of the genome," Genome Res, Oct 6. [Epub ahead of print], pubmed link
  • Keedy DA, Williams CJ, Headd JJ, Arendall WB 3rd, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS, 2009, "The other 90% of the protein: Assessment beyond the Calphas for CASP8 template-based and high-accuracy models," Proteins, Jul 20. [Epub ahead of print], pubmed link
  • Gordan R, Hartemink AJ, Bulyk ML, 2009, "Distinguishing direct versus indirect transcription factor-DNA interactions," Genome Res, Epub ahead of print, pubmed link
  • Quan J, Tian J, 2009, "Circular polymerase extension cloning of complex gene libraries and pathways," PLoS One, 4:e6441, pubmed link
  • Rach E, Yuan HY, Majoros WH, Tomancak P, Ohler U, 2009, "Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome," Genome Biol, 10:R73, pubmed link
  • Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN, 2009, "Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment," Methods Mol Biol, 553:57-77. pubmed link
  • Yokoyama KD, Ohler U, Wray GA, 2009, "Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships," Nucleic Acids Res, Jun 2. [Epub ahead of print], pubmed link.
  • Guo X, Hartemink AJ, 2009, "Domain-oriented edge-based alignment of protein interaction networks. Bioinformatics,". 25:i240-6, pubmed link.
  • Liao HX, Levesque MC, Nagel A, Dixon A, Zhang R, Walter E, Parks R, Whitesides J, Marshall DJ, Hwang KK, Yang Y, Chen X, Gao F, Munshaw S, Kepler TB, Denny T, Moody MA, Haynes BF, 2009, "High-throughput isolation of immunoglobulin genes from single human B cells and expression as monoclonal antibodies," J Virol Methods, 158:171-9, pubmed link .
  • Volpe JM, Kepler TB, 2009, "Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chains," Immunome Res, 5:1, pubmed link.
  • Mendiratta P, Mostaghel E, Guinney J, Tewari AK, Porrello A, Barry WT, Nelson PS, Febbo PG, 2009, "Genomic Strategy for Targeting Therapy in Castration-Resistant Prostate Cancer," J Clin Oncol, Mar 16. [Epub ahead of print], pubmed link
  • Crutchley J, King KM, Keaton MA, Szkotnicki L, Orlando DA, Zyla TR, Bardes ES, Lew DJ, 2009, "Molecular Dissection of the Checkpoint Kinase Hsl1p," Mol Biol Cell, 20:1926-36, pubmed link
  • Shah SH, Freedman NJ, Zhang L, Crosslin DR, Stone DH, Haynes C, Johnson J, Nelson S, Wang L, Connelly JJ, Muehlbauer M, Ginsburg GS, Crossman DC, Jones CJ, Vance J, Sketch MH, Granger CB, Newgard CB, Gregory SG, Goldschmidt-Clermont PJ, Kraus WE, Hauser ER, 2009, "Neuropeptide Y gene polymorphisms confer risk of early-onset atherosclerosis," PLoS Genet, 5:e1000318, Epub 2009 Jan 2, pubmed link
  • Crosslin DR, Shah SH, Nelson SC, Hayes C, Connelly JJ, Gadson S, Goldschmidt-Clermont PJ, Vance JM, Rose J, Granger CB, Seo D, Gregory SG, Kraus WE, Hauser ER, 2009, 2009, "Genetic Effects in the Leukotriene biosynthesis pathway and association with atherosclerosis," Hum Genet, Jan 8. [Epub ahead of print], pubmed link
  • Garman KS, Acharya CR, Edelman E, Grade M, Gaedcke J, Sud S, Barry W, Diehl AM, Provenzale D, Ginsburg GS, Ghadimi BM, Ried T, Nevins JR, Mukherjee S, Hsu D, Potti A, 2008, "A genomic approach to colon cancer risk stratification yields biologic insights into therapeutic opportunities," Proc Natl Acad Sci U S A, 105:19432-7. Epub 2008 Dec 2.pubmed link
  • Kavanaugh LA, Dietrich FS, 2009, "Non-coding RNA prediction and verification in Saccharomyces cerevisiae," PLoS Genet, 5:e1000321. Epub 2009 Jan 2, pubmed link
  • Sales AP, Tomaras GD, Kepler TB, 2008, "Improving peptide-MHC class I binding prediction for unbalanced datasets," BMC Bioinformatics, 9:385, pubmed link
  • Headd JJ, Immormino RM, Keedy DA, Emsley P, Richardson DC, Richardson JS, 2008, "Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place," J Struct Funct Genomics. Nov 11. [Epub ahead of print] pubmed link
  • Cooke B, Schmidler SC, 2008, "Preserving the Boltzmann Ensemble in Replica-Exchange Molecular Dynamics Simulations," J Chem Phys, 129: 1-17. pubmed link
  • Cooke B, Schmidler SC, 2008, "Statistical Prediction and Molecular Dynamics Simulation," Biophys J , 95: 4497-4511, pubmed link
  • Boyle AP, Guinney J, Crawford GE, Furey TS, 2008, “F-Seq: A Feature Density Estimator for High-Throughput Sequence Tags,” Bioinformatics, 24:2537-8, pubMed link
  • Simmons Kovacs LA, Orlando DA, Haase SB, 2008, "Transcription network and cyclin/CDKs: The yin and yang of cell cycle oscillators," Cell Cycle, 7:2626-9. pubmed link
  • Chaudhuri B, Hörmann F, Lalonde S, Brady SM, Orlando DA, Benfey P, Frommer WB, 2008, "Protonophore- and pH-insensitive glucose and sucrose accumulation detected by FRET nanosensors in Arabidopsis root tips," Plant J, Aug 12. [Epub ahead of print] pubmed link
  • Cárdenas-Navia LI, Mace DL, Richardson RA, Wilson DF, Shan S, Dewhirst MW, 2008, "The pervasive presence of fluctuating oxygenation in tumors," Cancer Res, 68:5812-9. pubmed link
  • Lalani T, Chu VH, Grussemeyer CA, Reed SD, Bolognesi MP, Friedman JY, Griffiths RI, Crosslin DR, Kanafani ZA, Kaye KS, Ralph Corey G, Fowler VG Jr, 2008, "Clinical outcomes and costs among patients with Staphylococcus aureus bacteremia and orthopedic device infections," Scand J Infect Dis, 10:1-5. pubmed link
  • Orlando DA, Lin CY, Bernard A, Wang JY, Socolar JE, Iversen ES, Hartemink AJ, Haase SB, 2008, “Global control of cell-cycle transcription by coupled CDK and networkoscillators,” Nature, 453:944-7. pubmed link
  • Dinneny JR, Long TA, Wang JY, Jung JW, Mace DL, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN, 2008, "Cell identity mediates the response of Arabidopsis roots to abiotic stress," Science, 320:942-5. pubmed link
  • Gordân R, Hartemink AJ, 2008, "Using DNA duplex stability information for transcription factor binding site discovery," Pac Symp Biocomput, 2008:453-64.  pubmed link
  • Buckley KM, Munshaw S, Kepler TB, Smith LC, 2008, "The 185/333 Gene Family Is a Rapidly Diversifying Host-Defense Gene Cluster in the Purple Sea Urchin Strongylocentrotus purpuratus," J Mol Biol, 379:912-28. pubmed link
  • Connelly JJ, Shah SH, Doss JF, Gadson S, Nelson S, Crosslin DR, Hale AB, Lou X, Wang T, Haynes C, Seo D, Crossman DC, Mooser V, Granger CB, Jones CJ, Kraus WE, Hauser ER, Gregory SG, 2008, "Genetic and functional association of FAM5C with myocardial infarction," BMC Med Genet. 9:33.  pubmed link
  • Munshaw S, Kepler TB, 2008, " An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics," Mol Biol Evol, 25:1199-208.  pubmed link
  • Shah SH, Hauser ER, Crosslin DR, Wang L, Haynes C, Connelly J, Nelson S, Johnson J, Gadson S, Nelson CL, Seo D, Gregory S, Kraus WE, Granger CB, Goldschmidt-Clermont P, Newby LK, 2008, "ALOX5AP variants are associated with in-stent restenosis after percutaneous coronary intervention,"  Atherosclerosis. [Epub ahead of print] pubmed link
  • Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE, 2008, " High-resolution mapping and characterization of open chromatin across the genome," Cell, 132:311-22, pubmed link
  • Volpe JM, Kepler TB, 2008, "Large-scale analysis of human heavy chain V(D)J recombination patterns," Immunome Res, 4:3. pubmed link
  • Edelman E, Guinney J, Chi JT, Febbo PG, Mukherjee S, 2008, "Modeling Cancer Progression via Pathway Dependencies," PLoS Comput Biol, 4:e28. pubmed link
  • Sutton BS, Crosslin DR, Shah SH, Nelson SC, Bassil A, Hale AB, Haynes C,
    Goldschmidt-Clermont PJ, Vance JM, Kraus WE, Gregory SG, Hauser ER, 2008, "Comprehensive Genetic Analysis of the Platelet Activating Factor cetylhydrolase (PLA2G7) Gene and Cardiovascular Disease in Case/Control and Family Datasets," Hum Mol Genet, 17:1318-28. pubmed link
  • Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM, 2008, "RNA Backbone: Consensus All-angle Conformers and Modular String Nomenclature," RNA, 14:465-81. pubmed link
  • Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ, 2007, " Computational and experimental identification of novel human imprinted genes," Genome Res, 17:1723-30. pubmed link
  • Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace DL, Ohler U,
    Benfey PN, 2007, "A high-resolution root spatiotemporal map reveals dominant expression patterns,"
    Science, 318:801-6. pubmed link
  • Malcolm WF, Lenfestey RW, Rice HE, Rach E, Goldberg RN, Cotten CM, 2007, "Dietary fat for infants with enterostomies," J Pediatr Surg, 42:1811-5. pubmed link
  • Haygood R, Fedrigo O, Hanson B, Yokoyama KD, Wray GA, 2007, "Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution," Nat Genet, 39:1140-4. pubmed link
  • Narlikar L, Gordân R, Hartemink AJ, 2007, "A nucleosome-guided map of transcription factor binding sites in yeast," PLoS Comput Biol, 3:e215. pubmed link
  • Reza F, Chandran K, Feltz M, Heinz A, Josephs E, O'Brien P, Dyke BV, Chung H, Indurkhya S, Lakhani N, Lee J, Lin S, Tang N, Labean T, You L, Yuan F, Tian J, 2007, "Engineering novel synthetic biological systems," Synthetic Biology, IET , .1:48-52.  IEEE Link
  • Tan C, Reza F, You L, 2007, "Noise-limited frequency signal transmission in gene circuits," Biophys J, 93:3753-61. pubmed link
  • Headd JJ, Ban YE, Brown P, Edelsbrunner H, Vaidya M, Rudolph J, 2007, "Protein-Protein Interfaces: Properties, Preferences, and Projections," J Proteome Res, 6:2576-86 . pubmed link
  • Reza F, Zuo P, Tian J, 2007, "Protein Interfacial Pocket Engineering via Coupled Computational Filtering and Biological Focusing Criterion," Ann Biomed Eng, 35:1026-36 . pubmed link
  • Orlando DA, Lin CY, Bernard A, Iversen ES, Hartemink AJ, Haase SB, 2007, "A probabilistic model for cell cycle distributions in synchrony experiments," Cell Cycle, 6:478-88. pubmed link
  • Wang L, Hauser ER, Shah SH, Pericak-Vance MA, Haynes C, Crosslin DR, Harris M, Nelson S, Hale AB, Granger CB, Haines JL, Jones CJ, Crossman D, Seo D, Gregory SG, Kraus WE, Goldschmidt-Clermont PJ, Vance JM, 2007, "Peakwide mapping on chromosome 3q13 identifies the kalirin gene as a novel candidate gene for coronary artery disease," Am J Hum Genet. 80:650-63. pubmed link
  • Connelly JJ, Wang T, Cox JE, Haynes C, Wang L, Shah SH, Crosslin DR, Hale AB, Nelson S, Crossman DC, Granger CB, Haines JL, Jones CJ, Vance JM, Goldschmidt-Clermont PJ, Kraus WE, Hauser ER, Gregory SG, 2006, "GATA2 is associated with familial early-onset coronary artery disease," PLoS Genet, 2:e139. pubmed link
  • Narlikar L, Gordân R, Ohler U, Hartemink AJ, 2006, "Informative priors based on transcription factor structural class improve de novo motif discovery," Bioinformatics, 22:e384-92. pubmed link
  • Edelman E, Porrello A, Guinney J, Balakumaran B, Bild A, Febbo PG, Mukherjee S, 2006, "Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles," Bioinformatics, 22:e108-16. pubmed link
  • Mace DL, Lee JY, Twigg RW, Colinas J, Benfey PN, Ohler U, 2006, "Quantification of transcription factor expression from Arabidopsis images," Bioinformatics, 22:e323-31. pubmed link
  • Lee JY, Colinas J, Wang JY, Mace D, Ohler U, Benfey PN, 2006, "Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots," Proc Natl Acad Sci U S A, 103:6055-60. pubmed link
  • Volpe JM, Cowell LG, Kepler TB, 2005, "SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations," Bioinformatics, 22:438-44. pubmed link
  • Larijani M, Chen S, Cunningham LA, Volpe JM, Cowell LG, Lewis SM, Wu GE, 2006, "The recombination difference between mouse kappa and lambda segments is mediated by a pair-wise regulation mechanism," Mol Immunol, 43:870-81. pubmed link
  • Luedi PP, Hartemink AJ, Jirtle RL, 2005, "Genome-wide prediction of imprinted murine genes," Genome Res, 15:875-84. pubmed link