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<h1 class="page-header">Publications
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<h3>
Journal Papers
</h3>
<p>
Piotrowski JS, Okada H, Lu F, Li SC, Hinchman L, Ranjan A, Smith DL, Higbee AJ, Ulbrich A, Coon JJ, Deshpande R, Bukhman YV, McIlwain S, Ong IM, Myers CL, Boone C, Landick R, Ralph J, Kabbage M, Ohya Y. Plant-derived antifungal agent poacic acid targets β-1,3-glucan. Proc. Natl. Acad. Sci. 9 March 2015 doi:10.1073/pnas.1410400112
</p>
<p>
Abbey DA, Funt J, Lurie-Weinberger MN, Thompson DA, Regev A, Myers CL, Berman J. YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens. Genome Medicine 20 Nov 2014 doi:10.1186/s13073-014-0100-8
</p>
<p>
Brown JCS, Nelson J, VanderSluis B, Desphande R, Butts A, Kagan S, Polacheck I, Krysan DJ, Myers CL, Madhani HD. Unraveling the biology of a fungal meningitis
</p>
<p>
pathogen using chemical genetics. Cell 20 Nov 2014 doi:10.1016/j.cell.2014.10.044
Wyche TP, Piotrowski JS, Hou Y, Braun D, Deshpande R, McIlwain S, Ong IM, Myers CL, Guzei IA, Westler WA, Andes DR, Bugni, TS. Forazoline A: Marine‐Derived Polyketide with Antifungal In Vivo Efficacy. Angewandte Chemie 4 Sept. 2014 doi:10.1002/anie.201405990
</p>
<p>
Stessman HAF, Lulla A, Xia T, Mitra A, Harding T, Mansoor A, Myers CL, Van Ness BG, Dolloff NG. High-throughput drug screening identifies compounds and molecular strategies for targeting proteasome inhibitor-resistant multiple myeloma. Leukemia 9 July 2014 doi:10.1038/leu.2014.214
</p>
<p>
DiPrima S, Haarer B, Viggiano S, Pons C, Myers CL, Amberg DC. Linking genetics to structural biology: complex heterozygosity screening with actin alanine scan alleles identifies functionally related surfaces on yeast actin. G3 17 June 2014 doi:10.1534/g3.114.012054
</p>
<p>
Robert J. Schaefer,Roman Briskine,Nathan M. Springer,Chad L. Myers Discovering Functional Modules across Diverse Maize Transcriptomes Using COB, the Co-Expression Browser PLoS ONE 12 June 2014 doi:10.1371/journal.pone.0099193
Benjamin VanderSluis, David C Hess, Colin Pesyna, Elias W Krumholz, Tahin Syed, Balázs Szappanos, Corey Nislow, Balázs Papp, Olga G Troyanskaya, Chad L Myers and Amy A Caudy Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection Genome Biology. 10 April 2014 doi:10.1186/gb-2014-15-4-r64
</p>
<p>
Shan-Yu Fung, Vladimir Sofiyev, Julia Schneiderman, Aaron F. Hirschfeld, Rachel E. Victor, Kate Wood, Jeff S. Piotrowski, Raamesh Deshpande, Sheena C. L, Nicole J. de Vood, Chad L. Myers, Charlie Boone, Raymond J. Anden, and Stuart E. Unbiased Screening of Marine Sponge Extracts for Anti-inflammatory Agents Combined with Chemical Genomics Identifies Girolline as an Inhibitor of Protein Synthesis ACS Chemical Biology October 2013 http://dx.doi.org/10.1021/cb400740c
</p>
<p>
Yungil Kim, Kenichi Tsuda, Daisuke Igarashi, Rachel A. Hillmer,Hitoshi Sakakibara, Chad L. Myers, Fumiaki Katagiri. Mechanisms Underlying Robustness and Tunability in a Plant Immune Signaling Network. Cell Host and Microbe. January 2014. http://dx.doi.org/11.1016/j.chom.2013.12.002.
</p>
<p>
Baryshnikova A, VanderSluis B, Costanzo M, Myers CL, Cha RS, Andrews B, Boone C. Global Linkage Map Connects Meiotic Centromere Function to Chromosome Size in Budding Yeast. G3 2013 Aug 26 doi:10.1534/g3.113.007377
</p>
<p>
Deshpande R, Asiedu M, Klebig M, Sutor S, Kuzmin E, Nelson J, Piotrowski J, Shin SH, Yoshida M, Costanzo M, Boone C, Wigle DA, Myers CL. A comparative genomic approach for identifying synthetic lethal interactions in human cancer. Cancer Res canres.3956.2012; Published OnlineFirst August 26, 2013; doi:10.1158/0008-5472.CAN-12-3956
</p>
<p>
Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM. Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations. Plant Cell August 2013 tpc.113.114793. doi:10.1105/tpc.113.114793
</p>
<p>
Deshpande R, VanderSluis B, Myers CL. Comparison of Profile Similarity Measures for Genetic Interaction Networks. PLoS ONE 2013 Jul 10; 8(7):e68664. doi:10.1371/journal.pone.0068664
</p>
<p>
Nguyen HD, Becker J, Thu YM, Costanzo M, Koch EN, Smith S, Myung K, Myers CL, Boone C, Bielinsky AK. Unligated Okazaki Fragments Induce PCNA Ubiquitination and a Requirement for Rad59-Dependent Replication Fork Progression. PLoS ONE 2013 Jun 18;8(6):e66379. doi:10.1371/journal.pone.0066379
</p>
<p>
Reece-Hoyes JS, Pons C, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, Diprima S, Dricot A, Lajoie BR, Ribeiro PS, Weirauch MT, Hill DE, Hughes TR, Myers CL, Walhout AJ. Extensive Rewiring and Complex Evolutionary Dynamics in a C. elegans Multiparameter Transcription Factor Network. Mol Cell. 2013, 51:116. doi:10.1016/j.molcel.2013.05.018
</p>
<p>
Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L: SGAtools: one-stop analysis and visualization of array-based genetic interaction screens. Nucleic Acids Research. 2013 doi:10.1093/nar/gkt400
</p>
<p>
Alver B, Jauert PA, Brosnan L, O'Hehir M, VanderSluis B, Myers CL, Kirkpatrick DT: A Whole Genome Screen for Minisatellite Stability Genes in Stationary Phase Yeast Cells. G3: Genes| Genomes| Genetics. 2013, 3(5):doi:10.1534/g3.112.005397
</p>
<p>
Colak R, Kim T, Michaut M, Sun M, Irimia M, Bellay J, Myers CL, Blencowe BJ, Kim PM. Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing. PLoS Comput Biol. 2013, 9(4): e1003030. doi:10.1371/journal.pcbi.1003030
</p>
<p>
Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, de Leon N, Kaeppler SM. Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays. PLoS ONE. 2013;8(4):e61005. doi:10.1371/journal.pone.0061005
</p>
<p>
Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM. Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27. The Plant Cell. 2013;25(3):780-793. doi:10.1105/tpc.112.106427
</p>
<p>
Stessman HAF, Baughn LB, Sarver A, Xia T, Deshpande R, Mansoor A, Walsh SA, Sunderland JJ, Dolloff NG, Linden MA, Zhan F, Janz S, Myers CL, and Van Ness BG. Profiling bortezomib resistance identifies secondary therapies in a mouse myeloma model. Molecular Cancer Therapeutics. 2013. doi:10.1158/1535-7163.MCT-12-1151
</p>
<p>
Koch E, Costanzo M, Bellay J, Deshpande R, Chatfield-Reed K, Chua G, D'Urso G, Andrews B, Boone C, Myers CL. Conserved rules govern genetic interaction degree across species. Genome Biology 2012, 13:R57. doi:10.1186/gb-2012-13-7-r57
</p>
<p>
Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM. Reshaping of the maize transcriptome by domestication. PNAS 2012 109: 11878-11883.doi:10.1073/pnas.1201961109
</p>
<p>
Sharifpoor S, van Dyk D, Costanzo M, Baryshnikova A, Friesen H, Douglas AC, Youn JY, VanderSluis B, Myers CL, Papp B, Boone C, Andrews BJ.Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs. Genome Res.2012 Feb 17. [Epub ahead of print]
</p>
<p>
Davidson MB, Katou Y, Keszthelyi A, Sing TL, Xia T, Ou J, Vaisica JA, Thevakumaran N, Marjavaara L, Myers CL, Chabes A, Shirahige K, Brown GW.Endogenous DNA replication stress results in expansion of dNTP pools and a mutator phenotype. EMBO J. 2012 Jan 10;31(4):895-907. doi: 10.1038/emboj.2011.485.
</p>
<p>
Cokol M, Chua HN, Tasan M, Mutlu B, Weinstein ZB, Suzuki Y, Nergiz ME, Costanzo M, Baryshnikova A, Giaever G, Nislow C, Myers CL, Andrews BJ, Boone C, Roth FP: Systematic exploration of synergistic drug pairs. Mol Syst Biol 2011 print; doi:10.1038/msb.2011.71
</p>
<p>
Reece-Hoyes JS, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S, Pesyna C, Dekker J, Myers CL, Walhout AJ: Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nat Meth 2011 online; doi:10.1038/nmeth.1748
</p>
<p>
Williams DE, Dalisay DS, Patrick BO, Matainaho T, Andrusiak K, Deshpande R, Myers CL, Piotrowski JS, Boone C, Yoshida M, Andersen RJ: Padanamides A and B, highly modified linear tetrapeptides produced in culture by a Streptomyces sp. isolated from a marine sediment. Org Lett. 2011 Aug 5;13(15):3936-9. Epub 2011 Jul 12. doi:10.1021/ol2014494
</p>
<p>
Bellay J, Atluri G, Sing TL, Toufighi K, Costanzo M, Ribeiro PS, Pandey G, Baller J, VanderSluis B, Michaut M, Han S, Kim P, Brown GW, Andrews BJ, Boone C, Kumar V, Myers CL: Putting genetic interactions in context through a global modular decomposition. Genome Res. 2011 Jun 29.
</p>
<p>
Szappanos B, Kovacs K, Szamecz B, Honti F, Costanzo M, Baryshnikova A, Gelius-Dietrich G, Lercher MJ, Jelasity M, Myers CL, Andrews BJ, Boone C, Oliver SG, Pal C, Papp B: An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet 2011 online; doi:10.1038/ng.846
</p>
<p>
Li Z, Vizeacoumar FJ, Bahr S, Li J, Warringer J, Vizeacoumar FS, Min R, VanderSluis B, Bellay J, Devit M, Fleming JA, Stephens A, Haase J, Lin ZY, Baryshnikova A, Lu H, Yan Z, Jin K, Barker S, Datti A, Giaever G, Nislow C, Bulawa C, Myers CL, Costanzo M, Gingras AC, Zhang Z, Blomberg A, Bloom K, Andrews B, Boone C: Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat Biotechnol. 2011 Mar 27.
</p>
<p>
Bellay J, Han S, Michaut M, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM: Bringing order to protein disorder through comparative genomics and genetic interactions. Genome Biol. 2011 Feb 15;12(2):R14.
</p>
<p>
Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD: Protein complexes are central in the yeast genetic landscape. PLoS Comput Biol, Vol. 7, No. 2. (24 February 2011), e1001092.
</p>
<p>
Desphande R, Sharma S, Hu WS, Verfaillie CM, Myers CL: A scalable approach for discovering conserved active subnetworks across species. PLoS Comput Biol 2010 Dec 9;6(12): e1001028.
</p>
<p>
Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL: Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods 2010, 7(12):1017-1024.
</p>
<p>
VanderSluis B, Bellay J, Musso G, Costanzo M, Papp B, Vizeacoumar FJ, Baryshnikova A, Andrews B, Boone C, Myers CL: Genetic interactions reveal the evolutionary trajectories of duplicate genes. Mol Syst Biol 2010, 6:429.
</p>
<p>
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pal C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C: The Genetic Landscape of a Cell. Science 2010, 327(5964):425-431.
</p>
<p>
Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C: DRYGIN: A database of quantitative genetic interaction networks in yeast. Nucleic Acids Res 2010, 38(Database issue):D502-507.
</p>
<p>
Hess DC, Myers CL, Huttenhower C, Hibbs MA, Hayes AP, Paw J, Clore JJ, Mendoza RM, Luis BS, Nislow C, Giaever G, Costanzo M, Troyanskaya OG, Caudy AA: Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet 2009, 5(3):e1000407.
</p>
<p>
Hibbs MA, Myers CL, Huttenhower C, Hess DC, Li K, Caudy AA, Troyanskaya OG: Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol 2009, 5(3):e1000322.
</p>
<p>
Huttenhower C, Hibbs MA, Myers CL, Caudy AA, Hess DC, Troyanskaya OG: The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. Bioinformatics 2009.
</p>
<p>
Pandey G, Myers CL, Kumar V: Incorporating functional inter-relationships into protein function prediction algorithms. BMC Bioinformatics 2009, 10:142.
Dixon SJ, Fedyshyn Y, Koh JL, Prasad TS, Chahwan C, Chua G, Toufighi K, Baryshnikova A, Hayles J, Hoe KL, Kim DU, Park HO, Myers CL, Pandey A, Durocher D, Andrews BJ, Boone C: Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes. Proc Natl Acad Sci USA 2008, 105(43):16653-16658.
</p>
<p>
Guan Y, Myers CL, Hess DC, Barutcuoglu Z, Caudy AA, Troyanskaya OG: Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol 2008, 9 Suppl 1:S3. Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG: A genomewide functional network for the laboratory mouse. PLoS Comput Biol 2008, 4(9):e1000165.
</p>
<p>
Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP: A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 2008, 9 Suppl 1:S2.
</p>
<p>
Myers CL, Troyanskaya OG: Context-sensitive data integration and prediction of biological networks. Bioinformatics 2007, 23(17):2322-2330.
</p>
<p>
Hibbs MA, Hess DC, Myers CL, Huttenhower C, Li K, Troyanskaya OG: Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics 2007, 23(20):2692-2699.
</p>
<p>
Miller DL, Myers C, Rickards B, Coller H, Flint J: Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence and survival. Genome Biol 2007, 8(4):R58.
</p>
<p>
Huttenhower C, Flamholz AI, Landis JN, Sahi S, Myers CL, Olszewski KL, Hibbs MA, Siemers NO, Troyanskaya OG, Coller HA: Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC Bioinformatics 2007, 8:250.
Huttenhower C, Hibbs M, Myers C, Troyanskaya OG: A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics 2006, 22(23):2890-2897.
</p>
<p>
Brown JA, Sherlock G, Myers CL, Burrows NM, Deng C, Wu HI, McCann KE, Troyanskaya OG, Brown JM: Global analysis of gene function in yeast by quantitative phenotypic profiling. Mol Syst Biol 2006, 2:2006 0001.
</p>
<p>
Myers CL, Barrett DR, Hibbs MA, Huttenhower C, Troyanskaya OG: Finding function: Evaluation methods for functional genomic data. BMC Genomics 2006, 7:187.
Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M: Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 2006, 5(4):11.
</p>
<p>
Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG: GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics 2006, 7:443.
</p>
<p>
Kung SY, Zhang X, Myers CL: A recursive QR approach to adaptive equalization of time-varying MIMO channels. Communications in Information and Systems 2005, 5(2):169-196.
</p>
<p>
Myers CL, Chen X, Troyanskaya OG: Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinformatics 2005, 6(1):146.
Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG: Discovery of biological networks from diverse functional genomic data. Genome Biol 2005, 6(13):R114.
</p>
<p>
Myers CL, Dunham MJ, Kung SY, Troyanskaya OG: Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics 2004, 20(18):3533-3543.
</p>
</div>
<div class="col-lg-12">
<h3>
Peer Reviewed
</h3>
<p>
Atluri G, Bellay J, Pandey G, Myers CL, Kumar V: Discovering coherent value bicliques in genetic interaction data. In: 9th International Workshop on Data Mining in Bioinformatics. (BIOKDD'10): July 2010; Washington D.C; 2010.
</p>
<p>
Fang G, Kuang R, Pandey G, Steinbach M, Myers CL, Kumar V: Subspace differential co-expression analysis: problem definition and a general approach. Pacific Symposium on Biocomputing. Hawaii, 2009.
</p>
<p>
Pandey G, Atluri G, Steinbach M, Myers C, Kumar V: An association analysis approach to biclustering. 15th ACM SIGKDD International Conference: 2009; 2009.
Bellay J, VanderSluis B, Kim Y, Bandyopadhyay S, Myers CL: Characterization of systems-level organization through mining large-scale genetic interaction networks. IEEE Workshop on Genomic Signal Processing and Statistics. Minneapolis, MN; 2009.
</p>
<p>
Zhang X, Myers CL, Kung SY: Cross-Weighted Fisher discriminant analysis for visualization of DNA microarray data. IEEE International Conference on Acoustics, Speech, and Signal Processing Proceedings (ICASSP) 2004.
</p>
<h3>
Technical Reports
</h3>
<p>
Atluri G, Pandey G, Bellay J, Myers C, Kumar V: Two-Dimensional Association Analysis For Finding Constant Value Biclusters In Real-Valued Data. vol. TR 09-020: Department of Computer Science and Engineering; 2009.
</p>
<p>
Myers CL: Context-sensitive methods for learning from genomic data. Doctoral dissertation. vol. TR-806-07. Princeton University; 2007.
</p>
<h3>
Book Chapters
</h3>
<p>
Costanzo M, Baryshnikova A, Myers CL, Andrews B, Boone C: Charting the genetic interaction map of a cell. Curr Opin Biotechnol 2010.
</p>
<p>
Baryshnikova A, Costanzo M, Dixon S, Vizeacoumar FJ, Myers CL, Andrews B, Boone C: Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Methods Enzymol 2010, 470:145-179.
</p>
<p>
Huttenhower C, Myers CL, Hibbs MA, Troyanskaya OG: Computational analysis of the yeast proteome: understanding and exploiting functional specificity in genomic data. Methods Mol Biol 2009, 548:273-293.
</p>
<p>
Myers CL, Chiriac C, Troyanskaya OG: Discovering biological networks from diverse functional genomic data. Methods Mol Biol 2009, 563:157-175.
</p>
<h3>
Reviews
</h3>
<p>
Bellay J, Michaut M, Kim T, Han S, Colak R, Myers CL, Kim PM.An omics perspective of protein disorder.Mol Biosyst. 2012, Jan 8;8(1):185-93. Epub 2011 Nov 18.
</p>
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