Student Publications
updated 1/24/2013
| Name | Publications |
|---|---|
| A. Aksoy |
Cancer Genome Atlas Network. (…Aksoy, A….). Comprehensive molecular portraits of human breast tumours. Nature. 2012 Oct 4;490(7418):61-70. doi: 10.1038/nature11412. Epub 2012 Sep 23.
Cancer Genome Atlas Research Network, Hammerman PS, Hayes DN, Wilkerson MD, Schultz N, Bose R, Chu A, Collisson EA, Cope L, Creighton CJ, Getz G, Herman JG, Johnson BE, Kucherlapati R, Ladanyi M, Maher CA, Robertson G, Sander C, Shen R, Sinha R, Sivachenko A, Thomas RK, Travis WD, Tsao MS, Weinstein JN, Wigle DA, Baylin SB, Govindan R, Meyerson M. & (…Aksoy, A….) Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27;489(7417):519-25. doi: 10.1038/nature11404. Epub 2012 Sep 9. Erratum in: Nature. 2012 Nov 8;491(7423):288. Rogers, Kristen [corrected to Rodgers, Kristen]. ' Cancer Genome Atlas Network. (….Aksoy, A….). Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252. |
| A. Basu |
Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, Garcia BA, Chait B, Zhao Y, Hunt DF, Segal E, Allis CD, Hake SB. Proteome-wide prediction of acetylation substrates. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13785-90. doi: 10.1073/pnas.0906801106. Epub 2009 Aug 3.
Whitcomb SJ, Basu A, Allis CD, Bernstein E. Polycomb Group proteins: an evolutionary perspective. Trends Genet. 2007 Oct;23(10):494-502. Epub 2007 Sep 7. |
| B.Barker |
Xu L, Barker B, Gu Z. Dynamic epistasis for different alleles of the same gene. Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10420-5. doi: 10.1073/pnas.1121507109. Epub 2012 Jun 11.
Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP. Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol. 2012 Jun 4;6:55. doi: 10.1186/1752-0509-6-55. Zanders S, Ma X, Roychoudhury A, Hernandez RD, Demogines A, Barker B, Gu Z, Bustamante CD, Alani E. Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach. Genetics. 2010 Oct;186(2):493-503. doi: 10.1534/genetics.110.120105. Epub 2010 Jul 26. |
| I. Bomash |
Pandarinath C, Bomash I, Victor J, Prusky G, Tschetter W, and Nirenberg S. A novel mechanism for switching a neural system fron one state to another. Frontiers in Computational Neuroscience, Mar 31 2010;4:2. PMID: 20407612
Nirenberg S, Bomash I, Pillow J, and Victor J. Heterogeneous response dynamics in retinal ganglion cells: the interplay of predictive coding and adaptation. J Neurophysiol. 2010 Jun;103(6):3184-94. Epub 2010 Mar 31. PMID: 20357061 |
| M. Carty | White P, Carty M. Reducing bias through process inventory dataset normalization. Int J Life Cycle Assess. 15(1):1-20 (2010). doi: 10.1007/s11367-010-0215-0 |
| E. Cerami |
Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL.Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010 Jul 13;18(1):11-22. Epub 2010 Jun 24.PMID: 20579941
Cerami E, Demir E, Schultz N, Taylor BS, Sander C., Automated network analysis identifies core pathways in glioblastoma. PLoS One. 2010 Feb 12; 5 (2): e8918. PMID: 20169195 Cancer Genome Atlas Research Network (...Cerami E,...). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8. Epub 2008 Sep 4. PubMed PMID: 18772890 MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007;2(10):2366-82.PMID: 17947979 Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 9;5:44. PMID: 17925023 Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. doi: 10.1093/nar/gkq1039. Epub 2010 Nov 10. |
| N. Chambwe |
Dorff KC, Chambwe N, Srdanovic M, Campagne F. BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets. Bioinformatics. 2010 Oct 1;26(19):2472-3. Epub 2010 Aug 11. PubMed PMID: 20702395
Dorff KC, Chambwe N, Srdanovic M, Campagne F. BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets. Bioinformatics. 2010 Oct 1;26(19):2472-3. doi: 10.1093/bioinformatics/btq463. Epub 2010 Aug 11. |
| D. Chang | Chang D, Keinan A. Predicting signatures of "synthetic associations" and "natural associations" from empirical patterns of human genetic variation. PLoS Comput Biol. 2012 Jul;8(7):e1002600. Epub 2012 Jul 5. PMID: 22792059 |
| Y. Cheng |
A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F. PLoS Comput Biol. 2012 Jan;8(1):e1002337. Epub 2012 Jan 5. PMID: 22241976 Hambardzumyan D, Cheng YK, Haeno H, Holland EC, Michor F. The probable cell of origin of NF1- and PDGF-driven glioblastomas. PLoS One. 2011;6(9):e24454. Epub 2011 Sep 9. PMID: 21931722 Attolini CS, Cheng YK, Beroukhim R, Getz G, Abdel-Wahab O, Levine RL, Mellinghoff IK, Michor F. A mathematical framework to determine the temporal sequence of somatic genetic events in cancer. Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17604-9. Epub 2010 Sep 23. PMID: 20864632 |
| SW Chi |
Chi SW, Zang JB, Mele A, Darnell RB. Argonaute HITS-CLIP decodes miRNA-mRNA interaction maps. Nature. 2009 Jul 23;460(7254):479-86. Epub 2009 Jun 17. PMID: 19536157 Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 2008 Nov 27;456(7221):464-9. Epub 2008 Nov 2. PMID: 18978773 Chang, J. H., Chi, S. W., and Zhang, B. T. Gene Expression Pattern Analysis via Latent Variable Models Coupled with Topographic Clustering. Genomics & Informatics, vol. 1, no. 1, pp. 32-39, 2003. PMID: not available. |
| L. DeVargas Roditi | De Vargas Roditi L, Michor F. Evolutionary dynamics of BRCA1 alterations in breast tumorigenesis. J Theor Biol. 2011 Mar 21;273(1):207-15. Epub 2010 Dec 29. PMID: 21194536 Hooker G, Ellner SP, Roditi Lde V, Earn DJ. J R Soc Interface. 2011 Jul 6;8(60):961-74. Epub 2010 Nov 17. Parameterizing state-space models for infectious disease dynamics by generalized profiling: measles in Ontario. PMID: 21084339 |
| Q. Hu | Mechler F, Victor JD, Ohiorhenuan I, Schmid AM, Hu Q. Three-dimensional localization of neurons in cortical tetrode recordings. J Neurophysiol. 2011 Aug;106(2):828-48. Epub 2011 May 25. PMID: 21613581 Ohiorhenuan, I.E., Mechler, F., Purpura, K.P., Schmid, A.M., Hu, Q., and Victor, J.D., 2010, Sparse coding and high-order correlations in fine-scale cortical networks. Nature. 2010 Jul 29;466(7306):617-21. Epub 2010 Jul 4. PMID: 20601940 Hu, Q., and Victor, J.D., 2010, A set of high-order spatiotemporal stimuli that elicit motion and reverse-phi percepts. J Vis. 2010 Mar 25;10(3):9.1-16. PMID: 20377286 |
| H. Hunter-Zinck | Hunter-Zinck H, Musharoff S, Salit J, Al-Ali KA, Chouchane L, Gohar A, Matthews R, Butler MW, Fuller J, Hackett NR, Crystal RG, Clark AG. Population genetic structure of the people of Qatar. Am J Hum Genet. 2010 Jul 9;87(1):17-25. Epub 2010 Jun 24. |
| H. Ingólfsson |
Ingólfsson HI, Sanford RL, Kapoor R, Andersen OS. Gramicidin-based fluorescence assay; for determining small molecules potential for modifying lipid bilayer properties. J Vis Exp. 2010 Oct 13;(44). pii: 2131. doi: 10.3791/2131. PMID: 20972414 Ingolfsson HI, Koeppe RE 2nd, Andersen OS. Curcumin is a modulator of bilayer material properties. Biochemistry. 2007 Sep 11;46(36):10384-91. Epub 2007 Aug 17. PMID: 17705403 |
| P. Kaushik |
Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010 Jul 13;18(1):11-22. doi: 10.1016/j.ccr.2010.05.026. Epub 2010 Jun 24.
Tasseff R, Nayak S, Salim S, Kaushik P, Rizvi N, Varner JD. Analysis of the molecular networks in androgen dependent and independent prostate cancer revealed fragile and robust subsystems. PLoS One. 2010 Jan 28;5(1):e8864. doi: 10.1371/journal.pone.0008864. |
| E. Kenny |
Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, Smith JG, Kovvali S, Min Kang H, Newton-Cheh C, Daly M, Stoffel M, Altshuler DM, Friedman JM, Eskin E, Breslow JL and Pe'er I. Increased power of mixed-models facilitates association mapping of 10 loci for metabolic traits in an isolated population. Hum Mol Genet. 2011 Feb 15;20(4):827-39. Epub 2010 Nov 30. PMID: 21118897 Kenny EE, Gusev A, Riegel K, Lutjohann D, Lowe JK, Salit J, Maller JB, Stoffel M, Daly MJ, Altshuler DM, Friedman JM, Breslow JL, Pe'er I and Sehayek E. Systematic haplotype analysis resoves a complex locus affecting plasma plant sterol levels in a Micronesian Island population. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13886-91. Epub 2009 Aug 10. PMID: 19667188 Lowe JK, Maller JB, Pe’er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, Ji W, Noel M, Nee Foo J, Blundell ML, Garcia L, Sullivan ML, Lee HE, Utterman A, Ferdowsian H, Lifton RP, Breslow JL, Stoffel M, Daly MJ, Altshuler DM, Friedman JM “Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae” PLoS Genet. 2009 Feb;5(2):e1000365. Epub 2009 Feb 6. PMID: 19197348 Burkhardt R, Kenny EE and Breslow JL “Genome-wide associations and lipid risk factors” Current Cardiovascular Lipid Reports 3(1):12-17 (2009) Burkhardt R, Kenny EE, Lowe JK, Birkeland A, Josowitz R, Noel M, Salit J, Maller JB, Pe’er I, Daly MJ, Altshuler D, Stoffel M, Friedman JM and Breslow JL “Common SNPs in HMGCR in Micronesians and Caucasians assciated with LDL-cholesterol levels affect alternative splicing of exon 13” Arterioscler Thromb Vasc Biol. 2008 Nov;28(11):2078-84. Epub 2008 Sep 18. PMID: 18802019 |
| A. Maoz | Maoz, A., Krogh-Madsen, T., and Christini, D. Instability in action potential morphology underlies phase-2 reentry-a mathematical modeling study. Heart Rhythm. 2009 Jun;6(6):813-22. Epub 2009 Mar 13. Erratum in: Heart Rhythm. 2009 Aug;6(8):1255. PMID: 19467510 |
| E. Molinelli | Wang Q, Navarro MVAS, Peng G, Molinelli E, Goh SL, Judson BL, Rajashankar KR, Sodermann H. Molecular mechanism of membrane constriction and tubulation mediated by the F-BAR protein Pacsin/Syndapin. Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12700-5. Epub 2009 Jun 19. PMID: 19549836 |
| J. Moore | Pohl C, Tiongson M, Moore JL, Santella A, Bao Z. Actomyosin-based Self-organization of cell internalization during C. elegans gastrulation. BMC Biol. 2012 Nov 30;10(1):94. [Epub ahead of print] |
| T. Nauvel | Schiff ND, Shah SA, Hudson AE, Nauvel T, Kalik SF, Purpura KP. Gating of attentional effort through the central thalamus. J Neurophysiol. 2012 Dec 5. [Epub ahead of print] |
| P. Ng |
Ng P, Keich U. Alignment constrained sampling. J Comput Biol. 2011 Feb;18(2):155-68. PMID: 21314455 Ng P and Keich U. GIMSAN: A Gibbs motif finder with significance analysis. Bioinformatics. 2008 Oct 1;24(19):2256-7. Epub 2008 Aug 14. PMID: 18703586 Keich U, Ng P. A conservative parametric approach to motif significance analysis. Genome Inform. 2007;19:61-72. PMID: 18546505 Ng P, Keich U. Factoring local sequence composition in motif significance analysis. Genome Inform. 2008;21:15-26. PMID: 19425144 Ng, P., Nagarajan, N., Jones, N., and Keich, U. Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone Bioinformatics. Bioinformatics. 2006 Jul 15;22(14):e393-401. PMID: 16873498 |
| Z. Nichols | Meytlis M, Nichols Z, Nirenberg S. Determining the role of correlated firing in large populations of neurons using white noise and natural scene stimuli. Vision Res. 2012 Oct 1;70:44-53. doi: 10.1016/j.visres.2012.07.007. Epub 2012 Aug 3. |
| J. Reichel | Singh D, Chan JM, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EM, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A. Transforming fusions of FGFR and TACC genes in human glioblastoma. Science. 2012 Sep 7;337(6099):1231-5. doi: 10.1126/science.1220834. Epub 2012 Jul 26. |
| B. Roberts | Roberts BN, Christini DJ. NHE inhibition does not improve Na(+) or Ca(2+) overload during reperfusion: using modeling to illuminate the mechanisms underlying a therapeutic failure. PLoS Comput Biol. 2011 Oct;7(10):e1002241. Epub 2011 Oct 20. PMID: 22028644
Roberts BN, Christini DJ. The relative influences of phosphometabolites and pH on action potential morphology during myocardial reperfusion: a simulation study. PLoS One. 2012;7(11):e47117. doi: 10.1371/journal.pone.0047117. Epub 2012 Nov 7. |
| Y. Saletore | Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE. The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol. 2012 Oct 31;13(10):175. [Epub ahead of print]
Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell. 2012 Jun 22;149(7):1635-46. doi: 10.1016/j.cell.2012.05.003. Epub 2012 May 17. |
| D. Terry |
Altman RB, Zheng Q, Zhou Z, Terry DS, Warren JD, Blanchard SC. Enhanced photostability of cyanine fluorophores across the visible spectrum. Nat Methods. 2012 Apr 27;9(5):428-9. doi: 10.1038/nmeth.1988. No abstract available. PMID: 22543373 Zhao Y, Terry DS, Shi L, Quick M, Weinstein H, Blanchard SC, Javitch JA. Substrate-modulated gating dynamics in a Na+-coupled neurotransmitter transporter homologue. Nature. 2011 Jun 2;474(7349):109-13. Epub 2011 Apr 24. PMID: 21516104 |
| S.Tischfield | Tischfield SE, Keeney S. Scale matters: the spatial correlation of yeast meiotic DNA breaks with histone H3 trimethylation is driven largely by independent colocalization at promoters. Cell Cycle. 2012 Apr 15;11(8):1496-503. doi: 10.4161/cc.19733. Epub 2012 Apr 15.
Pan J, Sasaki M, Kniewel R, Murakami H, Blitzblau HG, Tischfield SE, Zhu X, Neale MJ, Jasin M, Socci ND, Hochwagen A, Keeney S. A hierarchical combination of factors shapes the genome-wide topography of yeast meiotic recombination initiation. Cell. 2011 Mar 4;144(5):719-31. doi: 10.1016/j.cell.2011.02.009. |
| C. Wellock | Wellock CD, Reeke GN. Quantitative tools for examining the vocalizations of juvenile songbirds. Comput Intell Neurosci. 2012;2012:261010. doi: 10.1155/2012/261010. Epub 2012 Jun 4. PMID: 22701474 |