Publications

Computational Biology staff publications can be found below:

  • Involving Undergraduates in the Annotation and Analysis of Global Gene Expression Studies: Creation of a Maize Shoot Apical Meristem Expression Database. Genetics, April 2007. B. Buckner, J. Beck, K. F. Browning, A. E. Fritz, E. Hoxha, L. D. Grantham, Z. N. Kamvar, A. N. Lough, O. Nikolova, P. S. Schnable, M. J. Scanlon and D. Janick-Buckner.
  • Virk: an active learning-based system for bootstrapping knowledge base development in the neurosciences
  • Finna: A Paragraph Prioritization System for Biocuration in the Neurosciences
  • Wadhawan, S., Runz, H, Burchard, J. The genome as pharmacopeia: Association of genetic dose with phenotypic response. Biochemical pharmacology 94:229-240 (2015)
  • Abrams MT, Koser M, Burchard J, Strapps W, Mehmet H, Gindy M, Zaller D, Sepp-Lorenzino L, Stickens D. A Single Dose of EGLN1 siRNA Yields Increased Erythropoiesis in Nonhuman Primates. NAR 24:405-412. (2014)
  • Lindow M, Vornlocher HP, Riley D, Kornbrust DJ, Burchard J, Whiteley LO, Kamens J, Thompson JD, Nochur S, Younis H, Bartz S, Parry J, Ferrari N, Henry SP, Levin AA. Assessing unintended hybridization-induced biological effects of oligonucleotides. Nat Biotechnol. 30:920-923 (2012)
  • Buehler E, Khan AA, Marine S, Rajaram M, Bahl A, Burchard J, Ferrer M. siRNA off-target effects in genome-wide screens identify signaling pathway members. Sci Rep. 2:428 (2012)
  • Lamb JR, Zhang C, Xie T, Wang K, Zhang B, Hao K, Chudin E, Fraser HB, Millstein J, Ferguson M, Suver C, Ivanovska I, Scott M, Philippar U, Bansal D, Zhang Z, Burchard J, Smith R, Greenawalt D, Cleary M, Derry J, Loboda A, Watters J, Poon RT, Fan ST, Yeung C, Lee NP, Guinney J, Molony C, Emilsson V, Buser-Doepner C, Zhu J, Friend S, Mao M, Shaw PM, Dai H, Luk JM, Schadt EE. Predictive Genes in Adjacent Normal Tissue Are Preferentially Altered by sCNV during Tumorigenesis in Liver Cancer and May Rate Limiting. PLoS One 6 (2011)
  • Luk JM*, Burchard J*, Zhang C, Liu AM, Wong KF, Shek FH, Lee NP, Fan ST, Poon RT, Ivanovska I, Philippar U, Cleary MA, Buser CA, Shaw PM, Lee CN, Tenen DG, Dai H and Mao M. DLK1-DIO3 Genomic Imprinted MicroRNA Cluster at 14q32.2 Defines a Stemlike Subtype of Hepatocellular Carcinoma Associated with Poor Survival. JBC 286: 30706-30713 (2011).
  • Wang ML, Walsh R, Robinson KL, Burchard J, Bartz SR, Cleary M, Galloway DA and Grandori C. Gene expression signature of c-MYC-immortalized human fibroblasts reveals loss of growth inhibitory response to TGFβ. Cell Cycle 10: 2540 - 2548 (2011)
  • Wei J, Jones J, Kang J, Card A, Krimm M, Hancock P, Pei Y, Ason B, Payson E, Dubinina N, Cancilla M, Stroh M, Burchard J, Sachs AB, Hochman JH, Flanagan WM, Kuklin NA. RNA-Induced Silencing Complex-Bound Small Interfering RNA Is a Determinant of RNA Interference-Mediated Gene Silencing in Mice. Mol. Pharmacology 79:953-963 (2011)
  • Burchard J, Zhang C, Liu AM, Lee NPY, Wong KF, Poon RTP, Sham PC, Lam BY, Ferguson MD, Tokiwa G, Smith R, Leeson B, Beard R, Lamb JR, Lim L, Mao M, Dai H, Luk JM. miR-122 as a regulator of mitochondrial metabolic gene network in hepatocellular carcinoma. Mol. Sys. Biol. 6:402 (2010).
  • Burchard J, Jackson AL, Malkov V, Needham RH, Tan Y, Bartz SR, Dai H, Sachs AB, Linsley PS. MicroRNA-like off-target transcript regulation by siRNAs is species specific. RNA 15:308-15 (2009).
  • Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, Bartz SR, Johnson JM, Cummins JM, Raymond CK, Dai H, Chau N, Cleary M, Jackson AL, Carleton M, Lim L. Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression. Mol Cell Biol. 2007 27:2240-52.
  • Schwarz DS, Ding H, Kennington L, Moore JT, Schelter J, Burchard J, Linsley PS, Aronin N, Xu Z, Zamore PD. Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genet. 2006 2:e140.
  • Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, Johnson JM, Lim L, Karpilow J, Nichols K, Marshall W, Khvorova A, Linsley PS. Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. RNA. 2006 12:1197-205.
  • Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, Linsley PS. Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA. 2006 12:1179-87.
  • Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS. Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol. 2003 21:635-7.
  • Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey
  • Drug Susceptibility Prediction Against a Panel of Drugs Using Kernelized Bayesian Multitask Learning. Mehmet Gönen, Adam A. Margolin. Bioinformatics, vol. 30, no. 17, pp. i556–i563, 2014.
  • Integrative and Personalized QSAR Analysis in Cancer by Kernelized Bayesian Matrix Factorization. Muhammad Ammad-ud-din, Elisabeth Georgii, Mehmet Gönen, Tuomo Laitinen, Olli Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski. Journal of Chemical Information and Modeling, vol. 54, no. 8, pp. 2347–2359, 2014.
  • A Community Effort to Assess and Improve Drug Sensitivity Prediction Algorithms. James C. Costello, Laura M. Heiser, Elisabeth Georgii, Mehmet Gönen, Micheal P. Menden, Nicolas J. Wang, Mukesh Bansal, Muhammad Ammad-ud-din, Petteri Hintsanen, Suleiman A. Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Ait- tokallio, Krister Wennerberg, NCI Dream Community, James J. Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W. Gray, Gustavo Stolovitzky. Nature Biotechnology, vol. 32, no. 12, pp. 1202–1212, 2014.
  • Kernelized Bayesian Matrix Factorization. Mehmet Gönen, Samuel Kaski. IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 36, no. 10, pp. 2047–2060, 2014.
  • Predicting Drug–Target Interactions from Chemical and Genomic Kernels Using Bayesian Matrix Factorization. Mehmet Gönen. Bioinformatics, vol. 28, no. 18, pp. 2304–2310, 2012.