http://bmi217.stanford.edu/ Wed, 11 Mar 2009 00:41:40 -0700 FeedCreator 1.7.2-ppt DokuWiki http://bmi217.stanford.edu/lib/images/favicon.ico http://bmi217.stanford.edu/ http://bmi217.stanford.edu/doku.php?id=public:lecture14 Putting it All Together What to read ahead for this class For everyone: * Kohane IS, Masys DR, Altman RB. The incidentalome: a threat to genomic medicine. JAMA. 2006 Jul 12;296(2):212-5. Paper * Butte AJ, Kohane IS. Creation and implications of a phenome-genome network. Nat Biotechnol. 2006 Jan;24(1):55-62. Paper * Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR. Multiclass ca… abutte public Mon, 09 Mar 2009 14:29:36 -0700 http://bmi217.stanford.edu/doku.php?id=schedule_win0809 Google Calendar Version All times 3:15 pm to 4:30 pm in Alway M-106, unless otherwise specified. Monday Tuesday Wednesday Thursday Friday January 5 6 7 Lecture 1: Intro 8 9 12 Lecture 2: Review of eukaryotic molecular biology for the bioinformatician Problem set 1 out 13 TA session: Introduction to R 3 pm, MSOB x-275 (Lusted) 14 Lecture 3: Genomes and genome maps 15 TA session: Introduction to MySQL 3 pm, MSOB x-275 (Lust… tjchen Wed, 04 Mar 2009 15:33:18 -0700 http://bmi217.stanford.edu/doku.php?id=public:lecture13 Integrative Biology and Genomic Medicine What to read ahead for this class For everyone: * Mootha VK, Lepage P, Miller K, Bunkenborg J, Reich M, Hjerrild M, Delmonte T, Villeneuve A, Sladek R, Xu F, Mitchell GA, Morin C, Mann M, Hudson TJ, Robinson B, Rioux JD, Lander ES. Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A. 2003 Jan 21;100(2):605-10. Epub 2003 Jan 14. Paper * Schadt EE, Monks SA, Drake TA, Lusis AJ, Ch… abutte public Wed, 04 Mar 2009 14:25:50 -0700 http://bmi217.stanford.edu/doku.php?id=start [logo] News * Mar 3: Tomorrow's lecture will be held in CCSR 4105. We'll be back to our normal space next week. * Feb 26: Pathways and disease lecture slides available [ here]. * Feb 25: Midterm histogram here. Median 61, stdev 10.45. * Feb 19: Problem set 4 histogram here. Mean 90.5, stdev 19.23. * Feb 18: Example Question for the exam has been posted here. * Feb 11: Histogram for pset 3 is here. Mean: 87.45, Stdev: 16.80 * Feb 9: Lecture slides for today's lecture on prote… ecoronap Tue, 03 Mar 2009 14:51:08 -0700 http://bmi217.stanford.edu/doku.php?id=public:lecture11 Pathways and disease What to read ahead for this class For everyone: * Khatri P, Drăghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics. 2005 Sep 15;21(18):3587-95. Epub 2005 Jun 30. Paper * Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profil… ecoronap public Thu, 26 Feb 2009 15:12:30 -0700 http://bmi217.stanford.edu/doku.php?id=public:midtermgrades_win0809 tjchen public Wed, 25 Feb 2009 15:40:37 -0700 http://bmi217.stanford.edu/doku.php?id=public:final_project In the second half of the quarter, the students will research, design, and implement a translational bioinformatics project, with a topic of their choice. Due dates All times for due dates are 5:00 pm (Pacific), unless otherwise noted. Submissions should be emailed to bmi217submit@gmail.com. tjchen public Wed, 25 Feb 2009 12:54:34 -0700 http://bmi217.stanford.edu/doku.php?id=public:lecture10 Pharmacology What to read ahead for this class For everyone: * Fliri AF, Loging WT, Thadeio PF, Volkmann RA. Analysis of drug-induced effect patterns to link structure and side effects of medicines. Nat Chem Biol. 2005 Dec;1(7):389-97. Paper * Lamb, J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, Reich M, Hieronymus H, Wei G, Armstrong SA, Haggarty SJ, Clemons PA, Wei R, Carr SA, Lander ES, and TR Golub. The Connectivity Map: Using Gen… tjchen public Mon, 23 Feb 2009 11:06:56 -0700 http://bmi217.stanford.edu/doku.php?id=public:ps4_hist_win0809 ecoronap public Thu, 19 Feb 2009 10:36:42 -0700 http://bmi217.stanford.edu/doku.php?id=public:exam_questionex Example Exam Question 1. (3 points) The Netherlands breast-cancer study is described in John Quackenbush's article on Microarray Analysis and Tumor Classification. The Netherlands breast-cancer study differs from the study finding the BRCA1 gene, in both the medical question asked, biological method used, and statistical technique used. tjchen public Wed, 18 Feb 2009 11:16:06 -0700 http://bmi217.stanford.edu/doku.php?id=public:ps3_hist_win0809 ecoronap public Wed, 11 Feb 2009 17:14:03 -0700