Technion - Laboratory of Computational Biology

Laboratory of Computational Biology

People

Faculty Members

External Faculty

Research staff

Michael Shmoish

Graduate Students

Former Faculty Members

Alumni

Noa Henig(PhD, 2012)
Sivan Bercovici(PhD, 2010)
Ilan Gronau(PhD, 2010)
Itai Sharon(PhD, 2010)
Sasha Skolozub(MSc, 2009)
Oleg Rokhlenko(PhD, 2007)
Adi Mano(MSc, 2007)
Ydo Wexler(PhD, 2007)
Eran Eden(MSc, 2007)
Doron Lipson(PhD, 2007)
Amir Rubinstein(MSc, 2007)
Firas Swidan(PhD, 2006)
Chaya Ben Zaken(PhD, 2006)
Dolev Dotan(MSc, 2006)
Esti Yeger-Lotem (PhD, 2005)
Gideon Greenspan (PhD, 2005)
Ma'ayan Fishelzon (PhD, 2004)
Wisam Kadry (MSc, 2004)
Sagi Snir (PhD, 2004)
Ari Frank (MSc, 2002)
Ann Becker (PhD, 2000)
Dan Pelleg (MSc, 1998)
Amir Ben-Dor (PhD, 1997)

The Bioinformatics Forum
The Bioinformatics Forum - an open inter-departmental colloquium. BioForum-List - mailing list for bioinformatics-related events in the Technion.

Computational resources
Current status of the resources at the lab. Condor usage statistics of the resources at the lab. Please read the regulations for new users.

Courses
Introduction to Bioinformatics (236523) An introduction to several basic bioinformatics tools and databases. Algorithms in Computational Biology (236522) Sequence alignment, phylogeny, EM algorithms, Hidden Markov Models, Bayesian Networks. Projects in Bioinformatics(236524) Advanced Topics in Bioinformatics - Genetic Mapping(236633) Advanced Topics in Bioinformatics - Microarray Data Analysis(236632) Seminar in Bioinformatics (236818) Survey of computational methods (different from the ones discussed in 236522) and their application to problems in molecular biology, mainly focusing on genomic rearrangements and network analyses.

Student Projects
Geppetto - Population Synthesis Software by Amit Anvar and Amit Tzur Efficient calculation of interval scores for DNA copy number data analysis by Oren Levin and Amit Meshulam Weighted treewidth heuristics experimentsby Nikolay Dovgolevsky Visualization of SNP Outputby Sabbagh Wissam SNP analysisby Shay Gammer and Idan Ben-Harrush Non-Parametric Linkage (NPL) Analysisby Anisenia Andrei Non-Parametric Linkage (NPL) Analysisby Avihai Dgany Ubiquitin Portal Prototype by Amit Meshulam and Alexandra Skolozub Comparison of Metabolic Pathways by Amit Karp and Dana Silberklang Coloring Heuristics for Dotted Graphs by Talya Gendler and Shai Lubliner Polymorphism of Recombination Strategy in Evolutionary Games) by Oleg Rokhlenko and Doron Wexler Performing approximate inference by using a heuristic which ignores extreme markers by Mhameed Aez Aldeen and Qassem Ibrahem. Optimizing Variable Elimination Order in Bayesian Networks by Yaniv Ben-Zrihem and David Milman. Implementation of Genehunter's algorithm by Valeria Bodnya and Anna Kukuy. Implementation of Genehunter's algorithm by Nyqolay Dobgolbsqy and Anna Reitman. Finding approximate palindromes in genomic sequences by Tlalit Freund and Noga Engel. Clusters of Orthologous Genes by Evgeny Finkel and Eli Pozniansky. Fast Multinomial Bayes Network Inference with application in linkage analysis by Roman Feldman and Gideon Greenspan. Optimizing Variable Elimination Order in Bayesian Networks by Natalia Graiz and Marina Shteinberg. Haplotyping By MPE Query by Sofia Grinberg and Adi Mano. Approximate inference via a heuristic which ignores extreme markers by Firass Gzayil and Mohammed Zeidan. Analysis of Quality Weighted Gene Expression Data by Roni Kahana and Roy Navon. Applying GAs in Searching Motif Patterns in Gene Expression Data by Tal Kaminer and Nir Laor. Applying Ck Hybridization Arrays in Expression Profiling - A Theoretical Study by Yoav Pinsky and Idan Rubin. Performing approximate inference by using a heuristic which ignores extreme markers by Tatyana Polovets and Rita Shmukler. Implementation of the EM Algorithm for Linkage Recombination by Liat Ramati and Galia Shlezinger. Calculating Genetic Linkage using Monte Carlo Approximations by Guy Rom and Benjamin Zander. Checking Consistency of Pedigree Information by Osnat Tal and Noga Engel Template for Project Reports

Research
For the list of publications please refer to the personal home pages of the researchers.

Software
Gene Regulation Simulation - a tool for performing simulations for transcription regulation networks GDV_calc - GDV calculator for PPI networks MonoClad - Monoclad MPH - a tool for the alighment of metabolic pathways. MAGIC - a tool for integrative and accurate comparative genome mapping. HaarSeg - a segmentation algorithm for tiling microarrays. ATRHunter - find approximate tandem repeats in a genomic sequence. GeneSelector - find a small subset of genes for classification of expression data. HaploBlock - haplotype block identification and resolution for high-density SNP data. Superlink-online (former PedTool) - On-line distributed system for faster multipoint linkage analysis via parallel execution on thousands of personal computers. ProbeSpec - for mapping the specificity of all candidate probes for a given sequence. RHO Package - for radiation hybrid mapping, by Amir Ben-Dor. SDP Wizard - to make and run an SDP instance of a quartet problem. Sources for Sun OS/gcc. Superlink - highly optimized genetic linkage analysis software. SimTree - online tool for computing the similarity between RNA secondary structures. Stepgram - Application for aberration calling in aCGH data DRIM - a tool for discovering motifs in a list of ranked DNA sequences Superlink-GM - Genetic Linkage Analysis in the presence of GM

Links
Technion Bioinformatics Knowledge Unit Smoler Proteomics Center at the Technion Weizmann Institute Bioinformatics Unit Tel Aviv University Bioinformatics Unit Hebrew University Computational Biology Group Ben Gurion University Bioinformatics Support Unit Bar Ilan University Bioinformatics Unit Other bioinformatics links CS technical reports IBS 2010 - The 13th Israeli Bioinformatics Symposium was held in the Technion. IBS 2003 - The 6th Israeli Bioinformatics Symposium was held in the Technion.