yaelab.technion.ac.il
Mandel-Gutfreund Lab @ TechnionYael Mandel Gutfreund's lab for computational molecular biology, Technion - Israel Institute of Technology.
http://yaelab.technion.ac.il/
Yael Mandel Gutfreund's lab for computational molecular biology, Technion - Israel Institute of Technology.
http://yaelab.technion.ac.il/
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Mandel-Gutfreund Lab @ Technion | yaelab.technion.ac.il Reviews
https://yaelab.technion.ac.il
Yael Mandel Gutfreund's lab for computational molecular biology, Technion - Israel Institute of Technology.
yaelab.technion.ac.il
Mandel-Gutfreund Lab | People
http://yaelab.technion.ac.il/people.html
Yael Mandel-Gutfreund, Ph.D. Email: yaelmg@tx.technion.ac.il. Emerson building, room 3-4. Chen Lesnik, Ph.D. Email: lesnik@tx.technion.ac.il. ACCELLTA LTD., MALAT building, 3rd floor. Email: inbalos@tx.technion.ac.il. Emerson building, room 3-35. Hagay Enav, Ph.D. Emerson building, Beja lab. Maya Polishchuk, Ph.D. Email: pl.maya@gmail.com. Emerson building, room 3-1. Email: alonar@tx.technion.ac.il. Emerson building, room 3-1. ACCELLTA LTD., MALAT building, 3rd floor. Joint with Dr. Rachel Kolodny.
Mandel-Gutfreund Lab | Publications
http://yaelab.technion.ac.il/publications.html
2016) BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins. Pii: gkw454 [Epub ahead of print]. [PDF]. Rohs R, Mandel-Gutfreund Y. 2016) How motif environment influences transcription factor search dynamics: Finding a needle in a haystack. Doi: 10.1002/bies.201600005 [Epub ahead of print]. [PDF]. Golan T, Levy C, Rohs R, Mandel-Gutfreund Y. 2015) A widespread role of the motif environment on transcription factor binding across diverse protein families. Singer M*, Kosti I*.
Mandel-Gutfreund Lab | Tools
http://yaelab.technion.ac.il/tools.html
RBPmap: a web server for mapping binding sites of RNA-binding proteins. Paz et al., Nucleic Acids Res., 2014. DRIMust: a web server for Discovering Rank Imbalanced Motifs Using Suffix Trees. Leibovich et al., Nucleic Acids Res., 2013. SFmap: a web server for motif analysis and prediction of splicing factor binding sites. Paz et al., Nucleic Acids Res., 2010. NAbind: classifying NA-binding proteins based on electrostatic properties. Shazman et al., PLoS CB., 2008.
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SFmap - Motifs Analysis and Prediction of Splicing Factors
http://sfmap.technion.ac.il/versions.html
Version 1.8 (Jun. 19, 2013). The input size limitations have been changed:. The maximal sequence length is now 5,000 bp. The maximal number of entries per job was changed to 5,000. E-mail address is now an optional field. Version 1.7 (Jan. 27, 2013). HnRNP motifs were updated. Huelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue JP, Shiue L, Hoon S, Brenner S, Ares M Jr, Yeo GW. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Added an o...
SFmap - Motifs Analysis and Prediction of Splicing Factors
http://sfmap.technion.ac.il/overview.html
SFmap is a computational tool that enables accurate prediction and mapping of known splicing factor binding sites. For more detailed information about SFmap algorithm, read: Akerman et al., 2009. This web site is supported by Eliyahu Pen Research Fund.
RBPmap - Motifs Analysis and Prediction of RNA Binding Proteins
http://rbpmap.technion.ac.il/versions.html
Version 1.1 (Aug. 2016). Added the latest human genome assembly (GRCh38/hg38). The conservation filter's default has changed to not being applied. This web site is supported by Eliyahu Pen Research Fund.
Welcome to the Rohs Lab
http://rohslab.cmb.usc.edu/People.html
Remo Rohs, Ph.D. Professor of Biological Sciences, Chemistry, Physics and Astronomy, and Computer Science. Vice Chair of Biological Sciences. Head of Computational Biology and Bioinformatics. Email: rohs AT usc.edu. Email: tsupeich AT usc.edu. Ana Carolina Dantas Machado. Email: dantasma AT usc.edu. Email: jinsenli AT usc.edu. Joint with Prof. Daniel Lidar. Email: liry AT usc.edu. Email: satyanar AT usc.edu. Email: sagendor AT usc.edu. Email: xiaofei AT usc.edu. Email: bxin At usc.edu. Iris Dror, Ph.D.
Patch Finder Plus
http://pfp.technion.ac.il/versions.html
Jmol was upgraded to the latest version (Jmol-14.0.11). This version is compatible with the most updated security requirements of Java. What is new in version 2.2? The electrostatic potential calculation is now conducted by the APBS. Software. The grid size is now dynamically set for each protein chain and there is no limitation of the protein chain size. The Patch Finder algorithm was improved in terms of accuracy and efficiency. What is new in version 2.0? Grid spacing was changed to 1Å. Shula Shazman,...
Patch Finder Plus
http://pfp.technion.ac.il/overview.html
Patch Finder Plus is an automatic server to extract and display the largest positive electrostatic patch on a protein surface. The algorithm automatically assigns surface positive patches by looking for adjacent points on the protein surface that meet a given electrostatic potential cutoff. In the current version of Patch Finder Plus, the potential cutoff is fixed to 2 kT/e. The algorithm is built of five major steps:. Choosing the largest positive patch for each protein chain.
SFmap - Motifs Analysis and Prediction of Splicing Factors
http://sfmap.technion.ac.il/manual.html
Distinguishes between human, mouse and other genomes. For non-human/mouse genomes, the calculation is performed directly on the input sequence, without taking into account genomic information. Therefore, the following functions are restricted:. No database assembly selection. The input sequences must be loaded in FASTA format (The genomic coordinates option is not availabe). The COS(WR) scoring function is not available (Only the WR stage of the scoring function is applied). And the maximal is 5,000 bp.
SFmap - Motifs Analysis and Prediction of Splicing Factors
http://sfmap.technion.ac.il/index.html
We highly recommend to use our upgraded RBPmap. Web-server (including SFmap features and more) instead of SFmap. Human Feb. 2009 (hg19). Human Mar. 2006 (hg18). Sequence (In FASTA format). (View example). Genomic coordinates ( chromosome:start-end:strand. Paste your sequences/coordinates here:. Sequence length: 21-5,000 bp; Max. number of entries: 5,000). Note that the input size limitations have changed in version 1.8. Or, upload a file:. Motifs selection (optional, default: all motifs).
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Mandel-Gutfreund Lab @ Technion
In our laboratory we develop and apply computational and experimental approaches to study nucleic acid recognition and regulation. In the laboratory we integrate genomics, proteomics and high throughput binding experiments to study the co-regulation between transcription and post-transcriptional processes in human embryonic stem cells. Open positions for excellent and enthusiastic PhD/MSc students or Postdocs with the appropriate background are available.
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