Postdoctoral Fellow in Mike Eisen's lab,
QB3: California Institute for Quantitative Biosciences,
Department of Molecular and Cell Biology,
University of California, Berkeley
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Postdoctoral Fellow in Mike Eisen's lab, |
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Moran Yassour*, Tommy Kaplan*, Hunter B. Fraser, Joshua Z. Levine, Jenna Pfiffner, Xian Adiconis, Gary Schroth, Shujun Luo, Irina Khrebtukova, Andreas Gnirke, Chad Nusbaum, Dawn-Anne Thompson, Nir Friedman, and Aviv Regev Ab initio Construction of a Eukaryotic Transcriptome by Massively Parallel mRNA Sequencing [ Supp. Data ] PNAS, 2009, 106(9):3264-9 |
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Tommy Kaplan*, Chih Long Liu*, Judith A. Erkmann*, John Holik, Michael Grunstein, Paul D. Kaufman, Nir Friedman and Oliver J. Rando Cell Cycle- and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast PLoS Genetics, 2008, 4(11):e1000270 [ F1000 ] |
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Andrew P. Capaldi, Tommy Kaplan, Ying Liu, Naomi Habib, Aviv Regev, Nir Friedman and Erin K. O'Shea Structure and Function of a Transcriptional Network Activated by the MAPK Hog1 Nature Genetics, 2008, 40:1300-6 [ Abstract | Supp. information | Supp. webpage | ChIP-chip Peak Fitting Algorithm | F1000 | NBT's news and views ] |
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Moran Yassour, Tommy Kaplan, Ariel Jaimovich and Nir Friedman Nucleosome positioning from tiling microarray data Bioinformatics 2008 24: i139-i146 [ Proc Int Conf Intell Syst Mol Biol (ISMB), 2008 ] |
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Naomi Habib*, Tommy Kaplan*, Hanah Margalit, Nir Friedman A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval PLoS Comp. Biol., 2008, 4(2):e1000010 |
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Micheal F Dion*, Tommy Kaplan*, Minkyu Kim, Stephen Buratowski, Nir Friedman, and Oliver J. Rando Dynamics of Replication-Independent Histone Turnover in Budding Yeast Science, 2007, 315(5817):1405-8 [ Abstract | SOM | Data | Poster | F1000 ] |
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Chih Long Liu*, Tommy Kaplan*, Minkyu Kim, Stephen Buratowski, Stuart L. Schreiber, Nir Friedman, and Oliver J. Rando Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae PLoS Biol, 2005, 3(10):e328 [ synopsis | Interactive Map | Data | F1000 ] |
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Tommy Kaplan, Nir Friedman and Hanah Margalit ab initio Prediction of Transcription Factor Targets using Structural Knowledge PLoS Comp. Biol., 2005, 1(1):e1 |
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Tommy Kaplan, Nir Friedman and Hanah Margalit Predicting Transcription Factor Binding Sites Using Structural Knowledge Proc 9th Ann Int Conf in Comp Mol Bio (RECOMB), 2005 |
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Yoseph Barash*, Gal Elidan*, Tommy Kaplan*, and Nir Friedman CIS: Compound Importance Sampling Method for Transcription Factor Site p-value Estimation Bioinformatics, 21(5):596:600, 2005 |
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Yoseph Barash*, Gal Elidan*, Tommy Kaplan*, and Nir Friedman CIS: Compound Importance Sampling Method for Transcription Factor Site p-value Estimation Short Paper. Proc Int Conf Intell Syst Mol Biol (ISMB), 2004 |
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Yoseph Barash, Gal Elidan, Nir Friedman, and Tommy Kaplan Modeling Dependencies in Protein-DNA Binding Sites Proc 7th Ann Int Conf in Comp Mol Bio (RECOMB), 2003 |
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Iddo Friedberg, Tommy Kaplan, and Hanah Margalit Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold Proc Int Conf Intell Syst Mol Biol (ISMB), 2000: 162-170 |
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Iddo Friedberg, Tommy Kaplan, and Hanah Margalit Evaluation of PSI-BLAST alignment Accuracy in Comparison to Structural Alignments. Protein Science, 2000, (11):2278-84 |
