Menachem Fromer
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The Broad Institute of MIT and Harvard as a Computational Biologist in the Stanley Center for Psychiatric Research .
http://www.broadinstitute.org/~fromer
I'm a Ph.D. student in Computational Biology at the
School of Computer Science &
Engineering ,
The Hebrew University of Jerusalem .Prof. Michal
Linial (from the Life Sciences Department) andProf.
Nati Linial (from the Computer Science Department).
Contact Information:
The Hebrew University of Jerusalem
Bibliography
[FYH+10]
Menachem Fromer, Chen Yanover, Amir Harel, Ori Shachar, Yair Weiss, and Michal
Linial.
SPRINT: Side-chain prediction inference toolbox for multistate
protein design .
submitted , 2010.
[FL10]
Menachem Fromer and Michal Linial.
Exposing the coevolutionary potential of protein-protein interfaces
through computational design .
submitted , 2010.
[PFLL10]
Yosef Prat, Menachem Fromer, Nathan Linial, and Michal Linial.
Coplanarity analysis of gene expression leverages the inference of gene
function .
submitted , 2010.
[YFss]
Chen Yanover and Menachem Fromer.
Prediction of Low Energy Protein Side Chain Configurations using
Markov Random Fields .
In Thomas Hamelryck, Kanti V. Mardia, and Jesper Ferkinghoff-Borg, editors,
Bayesian Methods in Structural Bioinformatics . Springer-Verlag,
Berlin, Germany, 2010 (in press).
[RFSL10]
Nadav Rappoport, Menachem Fromer, Regev Schweiger, and Michal Linial.
PANDORA: analysis of protein and peptide sets through the hierarchical
integration of annotations Nucl. Acids Res. , page gkq320, 2010.
[FYL10]
Menachem Fromer, Chen Yanover, and Michal Linial.
Design of multispecific
protein sequences using probabilistic graphical modeling Proteins: Structure, Function, and Bioinformatics , 78:530-547, 2010.
[FG09]
Menachem Fromer and Amir Globerson.
An
LP view of the M-best MAP problem Advances in Neural Information Processing Systems (NIPS) 22
[Outstanding Student Paper Award] , pages 567-575. 2009.
[FS09]
Menachem Fromer and Julia M. Shifman.
Tradeoff
between stability and multispecificity in the design of promiscuous
proteins PLoS Comput Biol , 5(12):e1000627, 12 2009.
[NFL09]
Guy Naamati, Menachem Fromer, and Michal Linial.
Expansion of
tandem repeats in sea anemone nematostella vectensis proteome: A source for
gene novelty? BMC Genomics , 10(1):593, 2009.
[PFLL09]
Yosef Prat, Menachem Fromer, Nathan Linial, and Michal Linial.
Codon usage is
associated with the evolutionary age of genes in metazoan
genomes BMC Evolutionary Biology , 9(1):285, 2009.
[BFPL09]
Iris Bahir, Menachem Fromer, Yosef Prat, and Michal Linial.
Viral adaptation to
host: a proteome-based analysis of codon usage and amino acid
preferences Mol Syst Biol , 5, Oct 2009.
[SF09]
Julia M. Shifman and Menachem Fromer.
Search
Algorithms Protein Engineering
and Design . CRC Press, Boca Raton, FL, USA, 2009.
[FY09]
Menachem Fromer and Chen Yanover.
Accurate prediction for
atomic-level protein design and its application in diversifying the
near-optimal sequence space Proteins: Structure, Function, and Bioinformatics , 75:682-705, 2009.
[FY08]
Menachem Fromer and Chen Yanover.
A computational framework to empower probabilistic protein
design Bioinformatics , 24(13):i214-222, 2008.
[LPFL08]
Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, and Michal Linial.
Efficient algorithms for accurate hierarchical clustering of huge
datasets: tackling the entire protein space Bioinformatics , 24(13):i41-49, 2008.
[VFML07]
Roy Varshavsky, Menachem Fromer, Amit Man, and Michal Linial.
When less is
more: Improving classification of protein families with a minimal set of
global features Algorithms in Bioinformatics , Lecture Notes in Computer Science,
pages 12-24. Springer, 2007.
[YFS07]
Chen Yanover, Menachem Fromer, and Julia M. Shifman.
Dead-end elimination for
multistate protein design Journal of Computational Chemistry , 28:2122-2129, 2007.
[KSI+05]
Noam Kaplan, Ori Sasson, Uri Inbar, Moriah Friedlich, Menachem Fromer, Hillel
Fleischer, Elon Portugaly, Nathan Linial, and Michal Linial.
ProtoNet 4.0: A hierarchical classification of one million protein
sequences Nucl. Acids Res. , 33(suppl_1):D216-218, 2005.
[KFFL04]
Noam Kaplan, Moriah Friedlich, Menachem Fromer, and Michal Linial.
A functional
hierarchical organization of the protein sequence space BMC Bioinformatics , 5(1):196, 2004.
[HMWBS+03]
Hagit Hoch-Marchaim, Aryeh M. Weiss, Allan Bar-Sinai, Menachem Fromer, Knut
Adermann, and Jacob Hochman.
The leader peptide of MMTV Env precursor
localizes to the nucleoli in MMTV-derived T cell lymphomas and interacts with
nucleolar protein B23 Virology , 313:22-32, Aug 2003.
[ZYO+99]
Qinghong Zhang, Karina Yaniv, Froma Oberman, Uta Wolke, Anna Git, Menachem
Fromer, William L. Taylor, Dirk Meyer, Nancy Standart, Erez Raz, and Joel K.
Yisraeli.
Vg1 RBP intracellular distribution and
evolutionarily conserved expression at multiple stages during
development Mechanisms of Development , 88:101-106, Oct 1999.
Conference Presentations
Bibliography
[Fro10]
A probabilistic approach to the design of interfaces in proteins with
multiple partners: Tradeoff between stability and promiscuity Intelligent Systems for Molecular Biology (ISMB): Highlights Track .
2010.
[Fro09]
An LP view of
the M-best MAP problem Neural Information Processing Systems (NIPS) 22 [Outstanding Student
Paper Award] . 2009.
[Fro08]
A computational framework to empower probabilistic protein
design Intelligent Systems for Molecular Biology (ISMB): Proceedings
Track . 2008.
[Fro07]
When less is
more: Improving classification of protein families with a minimal set of
global features Workshop on Algorithms in Bioinformatics (WABI) . 2007.
Software
SPRINT: Side-chain PRediction INference Toolbox for Multistate Protein Design
