Menachem Fromer


I am a Computational Biologist at The Broad Institute of MIT and Harvard in the Stanley Center for Psychiatric Research.

I'm working with Pamela Sklar, Shaun Purcell, and the Genome Sequencing and Analysis Group of the Medical and Population Genetics Program.


I'm now an Associated Researcher here, as I've moved to New York as an Assistant Professor in Genetics and Genomic Sciences and Psychiatry at the Institute for Genomics and Multiscale Biology and Divisions of Psychiatric Genomics and Center for Statistical Genetics of the Mount Sinai School of Medicine.


Contact Information:

The Broad Institute of MIT and Harvard
Stanley Center for Psychiatric Research
415 Main Street
Cambridge, MA 02142

E-mail:


I completed my Ph.D. studies in Computational Biology at the
School of Computer Science & Engineering, The Hebrew University of Jerusalem.

My advisors were Prof. Michal Linial (from the Life Sciences Department) and
Prof. Nati Linial (from the Computer Science Department).



Curriculum Vitae



My publications in Pubmed


Publications (PDF)

Bibliography
[Autss]
Autism Sequencing Consortium. Synaptic, transcriptional, and chromatin genes disrupted in autism. Nature, 2014 (in press).

[GBI+14]
Joseph Glessner, Alexander G Bick, Kaoru Ito, Jason Homsy, Laura Rodriguez-Murillo, Menachem Fromer, Erica J Mazaika, Badri Vardarajan, Michael J Italia, Jeremy Leipzig, Steven DePalma, Ryan Golhar, Stephan J Sanders, Boris Yamrom, Michael Ronemus, Ivan Iossifov, A. J Willsey, Matthew W State, Jonathan R Kaltman, Peter S White, Yufeng Shen, Dorothy Warburton, Martina Brueckner, Christine Seidman, Elizabeth Goldmuntz, Bruce D Gelb, Richard Lifton, Jonathan G Seidman, Hakon Hakonarson, and Wendy K Chung. Increased frequency of de novo copy number variations in congenital heart disease by integrative analysis of SNP array and exome sequence data. Circulation Research, 2014.

[Sch14]
Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature, 511:421-427, Jul 2014.

[FPK+14]
Menachem Fromer, Andrew J. Pocklington, David H. Kavanagh, Hywel J. Williams, Sarah Dwyer, Padhraig Gormley, Lyudmila Georgieva, Elliott Rees, Priit Palta, Douglas M. Ruderfer, Noa Carrera, Isla Humphreys, Jessica S. Johnson, Panos Roussos, Douglas D. Barker, Eric Banks, Vihra Milanova, Seth G. Grant, Eilis Hannon, Samuel A. Rose, Kimberly Chambert, Milind Mahajan, Edward M. Scolnick, Jennifer L. Moran, George Kirov, Aarno Palotie, Steven A. McCarroll, Peter Holmans, Pamela Sklar, Michael J. Owen, Shaun M. Purcell, and Michael C. O'Donovan. De novo mutations in schizophrenia implicate synaptic networks. Nature, 506:179-184, Feb 2014.

[PMF+14]
Shaun M. Purcell, Jennifer L. Moran*, Menachem Fromer*, Douglas Ruderfer*, Nadia Solovieff, Panos Roussos, Colm O'Dushlaine, Kimberly Chambert, Sarah E. Bergen, Anna Kahler, Laramie Duncan, Eli Stahl, Giulio Genovese, Esperanza Fernandez, Mark O. Collins, Noboru H. Komiyama, Jyoti S. Choudhary, Patrik K. E. Magnusson, Eric Banks, Khalid Shakir, Kiran Garimella, Tim Fennell, Mark DePristo, Seth G. N. Grant, Stephen J. Haggarty, Stacey Gabriel, Edward M. Scolnick, Eric S. Lander, Christina M. Hultman, Patrick F. Sullivan, Steven A. McCarroll, and Pamela Sklar. A polygenic burden of rare disruptive mutations in schizophrenia. Nature, 506:185-190, Feb 2014.

[FP14a]
Menachem Fromer and Shaun M. Purcell. Using XHMM software to detect copy number variation in whole-exome sequencing data. Current Protocols in Human Genetics, 81:7.23.1-7.23.21, 2014.

[FP14b]
Menachem Fromer and Shaun M. Purcell. Rare structural variants. In Eleftheria Zeggini and Andrew Morris, editors, Assessing rare variation in complex traits: design and analysis of genetic studies. Springer-Verlag, Berlin, Germany, 2014.

[PGD+13]
Christopher S. Poultney, Arthur P. Goldberg, Elodie Drapeau, Yan Kou, Hala Harony-Nicolas, Yuji Kajiwara, Silvia De Rubeis, Simon Durand, Christine Stevens, Karola Rehnstrom, Aarno Palotie, Mark J. Daly, Avi Ma'ayan, Menachem Fromer, and Joseph D. Buxbaum. Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. The American Journal of Human Genetics, 93(4):607 - 619, 2013.

[ROC+13]
Stephan Ripke, Colm O'Dushlaine, Kimberly Chambert, Jennifer L. Moran, Anna K. Kahler, Susanne Akterin, Sarah E. Bergen, Ann L. Collins, James J. Crowley, Menachem Fromer, Yunjung Kim, Sang Hong Lee, Patrik K. E. Magnusson, Nick Sanchez, Eli A. Stahl, Stephanie Williams, Naomi R. Wray, Kai Xia, Francesco Bettella, Anders D. Borglum, Brendan K. Bulik-Sullivan, Paul Cormican, Nick Craddock, Christiaan de Leeuw, Naser Durmishi, Michael Gill, Vera Golimbet, Marian L. Hamshere, Peter Holmans, David M. Hougaard, Kenneth S. Kendler, Kuang Lin, Derek W. Morris, Ole Mors, Preben B. Mortensen, Benjamin M. Neale, Francis A. O'Neill, Michael J. Owen, Milica Pejovic Milovancevic, Danielle Posthuma, John Powell, Alexander L. Richards, Brien P. Riley, Douglas Ruderfer, Dan Rujescu, Engilbert Sigurdsson, Teimuraz Silagadze, August B. Smit, Hreinn Stefansson, Stacy Steinberg, Jaana Suvisaari, Sarah Tosato, Matthijs Verhage, James T. Walters, Multicenter Genetic Studies of Schizophrenia Consortium, Psychosis Endophenotypes International Consortium, Wellcome Trust Case Control Consortium 2, Elvira Bramon, Aiden P. Corvin, Michael C. O'Donovan, Kari Stefansson, Edward Scolnick, Shaun Purcell, Steven A. McCarroll, Pamela Sklar, Christina M. Hultman, and Patrick F. Sullivan. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nature Genetics, 45:1150-1159, Oct 2013.

[SNO+13]
J. P. Szatkiewicz, B. M. Neale, C. O'Dushlaine, M. Fromer, J. I. Goldstein, J. L. Moran, K. Chambert, A. Kahler, P. K. E. Magnusson, C. M. Hultman, P. Sklar, S. Purcell, S. A. McCarroll, and P. F. Sullivan. Detecting large copy number variants using exome genotyping arrays in a large Swedish schizophrenia sample. Mol Psychiatry, 18:1178-1184, Nov 2013.

[LRS+13]
Elaine T. Lim, Soumya Raychaudhuri, Stephan J. Sanders, Christine Stevens, Aniko Sabo, Daniel G. MacArthur, Benjamin M. Neale, Andrew Kirby, Douglas M. Ruderfer, Menachem Fromer, Monkol Lek, Li Liu, Jason Flannick, Stephan Ripke, Uma Nagaswamy, Donna Muzny, Jeffrey G. Reid, Alicia Hawes, Irene Newsham, Yuanqing Wu, Lora Lewis, Huyen Dinh, Shannon Gross, Li-San Wang, Chiao-Feng Lin, Otto Valladares, Stacey B. Gabriel, Mark dePristo, David M. Altshuler, Shaun M. Purcell, NHLBI Exome Sequencing Project, Matthew W. State, Eric Boerwinkle, Joseph D. Buxbaum, Edwin H. Cook, Richard A. Gibbs, Gerard D. Schellenberg, James S. Sutcliffe, Bernie Devlin, Kathryn Roeder, and Mark J. Daly. Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Neuron, 77:235-242, Jan 2013.

[BDD+12]
Joseph D. Buxbaum, Mark J. Daly, Bernie Devlin, Thomas Lehner, Kathryn Roeder, Matthew W. State, and The Autism Sequencing Consortium. The Autism Sequencing Consortium: Large-Scale, High-Throughput Sequencing in Autism Spectrum Disorders. Neuron, 76:1052-1056, 2012.

[FMC+12]
Menachem Fromer, Jennifer L. Moran, Kimberly Chambert, Eric Banks, Sarah E. Bergen, Douglas M. Ruderfer, Robert E. Handsaker, Steven A. McCarroll, Michael C. O'Donovan, Michael J. Owen, George Kirov, Patrick F. Sullivan, Christina M. Hultman, Pamela Sklar, and Shaun M. Purcell. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. American Journal of Human Genetics, 91:597-607, Oct 2012.

[GCC+12]
Jacqueline I. Goldstein, Andrew Crenshaw, Jason Carey, George B. Grant, Jared Maguire, Menachem Fromer, Colm O'Dushlaine, Jennifer L. Moran, Kimberly Chambert, Christine Stevens, Swedish Schizophrenia Consortium, ARRA Autism Sequencing Consortium, Pamela Sklar, Christina M. Hultman, Shaun Purcell, Steven A. McCarroll, Patrick F. Sullivan, Mark J. Daly, and Benjamin M. Neale. zCall: a rare variant caller for array-based genotyping. Bioinformatics, 28(19):2543-2545, 2012.

[NKL+12]
Benjamin M. Neale, Yan Kou, Li Liu, Avi Maáyan, Kaitlin E. Samocha, Aniko Sabo, Chiao-Feng Lin, Christine Stevens, Li-San Wang, Vladimir Makarov, Paz Polak, Seungtai Yoon, Jared Maguire, Emily L. Crawford, Nicholas G. Campbell, Evan T. Geller, Otto Valladares, Chad Schafer, Han Liu, Tuo Zhao, Guiqing Cai, Jayon Lihm, Ruth Dannenfelser, Omar Jabado, Zuleyma Peralta, Uma Nagaswamy, Donna Muzny, Jeffrey G. Reid, Irene Newsham, Yuanqing Wu, Lora Lewis, Yi Han, Benjamin F. Voight, Elaine Lim, Elizabeth Rossin, Andrew Kirby, Jason Flannick, Menachem Fromer, Khalid Shakir, Tim Fennell, Kiran Garimella, Eric Banks, Ryan Poplin, Stacey Gabriel, Mark DePristo, Jack R. Wimbish, Braden E. Boone, Shawn E. Levy, Catalina Betancur, Shamil Sunyaev, Eric Boerwinkle, Joseph D. Buxbaum, Edwin H. Cook Jr, Bernie Devlin, Richard A. Gibbs, Kathryn Roeder, Gerard D. Schellenberg, James S. Sutcliffe, and Mark J. Daly. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature, 485:242-245, May 2012.

[MBF+12]
Daniel G. MacArthur, Suganthi Balasubramanian, Adam Frankish, Ni Huang, James Morris, Klaudia Walter, Luke Jostins, Lukas Habegger, Joseph K. Pickrell, Stephen B. Montgomery, Cornelis A. Albers, Zhengdong D. Zhang, Donald F. Conrad, Gerton Lunter, Hancheng Zheng, Qasim Ayub, Mark A. DePristo, Eric Banks, Min Hu, Robert E. Handsaker, Jeffrey A. Rosenfeld, Menachem Fromer, Mike Jin, Xinmeng Jasmine Mu, Ekta Khurana, Kai Ye, Mike Kay, Gary Ian Saunders, Marie-Marthe Suner, Toby Hunt, If H. A. Barnes, Clara Amid, Denise R. Carvalho-Silva, Alexandra H. Bignell, Catherine Snow, Bryndis Yngvadottir, Suzannah Bumpstead, David N. Cooper, Yali Xue, Irene Gallego Romero, 1000 Genomes Project Consortium, Jun Wang, Yingrui Li, Richard A. Gibbs, Steven A. McCarroll, Emmanouil T. Dermitzakis, Jonathan K. Pritchard, Jeffrey C. Barrett, Jennifer Harrow, Matthew E. Hurles, Mark B. Gerstein, and Chris Tyler-Smith. A systematic survey of loss-of-function variants in human protein-coding genes. Science, 335(6070):823-828, 2012.

[YF12]
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, 2012.

[DAA+11]
Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin, and 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics, 27(15):2156-2158, 2011.

[PFLL11a]
Yosef Prat, Menachem Fromer, Michal Linial, and Nathan Linial. Geometric interpretation of gene expression by sparse reconstruction of transcript profiles. In V. Bafna and S. Sahinalp, editors, Research in Computational Molecular Biology, volume 6577 of Lecture Notes in Computer Science, pages 355-357. Springer, 2011.

[PFLL11b]
Yosef Prat, Menachem Fromer, Nathan Linial, and Michal Linial. Recovering key biological constituents through sparse representation of gene expression. Bioinformatics, 27(5):655-661, 2011.

[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. Bioinformatics, 26(19):2466-2467, 2010.

[FL10]
Menachem Fromer and Michal Linial. Exposing the co-adaptive potential of protein-protein interfaces through computational sequence design. Bioinformatics, 26(18):2266-2272, 2010.

[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. In Y. Bengio, D. Schuurmans, J. Lafferty, C. K. I. Williams, and A. Culotta, editors, 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. In Sheldon J. Park and Jennifer R. Cochran, editors, 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. In 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
[Fro14]
Integrating network analyses and genetics with large-scale RNA-sequencing of schizophrenia brains. In American Society of Human Genetics (ASHG). 2014.

[MEM14]
ONLY AVAILABLE TO ISCB MEMBERS. Statistical challenges in whole-exome sequencing of 7000 individuals with schizophrenia and controls. In Intelligent Systems for Molecular Biology (ISMB): Highlights Track. 2014.

[Fro13]
Large-scale RNA-sequencing of schizophrenia brains by the CommonMind Consortium. In XXIst annual World Congress of Psychiatric Genetics (WCPG). 2013.

[Fro12]
Integrating the spectrum of genetic variation and protein domain annotation in schizophrenia sequencing. In XXth annual World Congress of Psychiatric Genetics (WCPG). 2012.

[Fro11]
Robust discovery of copy number variation in matched Swedish schizophrenia case-control whole-exome targeted sequencing. In XIXth annual World Congress of Psychiatric Genetics (WCPG). 2011.

[Pra11]
Recovering key biological constituents through sparse representation of gene expression. In 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB). 2011.

[Fro10]
Finding multiple MAP solutions via LP relaxations. In Allerton Conference. 2010.

[MEM10]
ONLY AVAILABLE TO ISCB MEMBERS. A probabilistic approach to the design of interfaces in proteins with multiple partners: Tradeoff between stability and promiscuity. In Intelligent Systems for Molecular Biology (ISMB): Highlights Track. 2010.

[Fro10a]
A probabilistic approach to the design of interfaces in proteins with multiple partners: Tradeoff between stability and promiscuity. In Intelligent Systems for Molecular Biology (ISMB): Highlights Track. 2010.

[Fro10b]
Finding k-best solutions using LP relaxations. In IEEE Information Theory Workshop Program. 2010.

[Fro09a]
An LP view of the M-best MAP problem. In Neural Information Processing Systems (NIPS) 22 [Outstanding Student Paper Award]. 2009.

[Fro09b]
Finding k-best solutions using LP relaxations. In Physics of Algorithms. 2009.

[Fro08]
A computational framework to empower probabilistic protein design. In 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. In Workshop on Algorithms in Bioinformatics (WABI). 2007.





Software

XHMM (eXome-Hidden Markov Model) for calling and genotyping copy number variation (CNV) from exome sequencing


PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data


dnenrich framework for calculating recurrence and gene-set enrichment for de novo mutations


STRIPES (Spanning TRee Inequalities and Partitioning for Enumerating Solutions) for finding the M assignments with maximum probability in a probabilistic graphical model
See the NIPS 2009 paper here.



SPRINT: Side-chain PRediction INference Toolbox for Multistate Protein Design