Publications by authors named "Menachem Fromer"

54Publications

Characterization of Single Gene Copy Number Variants in Schizophrenia.

Biol Psychiatry 2020 Apr 4;87(8):736-744. Epub 2019 Oct 4.

Division of Genetic Medicine, Departments of Medicine, Psychiatry, and Biomedical Informatics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee. Electronic address:

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http://dx.doi.org/10.1016/j.biopsych.2019.09.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103483PMC
April 2020

The AURORA Study: a longitudinal, multimodal library of brain biology and function after traumatic stress exposure.

Mol Psychiatry 2020 02 19;25(2):283-296. Epub 2019 Nov 19.

Department of Health Care Policy, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41380-019-0581-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981025PMC
February 2020

Unperturbed expression bias of imprinted genes in schizophrenia.

Nat Commun 2018 07 25;9(1):2914. Epub 2018 Jul 25.

Department of Cell, Developmental and Regenerative Biology, ISMMS, New York, NY, 10029, USA.

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http://dx.doi.org/10.1038/s41467-018-04960-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060121PMC
July 2018

A framework for the detection of de novo mutations in family-based sequencing data.

Eur J Hum Genet 2017 02 23;25(2):227-233. Epub 2016 Nov 23.

Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/ejhg.2016.147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5255947PMC
February 2017

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects.

Authors:
Christian R Marshall Daniel P Howrigan Daniele Merico Bhooma Thiruvahindrapuram Wenting Wu Douglas S Greer Danny Antaki Aniket Shetty Peter A Holmans Dalila Pinto Madhusudan Gujral William M Brandler Dheeraj Malhotra Zhouzhi Wang Karin V Fuentes Fajarado Michelle S Maile Stephan Ripke Ingrid Agartz Margot Albus Madeline Alexander Farooq Amin Joshua Atkins Silviu A Bacanu Richard A Belliveau Sarah E Bergen Marcelo Bertalan Elizabeth Bevilacqua Tim B Bigdeli Donald W Black Richard Bruggeman Nancy G Buccola Randy L Buckner Brendan Bulik-Sullivan William Byerley Wiepke Cahn Guiqing Cai Murray J Cairns Dominique Campion Rita M Cantor Vaughan J Carr Noa Carrera Stanley V Catts Kimberley D Chambert Wei Cheng C Robert Cloninger David Cohen Paul Cormican Nick Craddock Benedicto Crespo-Facorro James J Crowley David Curtis Michael Davidson Kenneth L Davis Franziska Degenhardt Jurgen Del Favero Lynn E DeLisi Dimitris Dikeos Timothy Dinan Srdjan Djurovic Gary Donohoe Elodie Drapeau Jubao Duan Frank Dudbridge Peter Eichhammer Johan Eriksson Valentina Escott-Price Laurent Essioux Ayman H Fanous Kai-How Farh Martilias S Farrell Josef Frank Lude Franke Robert Freedman Nelson B Freimer Joseph I Friedman Andreas J Forstner Menachem Fromer Giulio Genovese Lyudmila Georgieva Elliot S Gershon Ina Giegling Paola Giusti-Rodríguez Stephanie Godard Jacqueline I Goldstein Jacob Gratten Lieuwe de Haan Marian L Hamshere Mark Hansen Thomas Hansen Vahram Haroutunian Annette M Hartmann Frans A Henskens Stefan Herms Joel N Hirschhorn Per Hoffmann Andrea Hofman Hailiang Huang Masashi Ikeda Inge Joa Anna K Kähler René S Kahn Luba Kalaydjieva Juha Karjalainen David Kavanagh Matthew C Keller Brian J Kelly James L Kennedy Yunjung Kim James A Knowles Bettina Konte Claudine Laurent Phil Lee S Hong Lee Sophie E Legge Bernard Lerer Deborah L Levy Kung-Yee Liang Jeffrey Lieberman Jouko Lönnqvist Carmel M Loughland Patrik K E Magnusson Brion S Maher Wolfgang Maier Jacques Mallet Manuel Mattheisen Morten Mattingsdal Robert W McCarley Colm McDonald Andrew M McIntosh Sandra Meier Carin J Meijer Ingrid Melle Raquelle I Mesholam-Gately Andres Metspalu Patricia T Michie Lili Milani Vihra Milanova Younes Mokrab Derek W Morris Bertram Müller-Myhsok Kieran C Murphy Robin M Murray Inez Myin-Germeys Igor Nenadic Deborah A Nertney Gerald Nestadt Kristin K Nicodemus Laura Nisenbaum Annelie Nordin Eadbhard O'Callaghan Colm O'Dushlaine Sang-Yun Oh Ann Olincy Line Olsen F Anthony O'Neill Jim Van Os Christos Pantelis George N Papadimitriou Elena Parkhomenko Michele T Pato Tiina Paunio Diana O Perkins Tune H Pers Olli Pietiläinen Jonathan Pimm Andrew J Pocklington John Powell Alkes Price Ann E Pulver Shaun M Purcell Digby Quested Henrik B Rasmussen Abraham Reichenberg Mark A Reimers Alexander L Richards Joshua L Roffman Panos Roussos Douglas M Ruderfer Veikko Salomaa Alan R Sanders Adam Savitz Ulrich Schall Thomas G Schulze Sibylle G Schwab Edward M Scolnick Rodney J Scott Larry J Seidman Jianxin Shi Jeremy M Silverman Jordan W Smoller Erik Söderman Chris C A Spencer Eli A Stahl Eric Strengman Jana Strohmaier T Scott Stroup Jaana Suvisaari Dragan M Svrakic Jin P Szatkiewicz Srinivas Thirumalai Paul A Tooney Juha Veijola Peter M Visscher John Waddington Dermot Walsh Bradley T Webb Mark Weiser Dieter B Wildenauer Nigel M Williams Stephanie Williams Stephanie H Witt Aaron R Wolen Brandon K Wormley Naomi R Wray Jing Qin Wu Clement C Zai Rolf Adolfsson Ole A Andreassen Douglas H R Blackwood Elvira Bramon Joseph D Buxbaum Sven Cichon David A Collier Aiden Corvin Mark J Daly Ariel Darvasi Enrico Domenici Tõnu Esko Pablo V Gejman Michael Gill Hugh Gurling Christina M Hultman Nakao Iwata Assen V Jablensky Erik G Jönsson Kenneth S Kendler George Kirov Jo Knight Douglas F Levinson Qingqin S Li Steven A McCarroll Andrew McQuillin Jennifer L Moran Bryan J Mowry Markus M Nöthen Roel A Ophoff Michael J Owen Aarno Palotie Carlos N Pato Tracey L Petryshen Danielle Posthuma Marcella Rietschel Brien P Riley Dan Rujescu Pamela Sklar David St Clair James T R Walters Thomas Werge Patrick F Sullivan Michael C O'Donovan Stephen W Scherer Benjamin M Neale Jonathan Sebat

Nat Genet 2017 01 21;49(1):27-35. Epub 2016 Nov 21.

Beyster Center for Psychiatric Genomics, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/ng.3725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737772PMC
January 2017

Analysis of protein-coding genetic variation in 60,706 humans.

Nature 2016 08;536(7616):285-91

Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

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http://www.nature.com/articles/nature19057
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http://dx.doi.org/10.1038/nature19057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018207PMC
August 2016

Patterns of genic intolerance of rare copy number variation in 59,898 human exomes.

Nat Genet 2016 10 17;48(10):1107-11. Epub 2016 Aug 17.

Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

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http://dx.doi.org/10.1038/ng.3638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5042837PMC
October 2016

Genetic Effect of Chemotherapy Exposure in Children of Testicular Cancer Survivors.

Clin Cancer Res 2016 05 2;22(9):2183-9. Epub 2015 Dec 2.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1078-0432.CCR-15-2317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4854770PMC
May 2016

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

A role for noncoding variation in schizophrenia.

Cell Rep 2014 Nov 6;9(4):1417-29. Epub 2014 Nov 6.

Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://www.cell.com/cell-reports/pdf/S2211-1247(14)00869-9.p
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http://linkinghub.elsevier.com/retrieve/pii/S221112471400869
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http://dx.doi.org/10.1016/j.celrep.2014.10.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255904PMC
November 2014

Synaptic, transcriptional and chromatin genes disrupted in autism.

Using XHMM Software to Detect Copy Number Variation in Whole-Exome Sequencing Data.

Curr Protoc Hum Genet 2014 Apr 24;81:7.23.1-21. Epub 2014 Apr 24.

Division of Psychiatric Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; Stanley Center for Psychiatric Research and Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Analytic and Translational Genetics Unit Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.

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http://dx.doi.org/10.1002/0471142905.hg0723s81DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065038PMC
April 2014

A polygenic burden of rare disruptive mutations in schizophrenia.

Nature 2014 Feb 22;506(7487):185-90. Epub 2014 Jan 22.

1] Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2] Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [3] Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.

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http://dx.doi.org/10.1038/nature12975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136494PMC
February 2014

Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder.

Am J Hum Genet 2013 Oct;93(4):607-19

Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

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http://dx.doi.org/10.1016/j.ajhg.2013.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791269PMC
October 2013

Genome-wide association analysis identifies 13 new risk loci for schizophrenia.

Authors:
Stephan Ripke Colm O'Dushlaine Kimberly Chambert Jennifer L Moran Anna K Kähler 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 Douglas F Levinson Pablo V Gejman Kenneth S Kendler Claudine Laurent Bryan J Mowry Michael C O'Donovan Michael J Owen Ann E Pulver Brien P Riley Sibylle G Schwab Dieter B Wildenauer Frank Dudbridge Peter Holmans Jianxin Shi Margot Albus Madeline Alexander Dominique Campion David Cohen Dimitris Dikeos Jubao Duan Peter Eichhammer Stephanie Godard Mark Hansen F Bernard Lerer Kung-Yee Liang Wolfgang Maier Jacques Mallet Deborah A Nertney Gerald Nestadt Nadine Norton Francis A O'Neill George N Papadimitriou Robert Ribble Alan R Sanders Jeremy M Silverman Dermot Walsh Nigel M Williams Brandon Wormley Maria J Arranz Steven Bakker Stephan Bender Elvira Bramon David Collier Benedicto Crespo-Facorro Jeremy Hall Conrad Iyegbe Assen Jablensky Rene S Kahn Luba Kalaydjieva Stephen Lawrie Cathryn M Lewis Kuang Lin Don H Linszen Ignacio Mata Andrew McIntosh Robin M Murray Roel A Ophoff John Powell Dan Rujescu Jim Van Os Muriel Walshe Matthias Weisbrod Durk Wiersma Peter Donnelly Ines Barroso Jenefer M Blackwell Elvira Bramon Matthew A Brown Juan P Casas Aiden P Corvin Panos Deloukas Audrey Duncanson Janusz Jankowski Hugh S Markus Christopher G Mathew Colin N A Palmer Robert Plomin Anna Rautanen Stephen J Sawcer Richard C Trembath Ananth C Viswanathan Nicholas W Wood Chris C A Spencer Gavin Band Céline Bellenguez Colin Freeman Garrett Hellenthal Eleni Giannoulatou Matti Pirinen Richard D Pearson Amy Strange Zhan Su Damjan Vukcevic Peter Donnelly Cordelia Langford Sarah E Hunt Sarah Edkins Rhian Gwilliam Hannah Blackburn Suzannah J Bumpstead Serge Dronov Matthew Gillman Emma Gray Naomi Hammond Alagurevathi Jayakumar Owen T McCann Jennifer Liddle Simon C Potter Radhi Ravindrarajah Michelle Ricketts Avazeh Tashakkori-Ghanbaria Matthew J Waller Paul Weston Sara Widaa Pamela Whittaker Ines Barroso Panos Deloukas Christopher G Mathew Jenefer M Blackwell Matthew A Brown Aiden P Corvin Mark I McCarthy Chris C A Spencer Elvira Bramon Aiden P Corvin Michael C O'Donovan Kari Stefansson Edward Scolnick Shaun Purcell Steven A McCarroll Pamela Sklar Christina M Hultman Patrick F Sullivan

Nat Genet 2013 Oct 25;45(10):1150-9. Epub 2013 Aug 25.

1] Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3].

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http://dx.doi.org/10.1038/ng.2742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827979PMC
October 2013

Recovering key biological constituents through sparse representation of gene expression.

Bioinformatics 2011 Mar 21;27(5):655-61. Epub 2011 Jan 21.

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.

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http://dx.doi.org/10.1093/bioinformatics/btr002DOI Listing
March 2011

SPRINT: side-chain prediction inference toolbox for multistate protein design.

Bioinformatics 2010 Oct 4;26(19):2466-7. Epub 2010 Aug 4.

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq445DOI Listing
October 2010

Exposing the co-adaptive potential of protein-protein interfaces through computational sequence design.

Bioinformatics 2010 Sep 2;26(18):2266-72. Epub 2010 Aug 2.

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq412DOI Listing
September 2010

PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations.

Nucleic Acids Res 2010 Jul 5;38(Web Server issue):W84-9. Epub 2010 May 5.

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkq320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896089PMC
July 2010

Tradeoff between stability and multispecificity in the design of promiscuous proteins.

PLoS Comput Biol 2009 Dec 24;5(12):e1000627. Epub 2009 Dec 24.

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.

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http://dx.doi.org/10.1371/journal.pcbi.1000627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790338PMC
December 2009

Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty?

BMC Genomics 2009 Dec 10;10:593. Epub 2009 Dec 10.

The Hebrew University of Jerusalem, Israel.

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http://dx.doi.org/10.1186/1471-2164-10-593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805694PMC
December 2009

Codon usage is associated with the evolutionary age of genes in metazoan genomes.

BMC Evol Biol 2009 Dec 8;9:285. Epub 2009 Dec 8.

Sudarsky Center for Computational Biology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.

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http://dx.doi.org/10.1186/1471-2148-9-285DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799417PMC
December 2009

Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences.

Mol Syst Biol 2009 13;5:311. Epub 2009 Oct 13.

Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.

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http://dx.doi.org/10.1038/msb.2009.71DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779085PMC
January 2010

Design of multispecific protein sequences using probabilistic graphical modeling.

Proteins 2010 Feb;78(3):530-47

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel.

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http://dx.doi.org/10.1002/prot.22575DOI Listing
February 2010

Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space.

Proteins 2009 May;75(3):682-705

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.

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http://dx.doi.org/10.1002/prot.22280DOI Listing
May 2009

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space.

Bioinformatics 2008 Jul;24(13):i41-9

School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.

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http://dx.doi.org/10.1093/bioinformatics/btn174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718652PMC
July 2008

A computational framework to empower probabilistic protein design.

Bioinformatics 2008 Jul;24(13):i214-22

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel.

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http://dx.doi.org/10.1093/bioinformatics/btn168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718646PMC
July 2008

Dead-end elimination for multistate protein design.

J Comput Chem 2007 Oct;28(13):2122-9

School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.

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http://dx.doi.org/10.1002/jcc.20661DOI Listing
October 2007

ProtoNet 4.0: a hierarchical classification of one million protein sequences.

Nucleic Acids Res 2005 Jan;33(Database issue):D216-8

Department of Biological Chemistry, Institute of Life Sciences and School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel.

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http://dx.doi.org/10.1093/nar/gki007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539961PMC
January 2005

A functional hierarchical organization of the protein sequence space.

BMC Bioinformatics 2004 Dec 14;5:196. Epub 2004 Dec 14.

Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.

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http://dx.doi.org/10.1186/1471-2105-5-196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC544566PMC
December 2004

The leader peptide of MMTV Env precursor localizes to the nucleoli in MMTV-derived T cell lymphomas and interacts with nucleolar protein B23.

Virology 2003 Aug;313(1):22-32

Department of Cell and Animal Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.

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http://dx.doi.org/10.1016/s0042-6822(03)00236-8DOI Listing
August 2003