Literature DB >> 26149713

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders.

Neelroop N Parikshak1, Michael J Gandal2, Daniel H Geschwind3.   

Abstract

Genetic and genomic approaches have implicated hundreds of genetic loci in neurodevelopmental disorders and neurodegeneration, but mechanistic understanding continues to lag behind the pace of gene discovery. Understanding the role of specific genetic variants in the brain involves dissecting a functional hierarchy that encompasses molecular pathways, diverse cell types, neural circuits and, ultimately, cognition and behaviour. With a focus on transcriptomics, this Review discusses how high-throughput molecular, integrative and network approaches inform disease biology by placing human genetics in a molecular systems and neurobiological context. We provide a framework for interpreting network biology studies and leveraging big genomics data sets in neurobiology.

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Year:  2015        PMID: 26149713      PMCID: PMC4699316          DOI: 10.1038/nrg3934

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  222 in total

Review 1.  Systems biology in neuroscience: bridging genes to cognition.

Authors:  Seth G N Grant
Journal:  Curr Opin Neurobiol       Date:  2003-10       Impact factor: 6.627

2.  Translational profiling of hypocretin neurons identifies candidate molecules for sleep regulation.

Authors:  Jasbir Dalal; Jee Hoon Roh; Susan E Maloney; Afua Akuffo; Samir Shah; Han Yuan; Brie Wamsley; Wendell B Jones; Cristina de Guzman Strong; Paul A Gray; David M Holtzman; Nathaniel Heintz; Joseph D Dougherty
Journal:  Genes Dev       Date:  2013-02-21       Impact factor: 11.361

Review 3.  The role of de novo mutations in the genetics of autism spectrum disorders.

Authors:  Michael Ronemus; Ivan Iossifov; Dan Levy; Michael Wigler
Journal:  Nat Rev Genet       Date:  2014-01-16       Impact factor: 53.242

Review 4.  Genotype to phenotype via network analysis.

Authors:  Hannah Carter; Matan Hofree; Trey Ideker
Journal:  Curr Opin Genet Dev       Date:  2013-11-14       Impact factor: 5.578

Review 5.  Neuroscience in the era of functional genomics and systems biology.

Authors:  Daniel H Geschwind; Genevieve Konopka
Journal:  Nature       Date:  2009-10-15       Impact factor: 49.962

6.  Exome sequencing supports a de novo mutational paradigm for schizophrenia.

Authors:  Bin Xu; J Louw Roos; Phillip Dexheimer; Braden Boone; Brooks Plummer; Shawn Levy; Joseph A Gogos; Maria Karayiorgou
Journal:  Nat Genet       Date:  2011-08-07       Impact factor: 38.330

7.  How complete are current yeast and human protein-interaction networks?

Authors:  G Traver Hart; Arun K Ramani; Edward M Marcotte
Journal:  Genome Biol       Date:  2006       Impact factor: 13.583

Review 8.  Prioritization of neurodevelopmental disease genes by discovery of new mutations.

Authors:  Alexander Hoischen; Niklas Krumm; Evan E Eichler
Journal:  Nat Neurosci       Date:  2014-05-27       Impact factor: 24.884

9.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

10.  De novo mutations in epileptic encephalopathies.

Authors:  Andrew S Allen; Samuel F Berkovic; Patrick Cossette; Norman Delanty; Dennis Dlugos; Evan E Eichler; Michael P Epstein; Tracy Glauser; David B Goldstein; Yujun Han; Erin L Heinzen; Yuki Hitomi; Katherine B Howell; Michael R Johnson; Ruben Kuzniecky; Daniel H Lowenstein; Yi-Fan Lu; Maura R Z Madou; Anthony G Marson; Heather C Mefford; Sahar Esmaeeli Nieh; Terence J O'Brien; Ruth Ottman; Slavé Petrovski; Annapurna Poduri; Elizabeth K Ruzzo; Ingrid E Scheffer; Elliott H Sherr; Christopher J Yuskaitis; Bassel Abou-Khalil; Brian K Alldredge; Jocelyn F Bautista; Samuel F Berkovic; Alex Boro; Gregory D Cascino; Damian Consalvo; Patricia Crumrine; Orrin Devinsky; Dennis Dlugos; Michael P Epstein; Miguel Fiol; Nathan B Fountain; Jacqueline French; Daniel Friedman; Eric B Geller; Tracy Glauser; Simon Glynn; Sheryl R Haut; Jean Hayward; Sandra L Helmers; Sucheta Joshi; Andres Kanner; Heidi E Kirsch; Robert C Knowlton; Eric H Kossoff; Rachel Kuperman; Ruben Kuzniecky; Daniel H Lowenstein; Shannon M McGuire; Paul V Motika; Edward J Novotny; Ruth Ottman; Juliann M Paolicchi; Jack M Parent; Kristen Park; Annapurna Poduri; Ingrid E Scheffer; Renée A Shellhaas; Elliott H Sherr; Jerry J Shih; Rani Singh; Joseph Sirven; Michael C Smith; Joseph Sullivan; Liu Lin Thio; Anu Venkat; Eileen P G Vining; Gretchen K Von Allmen; Judith L Weisenberg; Peter Widdess-Walsh; Melodie R Winawer
Journal:  Nature       Date:  2013-08-11       Impact factor: 49.962

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  159 in total

Review 1.  Genomics of Immune Diseases and New Therapies.

Authors:  Michael Lenardo; Bernice Lo; Carrie L Lucas
Journal:  Annu Rev Immunol       Date:  2015-12-23       Impact factor: 28.527

2.  Genetics of Gene Expression in the Aging Human Brain Reveal TDP-43 Proteinopathy Pathophysiology.

Authors:  Hyun-Sik Yang; Charles C White; Hans-Ulrich Klein; Lei Yu; Christopher Gaiteri; Yiyi Ma; Daniel Felsky; Sara Mostafavi; Vladislav A Petyuk; Reisa A Sperling; Nilüfer Ertekin-Taner; Julie A Schneider; David A Bennett; Philip L De Jager
Journal:  Neuron       Date:  2020-06-10       Impact factor: 17.173

Review 3.  Brain Connectivity and Neuroimaging of Social Networks in Autism.

Authors:  Ralph-Axel Müller; Inna Fishman
Journal:  Trends Cogn Sci       Date:  2018-10-31       Impact factor: 20.229

Review 4.  Genetics and genomics of psychiatric disease.

Authors:  Daniel H Geschwind; Jonathan Flint
Journal:  Science       Date:  2015-09-24       Impact factor: 47.728

5.  Gene expression shifts in yellow-bellied marmots prior to natal dispersal.

Authors:  Tiffany C Armenta; Steve W Cole; Daniel H Geschwind; Daniel T Blumstein; Robert K Wayne
Journal:  Behav Ecol       Date:  2018-12-17       Impact factor: 2.671

6.  Gene expression imputation across multiple brain regions provides insights into schizophrenia risk.

Authors:  Laura M Huckins; Amanda Dobbyn; Douglas M Ruderfer; Gabriel Hoffman; Weiqing Wang; Antonio F Pardiñas; Veera M Rajagopal; Thomas D Als; Hoang T Nguyen; Kiran Girdhar; James Boocock; Panos Roussos; Menachem Fromer; Robin Kramer; Enrico Domenici; Eric R Gamazon; Shaun Purcell; Ditte Demontis; Anders D Børglum; James T R Walters; Michael C O'Donovan; Patrick Sullivan; Michael J Owen; Bernie Devlin; Solveig K Sieberts; Nancy J Cox; Hae Kyung Im; Pamela Sklar; Eli A Stahl
Journal:  Nat Genet       Date:  2019-03-25       Impact factor: 38.330

Review 7.  The Central Nervous System and the Gut Microbiome.

Authors:  Gil Sharon; Timothy R Sampson; Daniel H Geschwind; Sarkis K Mazmanian
Journal:  Cell       Date:  2016-11-03       Impact factor: 41.582

Review 8.  Shared mechanisms among neurodegenerative diseases: from genetic factors to gene networks.

Authors:  Douglas Arneson; Yong Zhang; Xia Yang; Manikandan Narayanan
Journal:  J Genet       Date:  2018-07       Impact factor: 1.166

9.  Time-varying Hazards Model for Incorporating Irregularly Measured, High-Dimensional Biomarkers.

Authors:  Xiang Li; Quefeng Li; Donglin Zeng; Karen Marder; Jane Paulsen; Yuanjia Wang
Journal:  Stat Sin       Date:  2020-07       Impact factor: 1.261

10.  Brief Report: Genetic Links Between Autism and Suicidal Behavior-A Preliminary Investigation.

Authors:  Emily DiBlasi; Anne V Kirby; Eoin Gaj; Anna R Docherty; Brooks R Keeshin; Amanda V Bakian; Hilary Coon
Journal:  J Autism Dev Disord       Date:  2020-10
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