Literature DB >> 19805447

An overview of recent developments in genomics and associated statistical methods.

Peter J Bickel1, James B Brown, Haiyan Huang, Qunhua Li.   

Abstract

The landscape of genomics has changed drastically in the last two decades. Increasingly inexpensive sequencing has shifted the primary focus from the acquisition of biological sequences to the study of biological function. Assays have been developed to study many intricacies of biological systems, and publicly available databases have given rise to integrative analyses that combine information from many sources to draw complex conclusions. Such research was the focus of the recent workshop at the Isaac Newton Institute, 'High dimensional statistics in biology'. Many computational methods from modern genomics and related disciplines were presented and discussed. Using, as much as possible, the material from these talks, we give an overview of modern genomics: from the essential assays that make data-generation possible, to the statistical methods that yield meaningful inference. We point to current analytical challenges, where novel methods, or novel applications of extant methods, are presently needed.

Mesh:

Year:  2009        PMID: 19805447     DOI: 10.1098/rsta.2009.0164

Source DB:  PubMed          Journal:  Philos Trans A Math Phys Eng Sci        ISSN: 1364-503X            Impact factor:   4.226


  11 in total

1.  Advanced molecular biologic techniques in toxicologic disease.

Authors:  Jeanine Ward; Gyongyi Szabo; David McManus; Edward Boyer
Journal:  J Med Toxicol       Date:  2011-12

2.  Statistical challenges of high-dimensional data.

Authors:  Iain M Johnstone; D Michael Titterington
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2009-11-13       Impact factor: 4.226

3.  Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer.

Authors:  Catherine M Phelan; Karoline B Kuchenbaecker; Jonathan P Tyrer; Siddhartha P Kar; Kate Lawrenson; Stacey J Winham; Joe Dennis; Ailith Pirie; Marjorie J Riggan; Ganna Chornokur; Madalene A Earp; Paulo C Lyra; Janet M Lee; Simon Coetzee; Jonathan Beesley; Lesley McGuffog; Penny Soucy; Ed Dicks; Andrew Lee; Daniel Barrowdale; Julie Lecarpentier; Goska Leslie; Cora M Aalfs; Katja K H Aben; Marcia Adams; Julian Adlard; Irene L Andrulis; Hoda Anton-Culver; Natalia Antonenkova; Gerasimos Aravantinos; Norbert Arnold; Banu K Arun; Brita Arver; Jacopo Azzollini; Judith Balmaña; Susana N Banerjee; Laure Barjhoux; Rosa B Barkardottir; Yukie Bean; Matthias W Beckmann; Alicia Beeghly-Fadiel; Javier Benitez; Marina Bermisheva; Marcus Q Bernardini; Michael J Birrer; Line Bjorge; Amanda Black; Kenneth Blankstein; Marinus J Blok; Clara Bodelon; Natalia Bogdanova; Anders Bojesen; Bernardo Bonanni; Åke Borg; Angela R Bradbury; James D Brenton; Carole Brewer; Louise Brinton; Per Broberg; Angela Brooks-Wilson; Fiona Bruinsma; Joan Brunet; Bruno Buecher; Ralf Butzow; Saundra S Buys; Trinidad Caldes; Maria A Caligo; Ian Campbell; Rikki Cannioto; Michael E Carney; Terence Cescon; Salina B Chan; Jenny Chang-Claude; Stephen Chanock; Xiao Qing Chen; Yoke-Eng Chiew; Jocelyne Chiquette; Wendy K Chung; Kathleen B M Claes; Thomas Conner; Linda S Cook; Jackie Cook; Daniel W Cramer; Julie M Cunningham; Aimee A D'Aloisio; Mary B Daly; Francesca Damiola; Sakaeva Dina Damirovna; Agnieszka Dansonka-Mieszkowska; Fanny Dao; Rosemarie Davidson; Anna DeFazio; Capucine Delnatte; Kimberly F Doheny; Orland Diez; Yuan Chun Ding; Jennifer Anne Doherty; Susan M Domchek; Cecilia M Dorfling; Thilo Dörk; Laure Dossus; Mercedes Duran; Matthias Dürst; Bernd Dworniczak; Diana Eccles; Todd Edwards; Ros Eeles; Ursula Eilber; Bent Ejlertsen; Arif B Ekici; Steve Ellis; Mingajeva Elvira; Kevin H Eng; Christoph Engel; D Gareth Evans; Peter A Fasching; Sarah Ferguson; Sandra Fert Ferrer; James M Flanagan; Zachary C Fogarty; Renée T Fortner; Florentia Fostira; William D Foulkes; George Fountzilas; Brooke L Fridley; Tara M Friebel; Eitan Friedman; Debra Frost; Patricia A Ganz; Judy Garber; María J García; Vanesa Garcia-Barberan; Andrea Gehrig; Aleksandra Gentry-Maharaj; Anne-Marie Gerdes; Graham G Giles; Rosalind Glasspool; Gord Glendon; Andrew K Godwin; David E Goldgar; Teodora Goranova; Martin Gore; Mark H Greene; Jacek Gronwald; Stephen Gruber; Eric Hahnen; Christopher A Haiman; Niclas Håkansson; Ute Hamann; Thomas V O Hansen; Patricia A Harrington; Holly R Harris; Jan Hauke; Alexander Hein; Alex Henderson; Michelle A T Hildebrandt; Peter Hillemanns; Shirley Hodgson; Claus K Høgdall; Estrid Høgdall; Frans B L Hogervorst; Helene Holland; Maartje J Hooning; Karen Hosking; Ruea-Yea Huang; Peter J Hulick; Jillian Hung; David J Hunter; David G Huntsman; Tomasz Huzarski; Evgeny N Imyanitov; Claudine Isaacs; Edwin S Iversen; Louise Izatt; Angel Izquierdo; Anna Jakubowska; Paul James; Ramunas Janavicius; Mats Jernetz; Allan Jensen; Uffe Birk Jensen; Esther M John; Sharon Johnatty; Michael E Jones; Päivi Kannisto; Beth Y Karlan; Anthony Karnezis; Karin Kast; Catherine J Kennedy; Elza Khusnutdinova; Lambertus A Kiemeney; Johanna I Kiiski; Sung-Won Kim; Susanne K Kjaer; Martin Köbel; Reidun K Kopperud; Torben A Kruse; Jolanta Kupryjanczyk; Ava Kwong; Yael Laitman; Diether Lambrechts; Nerea Larrañaga; Melissa C Larson; Conxi Lazaro; Nhu D Le; Loic Le Marchand; Jong Won Lee; Shashikant B Lele; Arto Leminen; Dominique Leroux; Jenny Lester; Fabienne Lesueur; Douglas A Levine; Dong Liang; Clemens Liebrich; Jenna Lilyquist; Loren Lipworth; Jolanta Lissowska; Karen H Lu; Jan Lubinński; Craig Luccarini; Lene Lundvall; Phuong L Mai; Gustavo Mendoza-Fandiño; Siranoush Manoukian; Leon F A G Massuger; Taymaa May; Sylvie Mazoyer; Jessica N McAlpine; Valerie McGuire; John R McLaughlin; Iain McNeish; Hanne Meijers-Heijboer; Alfons Meindl; Usha Menon; Arjen R Mensenkamp; Melissa A Merritt; Roger L Milne; Gillian Mitchell; Francesmary Modugno; Joanna Moes-Sosnowska; Melissa Moffitt; Marco Montagna; Kirsten B Moysich; Anna Marie Mulligan; Jacob Musinsky; Katherine L Nathanson; Lotte Nedergaard; Roberta B Ness; Susan L Neuhausen; Heli Nevanlinna; Dieter Niederacher; Robert L Nussbaum; Kunle Odunsi; Edith Olah; Olufunmilayo I Olopade; Håkan Olsson; Curtis Olswold; David M O'Malley; Kai-Ren Ong; N Charlotte Onland-Moret; Nicholas Orr; Sandra Orsulic; Ana Osorio; Domenico Palli; Laura Papi; Tjoung-Won Park-Simon; James Paul; Celeste L Pearce; Inge Søkilde Pedersen; Petra H M Peeters; Bernard Peissel; Ana Peixoto; Tanja Pejovic; Liisa M Pelttari; Jennifer B Permuth; Paolo Peterlongo; Lidia Pezzani; Georg Pfeiler; Kelly-Anne Phillips; Marion Piedmonte; Malcolm C Pike; Anna M Piskorz; Samantha R Poblete; Timea Pocza; Elizabeth M Poole; Bruce Poppe; Mary E Porteous; Fabienne Prieur; Darya Prokofyeva; Elizabeth Pugh; Miquel Angel Pujana; Pascal Pujol; Paolo Radice; Johanna Rantala; Christine Rappaport-Fuerhauser; Gad Rennert; Kerstin Rhiem; Patricia Rice; Andrea Richardson; Mark Robson; Gustavo C Rodriguez; Cristina Rodríguez-Antona; Jane Romm; Matti A Rookus; Mary Anne Rossing; Joseph H Rothstein; Anja Rudolph; Ingo B Runnebaum; Helga B Salvesen; Dale P Sandler; Minouk J Schoemaker; Leigha Senter; V Wendy Setiawan; Gianluca Severi; Priyanka Sharma; Tameka Shelford; Nadeem Siddiqui; Lucy E Side; Weiva Sieh; Christian F Singer; Hagay Sobol; Honglin Song; Melissa C Southey; Amanda B Spurdle; Zsofia Stadler; Doris Steinemann; Dominique Stoppa-Lyonnet; Lara E Sucheston-Campbell; Grzegorz Sukiennicki; Rebecca Sutphen; Christian Sutter; Anthony J Swerdlow; Csilla I Szabo; Lukasz Szafron; Yen Y Tan; Jack A Taylor; Muy-Kheng Tea; Manuel R Teixeira; Soo-Hwang Teo; Kathryn L Terry; Pamela J Thompson; Liv Cecilie Vestrheim Thomsen; Darcy L Thull; Laima Tihomirova; Anna V Tinker; Marc Tischkowitz; Silvia Tognazzo; Amanda Ewart Toland; Alicia Tone; Britton Trabert; Ruth C Travis; Antonia Trichopoulou; Nadine Tung; Shelley S Tworoger; Anne M van Altena; David Van Den Berg; Annemarie H van der Hout; Rob B van der Luijt; Mattias Van Heetvelde; Els Van Nieuwenhuysen; Elizabeth J van Rensburg; Adriaan Vanderstichele; Raymonda Varon-Mateeva; Ana Vega; Digna Velez Edwards; Ignace Vergote; Robert A Vierkant; Joseph Vijai; Athanassios Vratimos; Lisa Walker; Christine Walsh; Dorothea Wand; Shan Wang-Gohrke; Barbara Wappenschmidt; Penelope M Webb; Clarice R Weinberg; Jeffrey N Weitzel; Nicolas Wentzensen; Alice S Whittemore; Juul T Wijnen; Lynne R Wilkens; Alicja Wolk; Michelle Woo; Xifeng Wu; Anna H Wu; Hannah Yang; Drakoulis Yannoukakos; Argyrios Ziogas; Kristin K Zorn; Steven A Narod; Douglas F Easton; Christopher I Amos; Joellen M Schildkraut; Susan J Ramus; Laura Ottini; Marc T Goodman; Sue K Park; Linda E Kelemen; Harvey A Risch; Mads Thomassen; Kenneth Offit; Jacques Simard; Rita Katharina Schmutzler; Dennis Hazelett; Alvaro N Monteiro; Fergus J Couch; Andrew Berchuck; Georgia Chenevix-Trench; Ellen L Goode; Thomas A Sellers; Simon A Gayther; Antonis C Antoniou; Paul D P Pharoah
Journal:  Nat Genet       Date:  2017-03-27       Impact factor: 38.330

Review 4.  A review of metabolomics approaches and their application in identifying causal pathways of childhood asthma.

Authors:  Kedir N Turi; Lindsey Romick-Rosendale; Kelli K Ryckman; Tina V Hartert
Journal:  J Allergy Clin Immunol       Date:  2017-05-04       Impact factor: 10.793

5.  Challenges of Big Data Analysis.

Authors:  Jianqing Fan; Fang Han; Han Liu
Journal:  Natl Sci Rev       Date:  2014-06       Impact factor: 17.275

6.  A pharmacogenomic study on the pharmacokinetics of tacrolimus in healthy subjects using the DMETTM Plus platform.

Authors:  Y Choi; F Jiang; H An; H J Park; J H Choi; H Lee
Journal:  Pharmacogenomics J       Date:  2016-02-16       Impact factor: 3.550

7.  VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in Genome-Wide Association Studies: applied to Alzheimer's Disease.

Authors:  Qiao Liu; Chen Chen; Annie Gao; Hang Hang Tong; Lei Xie
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2017-12-18

8.  Exploring massive, genome scale datasets with the GenometriCorr package.

Authors:  Alexander Favorov; Loris Mularoni; Leslie M Cope; Yulia Medvedeva; Andrey A Mironov; Vsevolod J Makeev; Sarah J Wheelan
Journal:  PLoS Comput Biol       Date:  2012-05-31       Impact factor: 4.475

9.  Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.

Authors:  Yuri V Kravatsky; Vladimir R Chechetkin; Nikolai A Tchurikov; Galina I Kravatskaya
Journal:  DNA Res       Date:  2015-01-27       Impact factor: 4.458

Review 10.  Discovery of biomarkers in rare diseases: innovative approaches by predictive and personalized medicine.

Authors:  Basri Gülbakan; Rıza Köksal Özgül; Ayşe Yüzbaşıoğlu; Matthias Kohl; Hans-Peter Deigner; Meral Özgüç
Journal:  EPMA J       Date:  2016-12-08       Impact factor: 6.543

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