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David Nix

Research Profile

Genes & Molecular Sequences

Chemicals & Drugs

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Molecular Sequence Data

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Chromatin Immunoprecipitation

Physiology

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Genomics

Anatomy

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Publications

TOP 3
Magdalena E Potok; David A Nix; Timothy J Parnell; Bradley R Cairns
Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern.
Shan-Fu Wu; Haiying Zhang; Saher Sue Hammoud; David A Jones; David A Nix; Magdalena Potok; Bradley R Cairns
DNA methylation profiling in zebrafish.
Noah C Welker; Derek M Pavelec; David A Nix; Thomas F Duchaine; Scott Kennedy; Brenda L Bass
Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs.

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All Publications

2013: Magdalena E Potok; David A Nix; Timothy J Parnell; Bradley R Cairns
Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern.
Cell 2013;153(4):759-72.
2011: Shan-Fu Wu; Haiying Zhang; Saher Sue Hammoud; David A Jones; David A Nix; Magdalena Potok; Bradley R Cairns
DNA methylation profiling in zebrafish.
Methods in cell biology 2011;104():327-39.
2010: Noah C Welker; Derek M Pavelec; David A Nix; Thomas F Duchaine; Scott Kennedy; Brenda L Bass
Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs.
RNA (New York, N.Y.) 2010;16(5):893-903.
2010: David A Nix; Tonya L Di Sera; Brian K Dalley; Brett A Milash; Robert M Cundick; Kevin S Quinn; Samir J Courdy
Next generation tools for genomic data generation, distribution, and visualization.
BMC bioinformatics 2010;11():455.
2009: Saher Sue Hammoud; David A Nix; Haiying Zhang; Jahnvi Purwar; Douglas T Carrell; Bradley R Cairns
Distinctive chromatin in human sperm packages genes for embryo development.
Nature 2009;460(7254):473-8.
2008: Natalie Dutrow; David A Nix; Derick Holt; Brett Milash; Brian Dalley; Erick Westbroek; Timothy J Parnell; Bradley R Cairns
Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping.
Nature genetics 2008;40(8):977-86.
2008: David S Johnson; Wei LI; D Benjamin Gordon; Arindam Bhattacharjee; Bo Curry; Jayati Ghosh; leonardo brizuela; Jason S Carroll; Myles Brown; Paul Flicek; Christoph M Koch; Ian Dunham; Mark Bieda; Xiaoqin Xu; Peggy J Farnham; Philipp Kapranov; David A Nix; Thomas Gingeras; Xinmin Zhang; Heather Holster; Nan Jiang; Roland D Green; Jun S Song; Scott A McCuine; Elizabeth Anton; Loan Nguyen; Nathan D Trinklein; Zhen Ye; Keith Ching; David Hawkins; Bing Ren; Peter C Scacheri; Joel Rozowsky; Alexander Karpikov; Ghia Euskirchen; Sherman Weissman; Mark Gerstein; Michael Snyder; Annie Yang; Zarmik Moqtaderi; Heather A. Hirsch; Hennady P Shulha; Yutao Fu; Zhiping Weng; Kevin Struhl; Richard Myers; Jason Dillon Lieb; X Shirley Liu
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Genome research 2008;18(3):393-403.
2008: Xiao-yong Li; Stewart MacArthur; Richard Bourgon; David A Nix; Daniel A Pollard; Venky N Iyer; Aaron Hechmer; Lisa Simirenko; Mark Stapleton; Cris L Luengo Hendriks; Hou Cheng Chu; Nobuo Ogawa; William Inwood; Victor Sementchenko; Amy Beaton; Richard Weiszmann; Susan E Celniker; David W Knowles; Tom Gingeras; Terence P Speed; Michael B Eisen; Mark D Biggin
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
PLoS biology 2008;6(2):e27.
2008: David A Nix; Samir J Courdy; Kenneth M Boucher
Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks.
BMC bioinformatics 2008;9():523.
2007: Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason Dillon Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A. Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jorg Hackermuller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; piero carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos Antonarakis; Yutao Fu; Eric Green; Ulaş Karaöz; Adam Siepel; James TAYLOR; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Richmond Todd; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Goncalo Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature 2007;447(7146):799-816.
2007: Philipp Kapranov; Jill Cheng; Sujit Dike; David A Nix; Radharani Duttagupta; Aarron T Willingham; Peter F Stadler; Jana Hertel; Jorg Hackermuller; Ivo L Hofacker; Ian Bell; Evelyn Cheung; Jorg Drenkow; Erica Dumais; Sandeep Patel; Gregg Helt; Madhavan Ganesh; Srinka Ghosh; Antonio Piccolboni; Victor Sementchenko; Hari Tammana; Thomas Gingeras
RNA maps reveal new RNA classes and a possible function for pervasive transcription.
Science (New York, N.Y.) 2007;316(5830):1484-8.
2006: Alan M Moses; Daniel A Pollard; David A Nix; Venky N Iyer; Xiao-Yong Li; Mark D Biggin; Michael B Eisen
Large-scale turnover of functional transcription factor binding sites in Drosophila.
PLoS computational biology 2006;2(10):e130.
2006: Frédéric Biemar; David A Nix; Jessica Piel; Brant Peterson; Matthew Ronshaugen; Victor Sementchenko; Ian Bell; J Robert Manak; Michael S Levine
Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(34):12763-8.
2006: Yuri B Schwartz; Tatyana G Kahn; David A Nix; Xiao-Yong Li; Richard Bourgon; Mark Biggin; Vincenzo Pirrotta
Genome-wide analysis of Polycomb targets in Drosophila melanogaster.
Nature genetics 2006;38(6):700-5.
2006: Aarron T Willingham; Sujit Dike; Jill Cheng; J Robert Manak; Ian Bell; Evelyn Cheung; Jorg Drenkow; E Dumais; Radharani Duttagupta; Madhavan Ganesh; Srinka Ghosh; Gregg Helt; David A Nix; Antonio Piccolboni; Victor Sementchenko; Hari Tammana; Philipp Kapranov; Thomas Gingeras
Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes.
Cold Spring Harbor symposia on quantitative biology 2006;71():101-10.
2006: Derek Chiang; David A Nix; Ryan K Shultzaberger; Audrey P Gasch; Michael B Eisen
Flexible promoter architecture requirements for coactivator recruitment.
BMC molecular biology 2006;7():16.
2005: David A Nix; Michael B Eisen
GATA: a graphic alignment tool for comparative sequence analysis.
BMC bioinformatics 2005;6():9.
2003: Kenneth R Henry; Kathleen D'Hondt; Ji Suk Chang; David A Nix; M Jamie T V Cope; Clarence S M Chan; David G Drubin; Sandra K Lemmon
The actin-regulating kinase Prk1p negatively regulates Scd5p, a suppressor of clathrin deficiency, in actin organization and endocytosis.
Current biology : CB 2003;13(17):1564-9.
2003: Laura M Hoffman; David A Nix; Beverly Benson; Ray Boot-Hanford; Erika Elisabet Gustafsson; Colin Jamora; A Sheila Menzies; Keow Lin Goh; Christopher C Jensen; Frank B Gertler; Elaine Fuchs; Reinhard Fässler; Mary C Beckerle
Targeted disruption of the murine zyxin gene.
Molecular and cellular biology 2003;23(1):70-9.
2001: David A Nix; J Fradelizi; S Bockholt; B Menichi; Daniel Louvard; Evelyne Friederich; Mary C Beckerle
Targeting of zyxin to sites of actin membrane interaction and to the nucleus.
The Journal of biological chemistry 2001;276(37):34759-67.
2000: Kristi L Neufeld; David A Nix; H Bogerd; Y Kang; Mary C Beckerle; B R Cullen; Raymond White
Adenomatous polyposis coli protein contains two nuclear export signals and shuttles between the nucleus and cytoplasm.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(22):12085-90.
1997: David A Nix; Mary C Beckerle
Nuclear-cytoplasmic shuttling of the focal contact protein, zyxin: a potential mechanism for communication between sites of cell adhesion and the nucleus.
The Journal of cell biology 1997;138(5):1139-47.