Publications by authors named "Chia-Lin Wei"

97Publications

Sox2-Dependent 3D Chromatin Interactomes in Transcription, Neural Stem Cell Proliferation and Neurodevelopmental Diseases.

J Exp Neurosci 2019 7;13:1179069519868224. Epub 2019 Aug 7.

Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy.

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http://dx.doi.org/10.1177/1179069519868224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686325PMC
August 2019

Ultra-long Read Sequencing for Whole Genomic DNA Analysis.

J Vis Exp 2019 03 15(145). Epub 2019 Mar 15.

Genome Technologies, Jackson Laboratory for Genomic Medicine;

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http://dx.doi.org/10.3791/58954DOI Listing
March 2019

Culture-independent analysis of liver abscess using nanopore sequencing.

PLoS One 2018 9;13(1):e0190853. Epub 2018 Jan 9.

Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190853PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760015PMC
February 2018

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.

Cell 2015 Dec 10;163(7):1611-27. Epub 2015 Dec 10.

The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA; National Key Laboratory of Crop Genetic Improvement, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA. Electronic address:

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http://www.cell.com/cell/pdf/S0092-8674(15)01504-4.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S009286741501504
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http://dx.doi.org/10.1016/j.cell.2015.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734140PMC
December 2015

Coherence analysis discriminates between retroviral integration patterns in CD34(+) cells transduced under differing clinical trial conditions.

Mol Ther Methods Clin Dev 2015 29;2:15015. Epub 2015 Apr 29.

Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead , Westmead, Australia ; The University of Sydney, Discipline of Paediatrics and Child Health , Westmead, Australia.

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http://dx.doi.org/10.1038/mtm.2015.15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445430PMC
June 2015

A genome-wide map of adeno-associated virus-mediated human gene targeting.

Nat Struct Mol Biol 2014 Nov 5;21(11):969-75. Epub 2014 Oct 5.

1] Department of Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Biochemistry, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nsmb.2895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405182PMC
November 2014

Marine algae and land plants share conserved phytochrome signaling systems.

Proc Natl Acad Sci U S A 2014 Nov 29;111(44):15827-32. Epub 2014 Sep 29.

Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039; Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON, Canada M5G 1Z8

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226090PMC
http://dx.doi.org/10.1073/pnas.1416751111DOI Listing
November 2014

Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles.

Nature 2014 Jul 9;511(7510):483-7. Epub 2014 Jul 9.

1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2] Comprehensive Cancer Center Mainfranken, University of Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany [3].

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http://dx.doi.org/10.1038/nature13473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879323PMC
July 2014

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

Sci Rep 2014 Mar 31;4:4519. Epub 2014 Mar 31.

1] Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA [2] Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1038/srep04519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3970191PMC
March 2014

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.

Nature 2013 Dec 10;504(7479):306-310. Epub 2013 Nov 10.

Sequencing Technology Group, Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California 94598, USA.

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http://dx.doi.org/10.1038/nature12716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954713PMC
December 2013

Genome-wide distribution of DNA methylation at single-nucleotide resolution.

Prog Mol Biol Transl Sci 2011 ;101:459-77

Genome Technology and Biology, Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1016/B978-0-12-387685-0.00015-9DOI Listing
August 2011

Multiplex parallel pair-end-ditag sequencing approaches in system biology.

Wiley Interdiscip Rev Syst Biol Med 2010 Mar-Apr;2(2):224-234

Genome Technology & Biology Group, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672.

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http://dx.doi.org/10.1002/wsbm.40DOI Listing
February 2011

A signal-noise model for significance analysis of ChIP-seq with negative control.

Bioinformatics 2010 May 5;26(9):1199-204. Epub 2010 Apr 5.

Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btq128DOI Listing
May 2010

Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages.

Immunity 2010 Mar 4;32(3):317-28. Epub 2010 Mar 4.

Department of Experimental Oncology, European Institute of Oncology (IEO), IFOM-IEO Campus, Via Adamello 16, Milan, Italy.

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http://dx.doi.org/10.1016/j.immuni.2010.02.008DOI Listing
March 2010

Dynamic changes in the human methylome during differentiation.

Genome Res 2010 Mar 4;20(3):320-31. Epub 2010 Feb 4.

UCSD Medical Center, Department of Reproductive Medicine, San Diego, California 92103, USA.

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http://dx.doi.org/10.1101/gr.101907.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840979PMC
March 2010

Chromatin interaction analysis using paired-end tag sequencing.

Curr Protoc Mol Biol 2010 Jan;Chapter 21:Unit 21.15.1-25

Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.

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http://dx.doi.org/10.1002/0471142727.mb2115s89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924956PMC
January 2010

ChIP'ing the mammalian genome: technical advances and insights into functional elements.

Genome Med 2009 Sep 23;1(9):89. Epub 2009 Sep 23.

Genome Technology and Biology Group, Genome Institute of Singapore, 138672 Singapore.

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http://dx.doi.org/10.1186/gm89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768996PMC
September 2009

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses.

Genome Res 2009 Apr;19(4):521-32

Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore.

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http://dx.doi.org/10.1101/gr.074906.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807531PMC
April 2009

Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages.

Cell Stem Cell 2008 Nov 18;3(5):543-54. Epub 2008 Sep 18.

Stem Cell and Developmental Biology, Genome Institute of Singapore, 138672 Singapore.

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http://dx.doi.org/10.1016/j.stem.2008.08.004DOI Listing
November 2008

Evolution of the mammalian transcription factor binding repertoire via transposable elements.

Genome Res 2008 Nov 5;18(11):1752-62. Epub 2008 Aug 5.

Computational and Mathematical Biology, Genome Institute of Singapore, Singapore 138672, Singapore.

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http://dx.doi.org/10.1101/gr.080663.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577865PMC
November 2008

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.

Bioinformatics 2008 Oct 29;24(20):2344-9. Epub 2008 Jul 29.

Computational & Mathematical Biology Group, Genome Institute of Singapore, 138672 Singapore.

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http://dx.doi.org/10.1093/bioinformatics/btn402DOI Listing
October 2008

Tackling the epigenome in the pluripotent stem cells.

J Genet Genomics 2008 Jul;35(7):403-12

Genome Technology and Biology Group, Genome Institute of Singapore, 138672, Singapore.

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http://dx.doi.org/10.1016/S1673-8527(08)60058-2DOI Listing
July 2008

Computational analysis and modeling of genome-scale avidity distribution of transcription factor binding sites in chip-pet experiments.

Genome Inform 2007 ;19:83-94

Genome Institute of Singapore, Biopolis street, 60, 138672 Singapore.

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July 2008

The use of multiple displacement amplification to amplify complex DNA libraries.

Nucleic Acids Res 2008 Mar 19;36(5):e32. Epub 2008 Feb 19.

Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore.

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http://dx.doi.org/10.1093/nar/gkn074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275127PMC
March 2008

Paired-end diTagging for transcriptome and genome analysis.

Curr Protoc Mol Biol 2007 Jul;Chapter 21:Unit 21.12

Genome Institute of Singapore, Singapore.

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http://dx.doi.org/10.1002/0471142727.mb2112s79DOI Listing
July 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R 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 D 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 Jörg Hackermüller 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 M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M 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 Todd A Richmond 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 Gonçalo R 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 M 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
June 2007

Global mapping of c-Myc binding sites and target gene networks in human B cells.

Proc Natl Acad Sci U S A 2006 Nov 8;103(47):17834-9. Epub 2006 Nov 8.

Department of Medicine and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0604129103
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http://dx.doi.org/10.1073/pnas.0604129103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635161PMC
November 2006

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

BMC Bioinformatics 2006 Aug 25;7:390. Epub 2006 Aug 25.

Information and Mathematical Sciences Group, Genome Institute of Singapore, 60 Biopolis Street, Genome #02-01, 138672, Singapore.

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http://dx.doi.org/10.1186/1471-2105-7-390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1564156PMC
August 2006

Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.

Nat Methods 2005 Feb 9;2(2):105-11. Epub 2005 Jan 9.

Genome Institute of Singapore, 60 Biopolis Street, Genome 02-01, Singapore 138672.

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http://dx.doi.org/10.1038/nmeth733DOI Listing
February 2005

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

Authors:
Daniela S Gerhard Lukas Wagner Elise A Feingold Carolyn M Shenmen Lynette H Grouse Greg Schuler Steven L Klein Susan Old Rebekah Rasooly Peter Good Mark Guyer Allison M Peck Jeffery G Derge David Lipman Francis S Collins Wonhee Jang Steven Sherry Mike Feolo Leonie Misquitta Eduardo Lee Kirill Rotmistrovsky Susan F Greenhut Carl F Schaefer Kenneth Buetow Tom I Bonner David Haussler Jim Kent Mark Kiekhaus Terry Furey Michael Brent Christa Prange Kirsten Schreiber Nicole Shapiro Narayan K Bhat Ralph F Hopkins Florence Hsie Tom Driscoll M Bento Soares Tom L Casavant Todd E Scheetz Michael J Brown-stein Ted B Usdin Shiraki Toshiyuki Piero Carninci Yulan Piao Dawood B Dudekula Minoru S H Ko Koichi Kawakami Yutaka Suzuki Sumio Sugano C E Gruber M R Smith Blake Simmons Troy Moore Richard Waterman Stephen L Johnson Yijun Ruan Chia Lin Wei S Mathavan Preethi H Gunaratne Jiaqian Wu Angela M Garcia Stephen W Hulyk Edwin Fuh Ye Yuan Anna Sneed Carla Kowis Anne Hodgson Donna M Muzny John McPherson Richard A Gibbs Jessica Fahey Erin Helton Mark Ketteman Anuradha Madan Stephanie Rodrigues Amy Sanchez Michelle Whiting Anup Madari Alice C Young Keith D Wetherby Steven J Granite Peggy N Kwong Charles P Brinkley Russell L Pearson Gerard G Bouffard Robert W Blakesly Eric D Green Mark C Dickson Alex C Rodriguez Jane Grimwood Jeremy Schmutz Richard M Myers Yaron S N Butterfield Malachi Griffith Obi L Griffith Martin I Krzywinski Nancy Liao Ryan Morin Ryan Morrin Diana Palmquist Anca S Petrescu Ursula Skalska Duane E Smailus Jeff M Stott Angelique Schnerch Jacqueline E Schein Steven J M Jones Robert A Holt Agnes Baross Marco A Marra Sandra Clifton Kathryn A Makowski Stephanie Bosak Joel Malek

Genome Res 2004 Oct;14(10B):2121-7

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http://dx.doi.org/10.1101/gr.2596504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528928PMC
October 2004

5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation.

Proc Natl Acad Sci U S A 2004 Aug 22;101(32):11701-6. Epub 2004 Jul 22.

Genome Institute of Singapore, 60 Biopolis Street, Genome 02-01, Singapore 138672.

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http://dx.doi.org/10.1073/pnas.0403514101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC511040PMC
August 2004

2001 GSAC meeting summary: from genome to transcriptome to proteome. Genome Sequencing and Analysis Conference.

OMICS 2002 ;6(1):131-4

Large Scale Biology Corporation, Vacaville, California 95688, USA.

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http://www.liebertpub.com/doi/10.1089/15362310252780889
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http://dx.doi.org/10.1089/15362310252780889DOI Listing
July 2002