Yi-Chieh Wu

Yi-Chieh Wu

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Yi-Chieh Wu

Yi-Chieh Wu

Publications by authors named "Yi-Chieh Wu"

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22Publications

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Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.

BMC Bioinformatics 2017 Jun 5;18(1):292. Epub 2017 Jun 5.

Department of Computer Science, Harvey Mudd College, Claremont, 91711, California, USA.

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http://dx.doi.org/10.1186/s12859-017-1701-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5460407PMC
June 2017

Doxorubicin Activates Hepatitis B Virus Replication by Elevation of p21 (Waf1/Cip1) and C/EBPα Expression.

PLoS One 2015 29;10(6):e0131743. Epub 2015 Jun 29.

Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan; Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131743PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4486450PMC
April 2016

Improved gene tree error correction in the presence of horizontal gene transfer.

Bioinformatics 2015 Apr 5;31(8):1211-8. Epub 2014 Dec 5.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge and Broad Institute, Cambridge, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4393519PMC
April 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Authors:
Daniel E Neafsey Robert M Waterhouse Mohammad R Abai Sergey S Aganezov Max A Alekseyev James E Allen James Amon Bruno Arcà Peter Arensburger Gleb Artemov Lauren A Assour Hamidreza Basseri Aaron Berlin Bruce W Birren Stephanie A Blandin Andrew I Brockman Thomas R Burkot Austin Burt Clara S Chan Cedric Chauve Joanna C Chiu Mikkel Christensen Carlo Costantini Victoria L M Davidson Elena Deligianni Tania Dottorini Vicky Dritsou Stacey B Gabriel Wamdaogo M Guelbeogo Andrew B Hall Mira V Han Thaung Hlaing Daniel S T Hughes Adam M Jenkins Xiaofang Jiang Irwin Jungreis Evdoxia G Kakani Maryam Kamali Petri Kemppainen Ryan C Kennedy Ioannis K Kirmitzoglou Lizette L Koekemoer Njoroge Laban Nicholas Langridge Mara K N Lawniczak Manolis Lirakis Neil F Lobo Ernesto Lowy Robert M MacCallum Chunhong Mao Gareth Maslen Charles Mbogo Jenny McCarthy Kristin Michel Sara N Mitchell Wendy Moore Katherine A Murphy Anastasia N Naumenko Tony Nolan Eva M Novoa Samantha O'Loughlin Chioma Oringanje Mohammad A Oshaghi Nazzy Pakpour Philippos A Papathanos Ashley N Peery Michael Povelones Anil Prakash David P Price Ashok Rajaraman Lisa J Reimer David C Rinker Antonis Rokas Tanya L Russell N'Fale Sagnon Maria V Sharakhova Terrance Shea Felipe A Simão Frederic Simard Michel A Slotman Pradya Somboon Vladimir Stegniy Claudio J Struchiner Gregg W C Thomas Marta Tojo Pantelis Topalis José M C Tubio Maria F Unger John Vontas Catherine Walton Craig S Wilding Judith H Willis Yi-Chieh Wu Guiyun Yan Evgeny M Zdobnov Xiaofan Zhou Flaminia Catteruccia George K Christophides Frank H Collins Robert S Cornman Andrea Crisanti Martin J Donnelly Scott J Emrich Michael C Fontaine William Gelbart Matthew W Hahn Immo A Hansen Paul I Howell Fotis C Kafatos Manolis Kellis Daniel Lawson Christos Louis Shirley Luckhart Marc A T Muskavitch José M Ribeiro Michael A Riehle Igor V Sharakhov Zhijian Tu Laurence J Zwiebel Nora J Besansky

Science 2015 Jan 27;347(6217):1258522. Epub 2014 Nov 27.

Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Sciences Building, Notre Dame, IN 46556, USA.

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http://dx.doi.org/10.1126/science.1258522DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380271PMC
January 2015

Highly conserved residues in the helical domain of dengue virus type 1 precursor membrane protein are involved in assembly, precursor membrane (prM) protein cleavage, and entry.

J Biol Chem 2014 Nov 17;289(48):33149-60. Epub 2014 Oct 17.

From the Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813 and

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http://dx.doi.org/10.1074/jbc.M114.610428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246076PMC
November 2014

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Pareto-optimal phylogenetic tree reconciliation.

Bioinformatics 2014 Jun;30(12):i87-95

Department of Computer Science, Harvey Mudd College, Claremont, CA 91711, Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 and Broad Institute, Cambridge, MA 02142, USADepartment of Computer Science, Harvey Mudd College, Claremont, CA 91711, Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 and Broad Institute, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu289DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058917PMC
June 2014

Analysis of cross-reactive antibodies recognizing the fusion loop of envelope protein and correlation with neutralizing antibody titers in Nicaraguan dengue cases.

PLoS Negl Trop Dis 2013 19;7(9):e2451. Epub 2013 Sep 19.

Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America.

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http://dx.doi.org/10.1371/journal.pntd.0002451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777924PMC
March 2014

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.

Genome Res 2014 Mar 5;24(3):475-86. Epub 2013 Dec 5.

Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;

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http://genome.cshlp.org/cgi/doi/10.1101/gr.161968.113
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http://dx.doi.org/10.1101/gr.161968.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941112PMC
March 2014

TreeFix: statistically informed gene tree error correction using species trees.

Syst Biol 2013 Jan 4;62(1):110-20. Epub 2012 Sep 4.

Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/sysbio/sys076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526801PMC
January 2013

Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny.

Mol Biol Evol 2012 Feb 7;29(2):689-705. Epub 2011 Sep 7.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Massachusetts, USA.

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http://dx.doi.org/10.1093/molbev/msr222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258039PMC
February 2012

Dynamics of HBV cccDNA expression and transcription in different cell growth phase.

J Biomed Sci 2011 Dec 30;18:96. Epub 2011 Dec 30.

Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.

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http://dx.doi.org/10.1186/1423-0127-18-96DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262020PMC
December 2011

HNF-4α determines hepatic differentiation of human mesenchymal stem cells from bone marrow.

World J Gastroenterol 2010 Oct;16(40):5092-103

Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 350, Taiwan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965287PMC
http://dx.doi.org/10.3748/wjg.v16.i40.5092DOI Listing
October 2010

Scutellariae radix suppresses hepatitis B virus production in human hepatoma cells.

Front Biosci (Elite Ed) 2010 Jun 1;2:1538-47. Epub 2010 Jun 1.

Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan, ROC.

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June 2010