Hai Fang - University of Bristol - Dr

Hai Fang

University of Bristol

Dr

Bristol | UK

Additional Specialties: Bioinformatics

ORCID logohttps://orcid.org/0000-0003-3961-8572

Hai Fang - University of Bristol - Dr

Hai Fang

Introduction

Primary Affiliation: University of Bristol - Bristol , UK

Additional Specialties:

Education

Jan 2003 - Jan 2009
Shanghai Institutes for Biological Sciences
Ph.D.

Experience

Jan 2010 - Jan 2015
University of Bristol
Jan 2015
University of Oxford

Wellcome Trust Centre for Human Genetics

Publications

37Publications

1352Reads

2Profile Views

1148PubMed Central Citations

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Authors:
Naihui Zhou Yuxiang Jiang Timothy R Bergquist Alexandra J Lee Balint Z Kacsoh Alex W Crocker Kimberley A Lewis George Georghiou Huy N Nguyen Md Nafiz Hamid Larry Davis Tunca Dogan Volkan Atalay Ahmet S Rifaioglu Alperen Dalkıran Rengul Cetin Atalay Chengxin Zhang Rebecca L Hurto Peter L Freddolino Yang Zhang Prajwal Bhat Fran Supek José M Fernández Branislava Gemovic Vladimir R Perovic Radoslav S Davidović Neven Sumonja Nevena Veljkovic Ehsaneddin Asgari Mohammad R K Mofrad Giuseppe Profiti Castrense Savojardo Pier Luigi Martelli Rita Casadio Florian Boecker Heiko Schoof Indika Kahanda Natalie Thurlby Alice C McHardy Alexandre Renaux Rabie Saidi Julian Gough Alex A Freitas Magdalena Antczak Fabio Fabris Mark N Wass Jie Hou Jianlin Cheng Zheng Wang Alfonso E Romero Alberto Paccanaro Haixuan Yang Tatyana Goldberg Chenguang Zhao Liisa Holm Petri Törönen Alan J Medlar Elaine Zosa Itamar Borukhov Ilya Novikov Angela Wilkins Olivier Lichtarge Po-Han Chi Wei-Cheng Tseng Michal Linial Peter W Rose Christophe Dessimoz Vedrana Vidulin Saso Dzeroski Ian Sillitoe Sayoni Das Jonathan Gill Lees David T Jones Cen Wan Domenico Cozzetto Rui Fa Mateo Torres Alex Warwick Vesztrocy Jose Manuel Rodriguez Michael L Tress Marco Frasca Marco Notaro Giuliano Grossi Alessandro Petrini Matteo Re Giorgio Valentini Marco Mesiti Daniel B Roche Jonas Reeb David W Ritchie Sabeur Aridhi Seyed Ziaeddin Alborzi Marie-Dominique Devignes Da Chen Emily Koo Richard Bonneau Vladimir Gligorijević Meet Barot Hai Fang Stefano Toppo Enrico Lavezzo Marco Falda Michele Berselli Silvio C E Tosatto Marco Carraro Damiano Piovesan Hafeez Ur Rehman Qizhong Mao Shanshan Zhang Slobodan Vucetic Gage S Black Dane Jo Erica Suh Jonathan B Dayton Dallas J Larsen Ashton R Omdahl Liam J McGuffin Danielle A Brackenridge Patricia C Babbitt Jeffrey M Yunes Paolo Fontana Feng Zhang Shanfeng Zhu Ronghui You Zihan Zhang Suyang Dai Shuwei Yao Weidong Tian Renzhi Cao Caleb Chandler Miguel Amezola Devon Johnson Jia-Ming Chang Wen-Hung Liao Yi-Wei Liu Stefano Pascarelli Yotam Frank Robert Hoehndorf Maxat Kulmanov Imane Boudellioua Gianfranco Politano Stefano Di Carlo Alfredo Benso Kai Hakala Filip Ginter Farrokh Mehryary Suwisa Kaewphan Jari Björne Hans Moen Martti E E Tolvanen Tapio Salakoski Daisuke Kihara Aashish Jain Tomislav Šmuc Adrian Altenhoff Asa Ben-Hur Burkhard Rost Steven E Brenner Christine A Orengo Constance J Jeffery Giovanni Bosco Deborah A Hogan Maria J Martin Claire O'Donovan Sean D Mooney Casey S Greene Predrag Radivojac Iddo Friedberg

Genome Biol 2019 11 19;20(1):244. Epub 2019 Nov 19.

Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.

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http://dx.doi.org/10.1186/s13059-019-1835-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930PMC
November 2019

The association between endometriosis and autoimmune diseases: a systematic review and meta-analysis.

Hum Reprod Update 2019 Jul;25(4):486-503

Oxford Endometriosis CaRe Centre, Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1093/humupd/dmz014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6601386PMC
July 2019
6 Reads
10.165 Impact Factor

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits.

Genome Med 2016 12 13;8(1):129. Epub 2016 Dec 13.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.

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http://dx.doi.org/10.1186/s13073-016-0384-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5154134PMC
December 2016
141 Reads
4 Citations
4.942 Impact Factor

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016
153 Reads
37 Citations

Evolution of the Calcium-Based Intracellular Signaling System.

Genome Biol Evol 2016 07 14;8(7):2118-32. Epub 2016 Jul 14.

Department of Computer Sciences, University of Bristol, United Kingdom.

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http://dx.doi.org/10.1093/gbe/evw139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987107PMC
July 2016
11 Reads
3 Citations
4.230 Impact Factor

Reactive oxygen species in eradicating acute myeloid leukemic stem cells.

Stem Cell Investig 2014 7;1:13. Epub 2014 Jun 7.

1 State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China ; 2 Pediatric department, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China.

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http://dx.doi.org/10.3978/j.issn.2306-9759.2014.04.03DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4923509PMC
June 2016
4 Reads
5 Citations

A derived network-based interferon-related signature of human macrophages responding to Mycobacterium tuberculosis.

Biomed Res Int 2014 31;2014:713071. Epub 2014 Aug 31.

Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai 201508, China ; Key Laboratory of Medical Molecular Virology of MOE/MOH, Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China.

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http://dx.doi.org/10.1155/2014/713071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209755PMC
May 2016
13 Reads
1 Citation

A predictive computational framework for direct reprogramming between human cell types.

Nat Genet 2016 Mar 18;48(3):331-5. Epub 2016 Jan 18.

Department of Computer Science, University of Bristol, Bristol, UK.

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http://dx.doi.org/10.1038/ng.3487DOI Listing
March 2016
76 Reads
35 Citations
29.352 Impact Factor

Genome-wide studies identify a novel interplay between AML1 and AML1/ETO in t(8;21) acute myeloid leukemia.

Blood 2016 Jan 6;127(2):233-42. Epub 2015 Nov 6.

State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; and Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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http://dx.doi.org/10.1182/blood-2015-03-626671DOI Listing
January 2016
54 Reads
6 Citations
10.452 Impact Factor

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.

Biochimie 2015 Dec 15;119:269-77. Epub 2015 May 15.

Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. Electronic address:

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http://dx.doi.org/10.1016/j.biochi.2015.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679076PMC
December 2015
16 Reads
2 Citations
2.963 Impact Factor

A proteome quality index.

Environ Microbiol 2015 Jan 22;17(1):4-9. Epub 2014 Oct 22.

Department of Computer Science, University of Bristol, Bristol, UK; Bristol Centre for Complexity Sciences, University of Bristol, Bristol, UK.

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http://dx.doi.org/10.1111/1462-2920.12622DOI Listing
January 2015
12 Reads
1 Citation
6.201 Impact Factor

The SUPERFAMILY 1.75 database in 2014: a doubling of data.

Nucleic Acids Res 2015 Jan 20;43(Database issue):D227-33. Epub 2014 Nov 20.

Computer Science, University of Bristol, Bristol, BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gku1041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383889PMC
January 2015
13 Reads
27 Citations
9.112 Impact Factor

dcGOR: an R package for analysing ontologies and protein domain annotations.

Authors:
Hai Fang

PLoS Comput Biol 2014 Oct 30;10(10):e1003929. Epub 2014 Oct 30.

Computational Genomics Group, Department of Computer Science, University of Bristol, Bristol, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214615PMC
October 2014
15 Reads
3 Citations

The 'dnet' approach promotes emerging research on cancer patient survival.

Genome Med 2014 26;6(8):64. Epub 2014 Aug 26.

Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol, BS8 1UB UK.

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http://dx.doi.org/10.1186/s13073-014-0064-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160547PMC
September 2014
56 Reads
15 Citations
4.942 Impact Factor

Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy.

Nat Commun 2014 Sep 3;5:4741. Epub 2014 Sep 3.

School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK.

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http://dx.doi.org/10.1038/ncomms5741DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167604PMC
September 2014
52 Reads
29 Citations
10.742 Impact Factor

The evolution of human cells in terms of protein innovation.

Mol Biol Evol 2014 Jun 1;31(6):1364-74. Epub 2014 Apr 1.

Department of Computer Science, University of Bristol, Bristol, United KingdomMedical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom

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http://dx.doi.org/10.1093/molbev/mst139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032124PMC
June 2014
7 Reads
6 Citations
9.110 Impact Factor

A daily-updated tree of (sequenced) life as a reference for genome research.

Sci Rep 2013 ;3:2015

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1038/srep02015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6504836PMC
June 2014
17 Reads
21 Citations
5.080 Impact Factor

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014
86 Reads
468 Citations
42.351 Impact Factor

supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map.

Biochem Biophys Res Commun 2014 Jan 2;443(1):285-9. Epub 2013 Dec 2.

Computational Genomics Group, Department of Computer Science, University of Bristol, Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1016/j.bbrc.2013.11.103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905187PMC
January 2014
2 Reads
10 Citations
2.300 Impact Factor

Endoplasmic reticulum stress-mediated apoptosis in imatinib-resistant leukemic K562-r cells triggered by AMN107 combined with arsenic trioxide.

Exp Biol Med (Maywood) 2013 Aug 24;238(8):932-42. Epub 2013 Jul 24.

Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.

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http://dx.doi.org/10.1177/1535370213492689DOI Listing
August 2013
22 Reads
3 Citations

A domain-centric solution to functional genomics via dcGO Predictor.

BMC Bioinformatics 2013 28;14 Suppl 3:S9. Epub 2013 Feb 28.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1186/1471-2105-14-S3-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584936PMC
July 2013
7 Reads
11 Citations
2.580 Impact Factor

A disease-drug-phenotype matrix inferred by walking on a functional domain network.

Mol Biosyst 2013 Jul 5;9(7):1686-96. Epub 2013 Mar 5.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1039/c3mb25495jDOI Listing
July 2013
4 Reads
6 Citations

Preferential eradication of acute myelogenous leukemia stem cells by fenretinide.

Proc Natl Acad Sci U S A 2013 Apr 19;110(14):5606-11. Epub 2013 Mar 19.

State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.

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http://dx.doi.org/10.1073/pnas.1302352110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619353PMC
April 2013
82 Reads
17 Citations
9.810 Impact Factor

A large-scale evaluation of computational protein function prediction.

Authors:
Predrag Radivojac Wyatt T Clark Tal Ronnen Oron Alexandra M Schnoes Tobias Wittkop Artem Sokolov Kiley Graim Christopher Funk Karin Verspoor Asa Ben-Hur Gaurav Pandey Jeffrey M Yunes Ameet S Talwalkar Susanna Repo Michael L Souza Damiano Piovesan Rita Casadio Zheng Wang Jianlin Cheng Hai Fang Julian Gough Patrik Koskinen Petri Törönen Jussi Nokso-Koivisto Liisa Holm Domenico Cozzetto Daniel W A Buchan Kevin Bryson David T Jones Bhakti Limaye Harshal Inamdar Avik Datta Sunitha K Manjari Rajendra Joshi Meghana Chitale Daisuke Kihara Andreas M Lisewski Serkan Erdin Eric Venner Olivier Lichtarge Robert Rentzsch Haixuan Yang Alfonso E Romero Prajwal Bhat Alberto Paccanaro Tobias Hamp Rebecca Kaßner Stefan Seemayer Esmeralda Vicedo Christian Schaefer Dominik Achten Florian Auer Ariane Boehm Tatjana Braun Maximilian Hecht Mark Heron Peter Hönigschmid Thomas A Hopf Stefanie Kaufmann Michael Kiening Denis Krompass Cedric Landerer Yannick Mahlich Manfred Roos Jari Björne Tapio Salakoski Andrew Wong Hagit Shatkay Fanny Gatzmann Ingolf Sommer Mark N Wass Michael J E Sternberg Nives Škunca Fran Supek Matko Bošnjak Panče Panov Sašo Džeroski Tomislav Šmuc Yiannis A I Kourmpetis Aalt D J van Dijk Cajo J F ter Braak Yuanpeng Zhou Qingtian Gong Xinran Dong Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Barbara Di Camillo Stefano Toppo Liang Lan Nemanja Djuric Yuhong Guo Slobodan Vucetic Amos Bairoch Michal Linial Patricia C Babbitt Steven E Brenner Christine Orengo Burkhard Rost Sean D Mooney Iddo Friedberg

Nat Methods 2013 Mar 27;10(3):221-7. Epub 2013 Jan 27.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1038/nmeth.2340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584181PMC
March 2013
176 Reads
215 Citations
32.072 Impact Factor

DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more.

Nucleic Acids Res 2013 Jan 17;41(Database issue):D536-44. Epub 2012 Nov 17.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gks1080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531119PMC
January 2013
3 Reads
31 Citations
9.112 Impact Factor

An interferon-related signature in the transcriptional core response of human macrophages to Mycobacterium tuberculosis infection.

PLoS One 2012 4;7(6):e38367. Epub 2012 Jun 4.

State Key Laboratory of Medical Genomics and Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038367PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366933PMC
October 2012
17 Reads
12 Citations
3.234 Impact Factor

A topology-preserving selection and clustering approach to multidimensional biological data.

OMICS 2011 Jul-Aug;15(7-8):483-94. Epub 2011 Jun 23.

State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (SJTU-SM), People's Republic of China.

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http://dx.doi.org/10.1089/omi.2010.0066DOI Listing
November 2011
8 Reads
3 Citations
2.362 Impact Factor

An organogenesis network-based comparative transcriptome analysis for understanding early human development in vivo and in vitro.

BMC Syst Biol 2011 Jul 6;5:108. Epub 2011 Jul 6.

State Key Laboratory of Medical Genomics, Sino-French Research Center for Life Sciences and Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Ruijin Rd, II, Shanghai 200025, China.

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http://dx.doi.org/10.1186/1752-0509-5-108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141417PMC
July 2011
9 Reads
1 Citation
2.440 Impact Factor

SUPERFAMILY 1.75 including a domain-centric gene ontology method.

Nucleic Acids Res 2011 Jan 9;39(Database issue):D427-34. Epub 2010 Nov 9.

Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.

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http://dx.doi.org/10.1093/nar/gkq1130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013712PMC
January 2011
7 Reads
60 Citations
9.112 Impact Factor

p21-activated kinase 3 is overexpressed in thymic neuroendocrine tumors (carcinoids) with ectopic ACTH syndrome and participates in cell migration.

Endocrine 2010 Aug 4;38(1):38-47. Epub 2010 May 4.

Shanghai Key Laboratory for Endocrine Tumors, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.

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http://dx.doi.org/10.1007/s12020-010-9324-6DOI Listing
August 2010
8 Reads
7 Citations
3.530 Impact Factor

Transcriptome analysis of early organogenesis in human embryos.

Dev Cell 2010 Jul;19(1):174-84

Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.

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