Publications by authors named "Ruibang Luo"

36Publications

Identification of Cooperative Gene Regulation Among Transcription Factors, LncRNAs, and MicroRNAs in Diabetic Nephropathy Progression.

Front Genet 2020 1;11:1008. Epub 2020 Sep 1.

Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.

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http://dx.doi.org/10.3389/fgene.2020.01008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7490338PMC
September 2020

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning.

iScience 2020 May 1;23(5):101128. Epub 2020 May 1.

Department of Computer Science, The University of Hong Kong, Hong Kong, China. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2020.101128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229283PMC
May 2020

A multi-task convolutional deep neural network for variant calling in single molecule sequencing.

Nat Commun 2019 03 1;10(1):998. Epub 2019 Mar 1.

Department of Computer Science, Johns Hopkins University, Baltimore, 21218, MD, USA.

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http://dx.doi.org/10.1038/s41467-019-09025-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397153PMC
March 2019

AC-DIAMOND v1: accelerating large-scale DNA-protein alignment.

Bioinformatics 2018 11;34(21):3744-3746

Department of Computer Science, University of Hong Kong, Hong Kong.

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https://academic.oup.com/bioinformatics/article/34/21/3744/4
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http://dx.doi.org/10.1093/bioinformatics/bty391DOI Listing
November 2018

Transcriptome Analysis of Acute Phase Liver Graft Injury in Liver Transplantation.

Biomedicines 2018 Apr 6;6(2). Epub 2018 Apr 6.

Department of Surgery, The University of Hong Kong, Hong Kong, China.

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http://dx.doi.org/10.3390/biomedicines6020041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027418PMC
April 2018

LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning.

Comput Struct Biotechnol J 2017 9;15:478-484. Epub 2017 Nov 9.

Department of Computer Science, Johns Hopkins University, United States.

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http://dx.doi.org/10.1016/j.csbj.2017.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5711661PMC
November 2017

MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs.

BMC Bioinformatics 2017 Oct 16;18(Suppl 12):408. Epub 2017 Oct 16.

Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong.

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http://dx.doi.org/10.1186/s12859-017-1825-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5657035PMC
October 2017

First Draft Genome Sequence of the Pathogenic Fungus (Formerly ).

G3 (Bethesda) 2017 11 6;7(11):3831-3836. Epub 2017 Nov 6.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

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http://dx.doi.org/10.1534/g3.117.300107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677167PMC
November 2017

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model.

Gigascience 2017 07;6(7):1-4

Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.

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http://dx.doi.org/10.1093/gigascience/gix045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570013PMC
July 2017

Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/β-catenin axis in hepatocellular carcinoma.

Cell Oncol (Dordr) 2017 Oct 19;40(5):443-456. Epub 2017 Jun 19.

Department of Surgery, The University of Hong Kong, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong.

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http://dx.doi.org/10.1007/s13402-017-0332-xDOI Listing
October 2017

BASE: a practical de novo assembler for large genomes using long NGS reads.

BMC Genomics 2016 08 31;17 Suppl 5:499. Epub 2016 Aug 31.

Bioinformatics Algorithms Research Laboratory, Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong.

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http://dx.doi.org/10.1186/s12864-016-2829-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009518PMC
August 2016

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.

Methods 2016 06 21;102:3-11. Epub 2016 Mar 21.

Department of Computer Science, University of Hong Kong, Hong Kong; L3 Bioinformatics Limited, Hong Kong. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.02.020DOI Listing
June 2016

database.bio: a web application for interpreting human variations.

Bioinformatics 2015 Dec 26;31(24):4035-7. Epub 2015 Aug 26.

HKU-BGI Bioinformatics Algorithms Research Laboratory and Department of Computer Science, University of Hong Kong, L3 Bioinformatics Limited.

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http://dx.doi.org/10.1093/bioinformatics/btv500DOI Listing
December 2015

De novo assembly of a haplotype-resolved human genome.

Nat Biotechnol 2015 Jun 25;33(6):617-22. Epub 2015 May 25.

1] BGI-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia. [4] Macau University of Science and Technology, Taipa, Macau, China. [5] Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China.

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http://dx.doi.org/10.1038/nbt.3200DOI Listing
June 2015

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.

Plant Cell 2015 Jun 22;27(6):1595-604. Epub 2015 May 22.

Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China

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http://dx.doi.org/10.1105/tpc.114.135848DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498199PMC
June 2015

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

Bioinformatics 2015 May 20;31(10):1674-6. Epub 2015 Jan 20.

HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan HKU-BGI Bioinformatics Algorithms Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, L3 Bioinformatics Limited, Hong Kong and National Institute of Informatics, Chiyoda-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btv033DOI Listing
May 2015

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.

PeerJ 2014 3;2:e421. Epub 2014 Jun 3.

HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong.

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http://dx.doi.org/10.7717/peerj.421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060040PMC
June 2014

FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data.

Bioinformatics 2014 Sep 14;30(17):2498-500. Epub 2014 May 14.

Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, Department of Pathology and Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, Department of Pathology and Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China Department of Biochemistry, LKS Faculty of Medicine, Hong Kong SAR, Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, Guangdong 518057, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, Department of Computer Science, Department of Pathology and Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.

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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/content/early/2014/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btu338DOI Listing
September 2014

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

Bioinformatics 2014 Jun 13;30(12):1660-6. Epub 2014 Feb 13.

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi ArabiaSchool of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawha

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http://dx.doi.org/10.1093/bioinformatics/btu077DOI Listing
June 2014

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner.

PLoS One 2013 31;8(5):e65632. Epub 2013 May 31.

HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065632PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669295PMC
January 2014

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly.

Bioinformatics 2012 Nov 8;28(22):2870-4. Epub 2012 Oct 8.

HKU-BGI BAL-Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong.

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http://dx.doi.org/10.1093/bioinformatics/bts563DOI Listing
November 2012

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression.

BMC Genomics 2012 Jul 2;13:300. Epub 2012 Jul 2.

CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.

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http://dx.doi.org/10.1186/1471-2164-13-300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447678PMC
July 2012

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.

Bioinformatics 2012 Mar 28;28(6):878-9. Epub 2012 Jan 28.

Department of Computer Science, The University of Hong Kong, Hong Kong, China.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts061DOI Listing
March 2012

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard Yann Joly Steven M Jones Arek Kasprzyk Mark Lathrop Nuria López-Bigas B F Francis Ouellette Paul T Spellman Jon W Teague Gilles Thomas Alfonso Valencia Teruhiko Yoshida Karen L Kennedy Myles Axton Stephanie O M Dyke P Andrew Futreal Daniela S Gerhard Chris Gunter Mark Guyer Thomas J Hudson John D McPherson Linda J Miller Brad Ozenberger Kenna M Shaw Arek Kasprzyk Lincoln D Stein Junjun Zhang Syed A Haider Jianxin Wang Christina K Yung Anthony Cros Anthony Cross Yong Liang Saravanamuttu Gnaneshan Jonathan Guberman Jack Hsu Martin Bobrow Don R C Chalmers Karl W Hasel Yann Joly Terry S H Kaan Karen L Kennedy Bartha M Knoppers William W Lowrance Tohru Masui Pilar Nicolás Emmanuelle Rial-Sebbag Laura Lyman Rodriguez Catherine Vergely Teruhiko Yoshida Sean M Grimmond Andrew V Biankin David D L Bowtell Nicole Cloonan Anna deFazio James R Eshleman Dariush Etemadmoghadam Brooke B Gardiner Brooke A Gardiner James G Kench Aldo Scarpa Robert L Sutherland Margaret A Tempero Nicola J Waddell Peter J Wilson John D McPherson Steve Gallinger Ming-Sound Tsao Patricia A Shaw Gloria M Petersen Debabrata Mukhopadhyay Lynda Chin Ronald A DePinho Sarah Thayer Lakshmi Muthuswamy Kamran Shazand Timothy Beck Michelle Sam Lee Timms Vanessa Ballin Youyong Lu Jiafu Ji Xiuqing Zhang Feng Chen Xueda Hu Guangyu Zhou Qi Yang Geng Tian Lianhai Zhang Xiaofang Xing Xianghong Li Zhenggang Zhu Yingyan Yu Jun Yu Huanming Yang Mark Lathrop Jörg Tost Paul Brennan Ivana Holcatova David Zaridze Alvis Brazma Lars Egevard Egor Prokhortchouk Rosamonde Elizabeth Banks Mathias Uhlén Anne Cambon-Thomsen Juris Viksna Fredrik Ponten Konstantin Skryabin Michael R Stratton P Andrew Futreal Ewan Birney Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Sancha Martin Jorge S Reis-Filho Andrea L Richardson Christos Sotiriou Hendrik G Stunnenberg Giles Thoms Marc van de Vijver Laura van't Veer Fabien Calvo Daniel Birnbaum Hélène Blanche Pascal Boucher Sandrine Boyault Christian Chabannon Ivo Gut Jocelyne D Masson-Jacquemier Mark Lathrop Iris Pauporté Xavier Pivot Anne Vincent-Salomon Eric Tabone Charles Theillet Gilles Thomas Jörg Tost Isabelle Treilleux Fabien Calvo Paulette Bioulac-Sage Bruno Clément Thomas Decaens Françoise Degos Dominique Franco Ivo Gut Marta Gut Simon Heath Mark Lathrop Didier Samuel Gilles Thomas Jessica Zucman-Rossi Peter Lichter Roland Eils Benedikt Brors Jan O Korbel Andrey Korshunov Pablo Landgraf Hans Lehrach Stefan Pfister Bernhard Radlwimmer Guido Reifenberger Michael D Taylor Christof von Kalle Partha P Majumder Rajiv Sarin T S Rao M K Bhan Aldo Scarpa Paolo Pederzoli Rita A Lawlor Massimo Delledonne Alberto Bardelli Andrew V Biankin Sean M Grimmond Thomas Gress David Klimstra Giuseppe Zamboni Tatsuhiro Shibata Yusuke Nakamura Hidewaki Nakagawa Jun Kusada Tatsuhiko Tsunoda Satoru Miyano Hiroyuki Aburatani Kazuto Kato Akihiro Fujimoto Teruhiko Yoshida Elias Campo Carlos López-Otín Xavier Estivill Roderic Guigó Silvia de Sanjosé Miguel A Piris Emili Montserrat Marcos González-Díaz Xose S Puente Pedro Jares Alfonso Valencia Heinz Himmelbauer Heinz Himmelbaue Victor Quesada Silvia Bea Michael R Stratton P Andrew Futreal Peter J Campbell Anne Vincent-Salomon Andrea L Richardson Jorge S Reis-Filho Marc van de Vijver Gilles Thomas Jocelyne D Masson-Jacquemier Samuel Aparicio Ake Borg Anne-Lise Børresen-Dale Carlos Caldas John A Foekens Hendrik G Stunnenberg Laura van't Veer Douglas F Easton Paul T Spellman Sancha Martin Anna D Barker Lynda Chin Francis S Collins Carolyn C Compton Martin L Ferguson Daniela S Gerhard Gad Getz Chris Gunter Alan Guttmacher Mark Guyer D Neil Hayes Eric S Lander Brad Ozenberger Robert Penny Jane Peterson Chris Sander Kenna M Shaw Terence P Speed Paul T Spellman Joseph G Vockley David A Wheeler Richard K Wilson Thomas J Hudson Lynda Chin Bartha M Knoppers Eric S Lander Peter Lichter Lincoln D Stein Michael R Stratton Warwick Anderson Anna D Barker Cindy Bell Martin Bobrow Wylie Burke Francis S Collins Carolyn C Compton Ronald A DePinho Douglas F Easton P Andrew Futreal Daniela S Gerhard Anthony R Green Mark Guyer Stanley R Hamilton Tim J Hubbard Olli P Kallioniemi Karen L Kennedy Timothy J Ley Edison T Liu Youyong Lu Partha Majumder Marco Marra Brad Ozenberger Jane Peterson Alan J Schafer Paul T Spellman Hendrik G Stunnenberg Brandon J Wainwright Richard K Wilson Huanming Yang

Nature 2010 Apr;464(7291):993-8

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http://dx.doi.org/10.1038/nature08987DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010