Ruibang Luo

发表

Restricted Boltzmann Machine and its Potential to Better Predict Cancer Survival

Ruibang Luo, Wen Ma, Tak-Wah Lam, 2018 .

ChromSeg: Two-Stage Framework for Overlapping Chromosome Segmentation and Reconstruction

Ruibang Luo, Xu Cao, Fangzhou Lan, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Database.bio: a Web Application for Interpreting Human Variations

Tak Wah Lam, Ruibang Luo, Min Ou, 2015, Bioinform..

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

Siu-Ming Yiu, Hao Zhang, Zhenyu Li, 2012, Bioinform..

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

Michael C. Schatz, Ruibang Luo, Steven L. Salzberg, 2017, bioRxiv.

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

Feng Xu, Weixin Wang, Tak Wah Lam, 2014, Bioinform..

MC-Explorer: Analyzing and Visualizing Motif-Cliques on Large Networks

Kevin Chen-Chuan Chang, Xuemin Lin, Reynold Cheng, 2020, 2020 IEEE 36th International Conference on Data Engineering (ICDE).

AC-DIAMOND: Accelerating Protein Alignment via Better SIMD Parallelization and Space-Efficient Indexing

Yifan Zhang, Tak Wah Lam, Hing-Fung Ting, 2016, IWBBIO.

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

Michael C. Schatz, Ruibang Luo, Fritz J. Sedlazeck, 2017, Computational and structural biotechnology journal.

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

Tak Wah Lam, Hing-Fung Ting, Henry C. M. Leung, 2017, BMC Bioinformatics.

Correction: SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

Siu-Ming Yiu, Haoxiang Lin, Thomas Wong, 2013, PLoS ONE.

Clair: Exploring the limit of using a deep neural network on pileup data for germline variant calling

Ruibang Luo, Chi-Man Liu, Tak-Wah Lam, 2019, bioRxiv.

RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature

Ye Wu, Tak Wah Lam, Hing-Fung Ting, 2019, RECOMB.

AC‐DIAMOND v1: accelerating large‐scale DNA‐protein alignment

Yifan Zhang, Tak Wah Lam, Hing-Fung Ting, 2018, Bioinform..

MegaPath: Low-Similarity Pathogen Detection from Metagenomic NGS Data (Extended Abstract)

Tak Wah Lam, Hing-Fung Ting, Yan Xin, 2018, 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

Michael C. Schatz, Ruibang Luo, Tak-Wah Lam, 2018, bioRxiv.

Exploring the limit of using a deep neural network on pileup data for germline variant calling

Ruibang Luo, Chi-Man Liu, Tak-Wah Lam, 2020, Nature Machine Intelligence.

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

Hing-Fung Ting, Ruibang Luo, Chi-Man Liu, 2016, Methods.

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)

Jun Wang, Shaoliang Peng, Tak Wah Lam, 2014, BMC Bioinformatics.

Inflammasome activation in airway epithelial cells after multi-walled carbon nanotube exposure mediates a profibrotic response in lung fibroblasts

Chang Yu, Wen Wang, Xiaoming Zheng, 2014, Particle and Fibre Toxicology.

MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics

Henry C. M. Leung, Yan Xin, Ruibang Luo, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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

Yifan Zhang, Henry C. M. Leung, Ruibang Luo, 2020, iScience.

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

Siu-Ming Yiu, Tak Wah Lam, Ruiqiang Li, 2012, Bioinform..

Efficient SNP-sensitive alignment and database-assisted SNP calling for low coverage samples

Siu-Ming Yiu, Tak Wah Lam, Ruiqiang Li, 2012, BCB.

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

Xun Xu, Jun Wang, Shanlin Liu, 2013, Bioinform..

From peer-reviewed to peer-reproduced: a role for data standards, models and computational workflows in scholarly publishing

M. S. Avila-Garcia, Rajaram Kaliyaperumal, Eelke van der Horst, 2014, bioRxiv.

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

Inanç Birol, Dominique Lavenier, Hamidreza Chitsaz, 2013, GigaScience.

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Jian Wang, Xiangke Liao, Yong Liu, 2012, GigaScience.

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

Lap-Kei Lee, Ruibang Luo, Chi-Man Liu, 2014, PeerJ.

Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads

Hing-Fung Ting, Ruibang Luo, Ye Wu, 2020, BCB.

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

Ruibang Luo, Tak-Wah Lam, Michael C Schatz, 2019, Nature Communications.

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

Kunihiko Sadakane, Tak Wah Lam, Ruibang Luo, 2014, Bioinform..

GPU-Accelerated BWT Construction for Large Collection of Short Reads pdf

Tak Wah Lam, Ruibang Luo, Chi-Man Liu, 2014, ArXiv.

Generalized radiograph representation learning via cross-supervision between images and free-text radiology reports

Ruibang Luo, Yizhou Yu, Hong-Yu Zhou, 2022, Nature Machine Intelligence.

BioNumQA-BERT: answering biomedical questions using numerical facts with a deep language representation model

Tak Wah Lam, Hing-Fung Ting, Ruibang Luo, 2021, BCB.

Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era

Dake Zhang, Ruibang Luo, Shoudong Zhang, 2021, Innovation.

RENET2: High-Performance Full-text Gene-Disease Relation Extraction with Iterative Training Data Expansion

Hing-Fung Ting, Ruibang Luo, Tak-Wah Lam, 2021, bioRxiv.

The oyster genome reveals stress adaptation and complexity of shell formation

Qiang Wang, Ye Yin, Wenjing Fu, 2012, Nature.

Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants

Michael C. Schatz, Ruibang Luo, Tak-Wah Lam, 2018, bioRxiv.

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

Shuai Li, Ruibang Luo, Honghe Sun, 2015, Plant Cell.

Building the sequence map of the human pan-genome

Lars Bolund, Ruiqiang Li, Xuan Zhu, 2010, Nature Biotechnology.

De novo assembly of a haplotype-resolved human genome

Jian Wang, Xun Xu, Lars Bolund, 2015, Nature Biotechnology.

Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073

Ken Chen, Joshua M. Korn, Afidalina Tumian, 2010 .

Title 16 GT : A fast and sensitive variant caller using a 16-genotypeprobabilistic model

Michael C. Schatz, Ruibang Luo, Steven L. Salzberg, 2017 .

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

Michael C. Schatz, Ruibang Luo, Steven L. Salzberg, 2017 .

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

M. S. Avila-Garcia, Rajaram Kaliyaperumal, Marco Roos, 2015, PloS one.

Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Siu-Ming Yiu, Xiangke Liao, Shaoliang Peng, 2015, GigaScience.