Zhong Wang

发表

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

M. Gerstein, Michael P. Snyder, U. Nagalakshmi, 2008, Science.

RNA-Seq: a revolutionary tool for transcriptomics

M. Gerstein, M. Snyder, Zhong Wang, 2009, Nature Reviews Genetics.

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

Philip D. Blood, Daniel A. Cuevas, Matthew Z. DeMaere, 2017, Nature Methods.

Next-generation transcriptome assembly

Zhong Wang, Jeffrey Martin, 2011, Nature Reviews Genetics.

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

S. Tringe, S. Luo, G. Schroth, 2011, Science.

Close association of RNA polymerase II and many transcription factors with Pol III genes

M. Gerstein, K. Struhl, M. Snyder, 2010, Proceedings of the National Academy of Sciences.

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

Dongwan D. Kang, Zhong Wang, J. Froula, 2015, PeerJ.

using RNA-seq Candida albicans fungal pathogen Comprehensive annotation of the transcriptome of the human Material

G. Sherlock, Michael P. Snyder, G. Euskirchen, 2010 .

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.

G. Sherlock, Michael P. Snyder, G. Euskirchen, 2010, Genome research.

A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome

Dongwan D. Kang, Derek N. Macklin, Zhong Wang, 2019 .

A robust statistical framework for reconstructing genomes from metagenomic data

Dongwan D. Kang, Zhong Wang, J. Froula, 2014, bioRxiv.

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

G. Sherlock, Michael P. Snyder, Tao Zhang, 2010, BMC Genomics.

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Dongwan D. Kang, Zhong Wang, R. Egan, 2019 .

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

Xiandong Meng, Feng Chen, Dongwan D. Kang, 2015, PloS one.

De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

Axel Visel, Zhong Wang, A. Visel, 2013, BMC Genomics.

Widespread polycistronic transcripts in mushroom-forming fungi revealed by single-molecule long-read mRNA sequencing

Xiandong Meng, Feng Chen, Dongwan D. Kang, 2014, bioRxiv.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Dominique Lavenier, Alexander Sczyrba, Mihai Pop, 2017, bioRxiv.

Lawrence Berkeley National Laboratory Recent Work Title Combining Hadoop with MPI to Solve Metagenomics Problems that are both Data-and Compute-intensive Permalink

Zhong Wang, Xiandong Meng, Hong An, 2017 .

Sequence analysis SpaRC : scalable sequence clustering using Apache Spark

M. Mascagni, Zhong Wang, E. Tseng, 2019 .

Lawrence Berkeley National Laboratory Recent Work Title SpaRC : scalable sequence clustering using Apache Spark

M. Mascagni, Zhong Wang, E. Tseng, 2018 .

Persistent memory as an effective alternative to random access memory in metagenome assembly

Zhong Wang, R. Egan, H. Ho, 2022, bioRxiv.

Combining Hadoop with MPI to Solve Metagenomics Problems that are both Data- and Compute-intensive

Zhong Wang, Xiandong Meng, Han Lin, 2018, International Journal of Parallel Programming.

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

Zhong Wang, Peter I. Frazier, Rob Egan, 2013, Bioinform..

Hybrid error correction and de novo assembly of single-molecule sequencing reads

M. Schatz, S. Koren, A. Phillippy, 2012, Nature Biotechnology.

Computational Strategies for Scalable Genomics Analysis

Lizhen Shi, Zhong Wang, Zhong Wang, 2019, Genes.

Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis

Lisa M. Chung, M. Gerstein, Michael P. Snyder, 2013, Viruses.

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

Xiandong Meng, Feng Chen, James Schnable, 2014, Scientific Reports.

Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome

Dongwan D. Kang, A. Visel, S. Deutsch, 2014, Genome research.

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Feng Li, Hong An, Dongwan D. Kang, 2019, PeerJ.

Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave

A. Visel, T. Tschaplinski, Zhong Wang, 2018, BMC Genomics.

Reconstructing single genomes from complex microbial communities

Zhong Wang, Dongwan D. Kang, Edward M. Rubin, 2016, it Inf. Technol..

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data

Kai Wang, Zhong Wang, Karan Bhatia, 2013, Bioinform..

MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequence

Jeff Froula, Dongwan D. Kang, Rob Egan, 2014 .

Supplementary Data for " Hybrid Error Correction and De Novo Assembly of Single-molecule Sequencing Reads " Online Resources

M. Schatz, S. Koren, A. Phillippy, 2022 .

SpaRC: Scalable Sequence Clustering using Apache Spark

Xiandong Meng, Zhong Wang, Michael Mascagni, 2018, bioRxiv.

Identification of novel biomass‐degrading enzymes from genomic dark matter: Populating genomic sequence space with functional annotation

H. Klenk, Zhong Wang, J. Froula, 2014, Biotechnology and bioengineering.

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments

Zhong Wang, Jeffrey Martin, Zhide Fang, 2012, Cell & Bioscience.

the sheep rumen microbiome Methane yield phenotypes linked to differential gene expression in

Axel Visel, Jeff Froula, William J. Kelly, 2014 .

Deconvolute individual genomes from metagenome sequences through short read clustering

Lili Wang, Li Deng, Zhong Wang, 2020, PeerJ.

Deconvolute individual genomes from metagenome sequences through read clustering

Lizhen Shi, Zhong Wang, Kexue Li, 2019, bioRxiv.

Hybrid Clustering of Long and Short-read for Improved Metagenome Assembly

M. Mascagni, Zhong Wang, Marc Warwick Van Goethem, 2021, bioRxiv.

A Scalable Pipeline for Transcriptome Profiling Tasks with On-Demand Computing Clouds

Shantenu Jha, Xiandong Meng, Zhong Wang, 2016, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

Transcriptome Analysis of Drought-Tolerant CAM plants Agave deserti and Agave tequilana

A. Visel, Zhong Wang, Jeffrey Martin, 2013 .

Deep sequencing of a plant transcriptome

Mei Wang, Zhong Wang, Jeffrey Martin, 2012 .

Prediction of protein solubility in E. coli

Zhong Wang, Dan Gunter, Taghrid Samak, 2012, 2012 IEEE 8th International Conference on E-Science.

De novo Nanopore read quality improvement using deep learning

Rob Egan, Nathan LaPierre, Wei Wang, 2019, BMC Bioinformatics.

MiniScrub: de novo long read scrubbing using approximate alignment and deep learning

Wei Wang, Zhong Wang, Rob Egan, 2018, bioRxiv.

A bi-Poisson model for clustering gene expression profiles by RNA-seq

Rongling Wu, Jianxin Wang, Zhong Wang, 2014, Briefings Bioinform..

Lawrence Berkeley National Laboratory Recent Work Title Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis Permalink

Lisa M. Chung, M. Gerstein, Michael P. Snyder, 2013 .

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

S. Tringe, G. Schroth, A. Visel, 2011, Science.

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.

G. Sherlock, Michael P. Snyder, G. Euskirchen, 2010, Genome research.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Dongwan D. Kang, Philip D. Blood, Daniel A. Cuevas, 2017, bioRxiv.