DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

Likun Wang, Zhixing Feng, Xi Wang, +2

Bioinformatics

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

Gang Fang, Diana Munera, David I. Friedman, +20

Nature Biotechnology

Long-read SequencingDna SequencingSequencingSingle-molecule Real-time SequencingSequence Analysis +10

Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae

Jing Li, Jing Li, Zhixing Feng, +12

PLoS Pathogens

GeneticsDna MethylationDna AnalysisMolecular BiologyGenomics +15

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

Eric E. Schadt, Onureena Banerjee, Gang Fang, +13

Genome Research

EngineeringConditional Random FieldGeneticsDna AnalysisMolecular Biology +20

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic

Zhixing Feng, Gang Fang, Jonas Korlach, +5

PLoS Computational Biology

GeneticsMolecular BiologyGenomicsHigh Throughput SequencingSequence Context Dependence +18

Identifying differentially spliced genes from two groups of RNA-seq samples

Weichen Wang, Zhiyi Qin, Zhixing Feng, +2

Gene

Rna-seq SamplesFunctional GenomicsNatural SciencesGeneticsSequence Analysis +8

Detecting and phasing minor single-nucleotide variants from long-read sequencing data

Zhixing Feng, José C. Clemente, Brandon Wong, +1

Nature Communications

qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data

Zhixing Feng, Jing Li, Jing-Ren Zhang, +1

Nucleic Acids Research

Transcriptional Repressor PtvR Regulates Phenotypic Tolerance to Vancomycin in Streptococcus pneumoniae

Xue Liu, Jing Li, Zhixing Feng, +3

Journal of Bacteriology