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ISEScan: automated identification of insertion sequence elements in prokaryotic genomes

Bioinformatics (Oxford, England), 2017-11, Vol.33 (21), p.3340-3347

2017

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FragGeneScan: predicting genes in short and error-prone reads

Nucleic acids research, 2010-11, Vol.38 (20), p.e191-e191

2010

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RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

Bioinformatics, 2012-01, Vol.28 (1), p.125-126

2012

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Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

eLife, 2015-10, Vol.4, p.e09591-e09591

2015

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RAPSearch: a fast protein similarity search tool for short reads

BMC bioinformatics, 2011-05, Vol.12 (1), p.159-159, Article 159

2011

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Computational Framework for Identification of Intact Glycopeptides in Complex Samples

Analytical chemistry (Washington), 2014-01, Vol.86 (1), p.453-463

2014

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Glycoproteomics: Identifying the Glycosylation of Prostate Specific Antigen at Normal and High Isoelectric Points by LC–MS/MS

Journal of proteome research, 2014-12, Vol.13 (12), p.5570-5580

2014

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A Two-Step Process for Epigenetic Inheritance in Arabidopsis

Molecular cell, 2014-04, Vol.54 (1), p.30-42

2014

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Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome

Genes & development, 2012-08, Vol.26 (16), p.1825-1836

2012

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Automated Glycan Sequencing from Tandem Mass Spectra of N‑Linked Glycopeptides

Analytical chemistry (Washington), 2016-06, Vol.88 (11), p.5725-5732

2016

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Automated annotation and quantitation of glycans by liquid chromatography/electrospray ionization mass spectrometric analysis using the MultiGlycan-ESI computational tool

Rapid communications in mass spectrometry, 2015-01, Vol.29 (1), p.135-142

2015

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Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

PloS one, 2016-01, Vol.11 (1), p.e0147229-e0147229

2016

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MGEScan: a Galaxy-based system for identifying retrotransposons in genomes

Bioinformatics (Oxford, England), 2016-08, Vol.32 (16), p.2502-2504

2016

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The transcriptional diversity of 25 Drosophila cell lines

Genome research, 2011-02, Vol.21 (2), p.301-314

2011

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Quantitative Measurement of Phosphoproteome Response to Osmotic Stress in Arabidopsis Based on Library-Assisted eXtracted Ion Chromatogram (LAXIC)

Molecular & cellular proteomics, 2013-08, Vol.12 (8), p.2354-2369

2013

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SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations

PloS one, 2013-12, Vol.8 (12), p.e83356-e83356

2013

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An Eulerian Path Approach to DNA Fragment Assembly

Proceedings of the National Academy of Sciences - PNAS, 2001-08, Vol.98 (17), p.9748-9753

2001

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Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry

Bioinformatics, 2013-07, Vol.29 (13), p.1706-1707

2013

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Next-generation sequencing technologies and fragment assembly algorithms

Methods in molecular biology (Clifton, N.J.), 2012, Vol.855, p.155

2012

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On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

Analytical chemistry (Washington), 2011-02, Vol.83 (3), p.790-796

2011

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Improving confidence in detection and characterization of protein N-glycosylation sites and microheterogeneity

Rapid communications in mass spectrometry, 2011-07, Vol.25 (14), p.2007-2019

2011

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Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences

PLoS computational biology, 2013-03, Vol.9 (3), p.e1002981-e1002981

2013

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De novo repeat classification and fragment assembly

Genome research, 2004-09, Vol.14 (9), p.1786-1796

2004

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N-Glycan Profiling by Microchip Electrophoresis to Differentiate Disease States Related to Esophageal Adenocarcinoma

Analytical chemistry (Washington), 2012-04, Vol.84 (8), p.3621-3627

2012

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De novo identification of LTR retrotransposons in eukaryotic genomes

BMC genomics, 2007-04, Vol.8 (1), p.90-90, Article 90

2007

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ISEScan: automated identification of insertion sequence elements in prokaryotic genomes

FragGeneScan: predicting genes in short and error-prone reads

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

RAPSearch: a fast protein similarity search tool for short reads

Computational Framework for Identification of Intact Glycopeptides in Complex Samples

Glycoproteomics: Identifying the Glycosylation of Prostate Specific Antigen at Normal and High Isoelectric Points by LC–MS/MS

A Two-Step Process for Epigenetic Inheritance in Arabidopsis

Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome

Automated Glycan Sequencing from Tandem Mass Spectra of N‑Linked Glycopeptides

Automated annotation and quantitation of glycans by liquid chromatography/electrospray ionization mass spectrometric analysis using the MultiGlycan-ESI computational tool

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing

MGEScan: a Galaxy-based system for identifying retrotransposons in genomes

The transcriptional diversity of 25 Drosophila cell lines

Quantitative Measurement of Phosphoproteome Response to Osmotic Stress in Arabidopsis Based on Library-Assisted eXtracted Ion Chromatogram (LAXIC)

SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations

An Eulerian Path Approach to DNA Fragment Assembly

Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry

Next-generation sequencing technologies and fragment assembly algorithms

On the Accuracy and Limits of Peptide Fragmentation Spectrum Prediction

Improving confidence in detection and characterization of protein N-glycosylation sites and microheterogeneity

Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences

De novo repeat classification and fragment assembly

N-Glycan Profiling by Microchip Electrophoresis to Differentiate Disease States Related to Esophageal Adenocarcinoma

De novo identification of LTR retrotransposons in eukaryotic genomes

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