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HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Genome research, 2017-05, Vol.27 (5), p.801-812

2017

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Exploring the landscape of focal amplifications in cancer using AmpliconArchitect

Nature communications, 2019-01, Vol.10 (1), p.392-14, Article 392

2019

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Extrachromosomal oncogene amplification in tumour pathogenesis and evolution

Nature reviews. Cancer, 2019-05, Vol.19 (5), p.283-288

2019

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HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

Bioinformatics, 2008-08, Vol.24 (16), p.i153-i159

2008

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Proteogenomics to discover the full coding content of genomes: A computational perspective

Journal of proteomics, 2010-10, Vol.73 (11), p.2124-2135

2010

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Variable number tandem repeats mediate the expression of proximal genes

Nature communications, 2021-04, Vol.12 (1), p.2075-2075, Article 2075

2021

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Learning natural selection from the site frequency spectrum

Genetics (Austin), 2013-09, Vol.195 (1), p.181-193

2013

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AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications

Nature communications, 2020-09, Vol.11 (1), p.4374-14, Article 4374

2020

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Skmer: assembly-free and alignment-free sample identification using genome skims

Genome Biology, 2019-02, Vol.20 (1), p.34-20, Article 34

2019

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Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009449-e1009449

2021

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Inferring gene ontologies from pairwise similarity data

Bioinformatics (Oxford, England), 2014-06, Vol.30 (12), p.i34-i42

2014

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De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly

Nature genetics, 2012-08, Vol.44 (8), p.941-945

2012

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Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors

eLife, 2024-06, Vol.12

2024

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Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells

Nature communications, 2020-01, Vol.11 (1), p.550-550, Article 550

2020

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Clear: Composition of Likelihoods for Evolve and Resequence Experiments

Genetics (Austin), 2017-06, Vol.206 (2), p.1011-1023

2017

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Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

Genome research, 2012-02, Vol.22 (2), p.246-258

2012

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ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer

Nucleic acids research, 2018-04, Vol.46 (7), p.3309-3325

2018

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Multiple mechanisms drive genomic adaptation to extreme O2 levels in Drosophila melanogaster

Nature communications, 2021-02, Vol.12 (1), p.1-10, Article 997

2021

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Ultraaccurate genome sequencing and haplotyping of single human cells

Proceedings of the National Academy of Sciences - PNAS, 2017-11, Vol.114 (47), p.12512-12517

2017

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algorithmic approach for breakage-fusion-bridge detection in tumor genomes

Proceedings of the National Academy of Sciences - PNAS, 2013-04, Vol.110 (14), p.5546-5551

2013

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Discovery and revision of Arabidopsis genes by proteogenomics

Proceedings of the National Academy of Sciences - PNAS, 2008-12, Vol.105 (52), p.21034-21038

2008

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Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

Journal of proteome research, 2014-01, Vol.13 (1), p.21-28

2014

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A Multidimensional Chromatography Technology for In-depth Phosphoproteome Analysis

Molecular & cellular proteomics, 2008-07, Vol.7 (7), p.1389-1396

2008

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A deep population reference panel of tandem repeat variation

Nature communications, 2023-10, Vol.14 (1), p.6711-6711, Article 6711

2023

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Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

Applied and environmental microbiology, 2016-04, Vol.82 (8), p.2494-2505

2016

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HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Exploring the landscape of focal amplifications in cancer using AmpliconArchitect

Extrachromosomal oncogene amplification in tumour pathogenesis and evolution

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

Proteogenomics to discover the full coding content of genomes: A computational perspective

Variable number tandem repeats mediate the expression of proximal genes

Learning natural selection from the site frequency spectrum

AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications

Skmer: assembly-free and alignment-free sample identification using genome skims

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT

Inferring gene ontologies from pairwise similarity data

De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly

Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors

Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells

Clear: Composition of Likelihoods for Evolve and Resequence Experiments

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer

Multiple mechanisms drive genomic adaptation to extreme O2 levels in Drosophila melanogaster

Ultraaccurate genome sequencing and haplotyping of single human cells

algorithmic approach for breakage-fusion-bridge detection in tumor genomes

Discovery and revision of Arabidopsis genes by proteogenomics

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

A Multidimensional Chromatography Technology for In-depth Phosphoproteome Analysis

A deep population reference panel of tandem repeat variation

Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem

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