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scds: computational annotation of doublets in single-cell RNA sequencing data

Bioinformatics, 2020-02, Vol.36 (4), p.1150-1158

2020

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Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function

BMC genomics, 2019-06, Vol.20 (1), p.511-511, Article 511

2019

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Single-cell transcriptomic analysis identifies murine heart molecular features at embryonic and neonatal stages

Nature communications, 2022-12, Vol.13 (1), p.7960-7960, Article 7960

2022

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Integrating diverse datasets improves developmental enhancer prediction

PLoS computational biology, 2014-06, Vol.10 (6), p.e1003677-e1003677

2014

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DAF-16 and TCER-1 Facilitate Adaptation to Germline Loss by Restoring Lipid Homeostasis and Repressing Reproductive Physiology in C. elegans

PLoS genetics, 2016-02, Vol.12 (2), p.e1005788-e1005788

2016

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Regulatory networks define phenotypic classes of human stem cell lines

Nature, 2008-09, Vol.455 (7211), p.401-405

2008

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Finding disease specific alterations in the co-expression of genes

Bioinformatics, 2004-08, Vol.20 (suppl-1), p.i194-i199

2004

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Single-cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis

Scientific reports, 2021-11, Vol.11 (1), p.22434-22434, Article 22434

2021

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Computational profiling of hiPSC-derived heart organoids reveals chamber defects associated with NKX2-5 deficiency

Communications biology, 2022-04, Vol.5 (1), p.399-399, Article 399

2022

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Vaeda computationally annotates doublets in single-cell RNA sequencing data

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes

PLoS genetics, 2013-08, Vol.9 (8), p.e1003684-e1003684

2013

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Random forest based similarity learning for single cell RNA sequencing data

Bioinformatics, 2018-07, Vol.34 (13), p.i79-i88

2018

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The importance of being cis: evolution of orthologous fish and mammalian enhancer activity

Molecular biology and evolution, 2010-10, Vol.27 (10), p.2322-2332

2010

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Microarray based diagnosis profits from better documentation of gene expression signatures

PLoS computational biology, 2008-02, Vol.4 (2), p.e22-e22

2008

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Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data

Bioinformatics (Oxford, England), 2022-05, Vol.38 (10), p.2749-2756

2022

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Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data

Bioinformatics, 2022-05, Vol.38 (10), p.2749-2756

2022

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Large-scale inference of competing endogenous RNA networks with sparse partial correlation

Bioinformatics, 2019-07, Vol.35 (14), p.i596-i604

2019

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aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants

Bioinformatics (Oxford, England), 2023-09, Vol.39 (9)

2023

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Expression of Late Cell Cycle Genes and an Increased Proliferative Capacity Characterize Very Early Relapse of Childhood Acute Lymphoblastic Leukemia

Clinical cancer research, 2006-08, Vol.12 (15), p.4553-4561

2006

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Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages

Molecular biology and evolution, 2018-08, Vol.35 (8), p.2034-2045

2018

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An intrinsically interpretable neural network architecture for sequence-to-function learning

Bioinformatics (Oxford, England), 2023-06, Vol.39 (Supplement_1), p.i413-i422

2023

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Modeling DNA methylation dynamics with approaches from phylogenetics

Bioinformatics, 2014-09, Vol.30 (17), p.i408-i414

2014

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The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

Molecular biology and evolution, 2012-03, Vol.29 (3), p.1047-1057

2012

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Gibbon genome and the fast karyotype evolution of small apes

Nature (London), 2014-09, Vol.513 (7517), p.195-201

2014

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scds: computational annotation of doublets in single-cell RNA sequencing data

Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function

Single-cell transcriptomic analysis identifies murine heart molecular features at embryonic and neonatal stages

Integrating diverse datasets improves developmental enhancer prediction

DAF-16 and TCER-1 Facilitate Adaptation to Germline Loss by Restoring Lipid Homeostasis and Repressing Reproductive Physiology in C. elegans

Regulatory networks define phenotypic classes of human stem cell lines

Finding disease specific alterations in the co-expression of genes

Single-cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis

Computational profiling of hiPSC-derived heart organoids reveals chamber defects associated with NKX2-5 deficiency

Vaeda computationally annotates doublets in single-cell RNA sequencing data

A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes

Random forest based similarity learning for single cell RNA sequencing data

The importance of being cis: evolution of orthologous fish and mammalian enhancer activity

Microarray based diagnosis profits from better documentation of gene expression signatures

Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data

Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data

Large-scale inference of competing endogenous RNA networks with sparse partial correlation

aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants

Expression of Late Cell Cycle Genes and an Increased Proliferative Capacity Characterize Very Early Relapse of Childhood Acute Lymphoblastic Leukemia

Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages

An intrinsically interpretable neural network architecture for sequence-to-function learning

Modeling DNA methylation dynamics with approaches from phylogenetics

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

The complex genetics of hypoplastic left heart syndrome

Gibbon genome and the fast karyotype evolution of small apes

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