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A scalable SCENIC workflow for single-cell gene regulatory network analysis

Nature protocols, 2020-07, Vol.15 (7), p.2247-2276

2020

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Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Nature communications, 2014-09, Vol.5 (1), p.4767-4767, Article 4767

2014

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Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

Nature methods, 2010-03, Vol.7 (3), p.237

2010

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Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce

PloS one, 2017-03, Vol.12 (3), p.e0174575-e0174575

2017

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Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

Nature biotechnology, 2012-01, Vol.30 (1), p.61-68

2012

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Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

Genome Biology, 2022-02, Vol.23 (1), p.55-55, Article 55

2022

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elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

PloS one, 2015-07, Vol.10 (7), p.e0132868-e0132868

2015

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VEGF pathway genetic variants as biomarkers of treatment outcome with bevacizumab: an analysis of data from the AViTA and AVOREN randomised trials

The lancet oncology, 2012-07, Vol.13 (7), p.724-733

2012

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Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

eLife, 2014-08, Vol.3, p.e02725

2014

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PepX: a structural database of non-redundant protein-peptide complexes

Nucleic acids research, 2010-01, Vol.38 (Database issue), p.D545

2010

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Efficiency of whole genome amplification of single circulating tumor cells enriched by CellSearch and sorted by FACS

Genome medicine, 2013-11, Vol.5 (11), p.106-106, Article 106

2013

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VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

Bioinformatics (Oxford, England), 2015-01, Vol.31 (1), p.94-101

2015

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Genetically Engineered iPSC-Derived FTDP-17 MAPT Neurons Display Mutation-Specific Neurodegenerative and Neurodevelopmental Phenotypes

Stem cell reports, 2018-08, Vol.11 (2), p.363-379

2018

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An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins

PLoS computational biology, 2011-06, Vol.7 (6), p.e1002090-e1002090

2011

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Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

Genome medicine, 2017-08, Vol.9 (1), p.80-80, Article 80

2017

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A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

BMC bioinformatics, 2017-05, Vol.18 (1), p.273-273, Article 273

2017

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Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

BMC bioinformatics, 2009-08, Vol.10 Suppl 8 (S8), p.S9-S9, Article S9

2009

Volltextzugriff (PDF)

Sequencing of DISC1 pathway genes reveals increased burden of rare missense variants in schizophrenia patients from a northern Swedish population

PloS one, 2011-08, Vol.6 (8), p.e23450-e23450

2011

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Halvade: scalable sequence analysis with MapReduce

Bioinformatics, 2015-08, Vol.31 (15), p.2482-2488

2015

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Reconstruction of protein backbones from the BriX collection of canonical protein fragments

PLoS computational biology, 2008-05, Vol.4 (5), p.e1000083-e1000083

2008

Volltextzugriff (PDF)

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

Nucleic acids research, 2012-01, Vol.40 (Database issue), p.D935

2012

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Gain of function of mutant p53 by coaggregation with multiple tumor suppressors

Nature chemical biology, 2011-05, Vol.7 (5), p.285

2011

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Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development

Nature medicine, 2024-05, Vol.30 (5), p.1339-1348

2024

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Diversity and Clonality of T Cell Receptor Repertoire and Antigen Specificities in Small Joints of Early Rheumatoid Arthritis

Arthritis & rheumatology (Hoboken, N.J.), 2023-05, Vol.75 (5), p.673-684

2023

Volltextzugriff (PDF)

Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers

Proceedings of the National Academy of Sciences - PNAS, 2023-08, Vol.120 (31), p.e2301536120-e2301536120

2023

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A scalable SCENIC workflow for single-cell gene regulatory network analysis

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

VEGF pathway genetic variants as biomarkers of treatment outcome with bevacizumab: an analysis of data from the AViTA and AVOREN randomised trials

Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks

PepX: a structural database of non-redundant protein-peptide complexes

Efficiency of whole genome amplification of single circulating tumor cells enriched by CellSearch and sorted by FACS

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

Genetically Engineered iPSC-Derived FTDP-17 MAPT Neurons Display Mutation-Specific Neurodegenerative and Neurodevelopmental Phenotypes

An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins

Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

Sequencing of DISC1 pathway genes reveals increased burden of rare missense variants in schizophrenia patients from a northern Swedish population

Halvade: scalable sequence analysis with MapReduce

Reconstruction of protein backbones from the BriX collection of canonical protein fragments

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

Gain of function of mutant p53 by coaggregation with multiple tumor suppressors

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development

Diversity and Clonality of T Cell Receptor Repertoire and Antigen Specificities in Small Joints of Early Rheumatoid Arthritis

Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers

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