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Mechanisms of tissue and cell-type specificity in heritable traits and diseases

Nature reviews. Genetics, 2020-03, Vol.21 (3), p.137-150

2020

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The landscape of molecular chaperones across human tissues reveals a layered architecture of core and variable chaperones

Nature communications, 2021-04, Vol.12 (1), p.2180-2180, Article 2180

2021

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Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data

eLife, 2024-01, Vol.13

2024

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Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation

Molecular systems biology, 2023-08, Vol.19 (8), p.e11407-n/a

2023

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Small heat-shock protein HSPB3 promotes myogenesis by regulating the lamin B receptor

Cell death & disease, 2021-05, Vol.12 (5), p.452-452, Article 452

2021

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A combination of gene expression ranking and co‐expression network analysis increases discovery rate in large‐scale mutant screens for novel Arabidopsis thaliana abiotic stress genes

Plant biotechnology journal, 2015-05, Vol.13 (4), p.501-513

2015

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The DifferentialNet database of differential protein-protein interactions in human tissues

Nucleic acids research, 2018-01, Vol.46 (D1), p.D522-D526

2018

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Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes

Genome Biology, 2024-04, Vol.25 (1), p.95-29, Article 95

2024

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Role of duplicate genes in determining the tissue-selectivity of hereditary diseases

PLoS genetics, 2018-05, Vol.14 (5), p.e1007327

2018

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Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases

PLoS computational biology, 2014-06, Vol.10 (6), p.e1003632

2014

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Cancer evolution is associated with pervasive positive selection on globally expressed genes

PLoS genetics, 2014-03, Vol.10 (3), p.e1004239

2014

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An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts

PLoS computational biology, 2017-01, Vol.13 (1), p.e1005221-e1005221

2017

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Network Motifs in Integrated Cellular Networks of Transcription-Regulation and Protein-Protein Interaction

Proceedings of the National Academy of Sciences - PNAS, 2004-04, Vol.101 (16), p.5934-5939

2004

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A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans

PLoS genetics, 2016-12, Vol.12 (12), p.e1006531-e1006531

2016

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Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

Nature genetics, 2009-03, Vol.41 (3), p.316-323

2009

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Dosage-sensitive molecular mechanisms are associated with the tissue-specificity of traits and diseases

Computational and structural biotechnology journal, 2020-01, Vol.18, p.4024-4032

2020

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sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human adipose tissues

iScience, 2024-07, Vol.27 (7), p.110368, Article 110368

2024

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Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation

Nucleic acids research, 2003-10, Vol.31 (20), p.6053-6061

2003

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Large-scale analysis of human gene expression variability associates highly variable drug targets with lower drug effectiveness and safety

Bioinformatics (Oxford, England), 2019-09, Vol.35 (17), p.3028-3037

2019

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Alignment of metabolic pathways

Bioinformatics, 2005-08, Vol.21 (16), p.3401-3408

2005

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ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

Nucleic acids research, 2011-07, Vol.39 (suppl), p.W424-W429

2011

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A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks

Bioinformatics, 2013-07, Vol.29 (13), p.i210-i216

2013

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ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts

Nucleic acids research, 2023-07, Vol.51 (W1), p.W478-W483

2023

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The TissueNet v.3 Database: Protein-protein Interactions in Adult and Embryonic Human Tissue contexts

Journal of molecular biology, 2022-06, Vol.434 (11), p.167532-167532, Article 167532

2022

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The Organ-Disease Annotations (ODiseA) Database of Hereditary Diseases and Inflicted Tissues

Journal of molecular biology, 2022-06, Vol.434 (11), p.167619-167619, Article 167619

2022

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Mechanisms of tissue and cell-type specificity in heritable traits and diseases

The landscape of molecular chaperones across human tissues reveals a layered architecture of core and variable chaperones

Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data

Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation

Small heat-shock protein HSPB3 promotes myogenesis by regulating the lamin B receptor

A combination of gene expression ranking and co‐expression network analysis increases discovery rate in large‐scale mutant screens for novel Arabidopsis thaliana abiotic stress genes

The DifferentialNet database of differential protein-protein interactions in human tissues

Machine-learning analysis reveals an important role for negative selection in shaping cancer aneuploidy landscapes

Role of duplicate genes in determining the tissue-selectivity of hereditary diseases

Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases

Cancer evolution is associated with pervasive positive selection on globally expressed genes

An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts

Network Motifs in Integrated Cellular Networks of Transcription-Regulation and Protein-Protein Interaction

A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

Dosage-sensitive molecular mechanisms are associated with the tissue-specificity of traits and diseases

sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human adipose tissues

Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation

Large-scale analysis of human gene expression variability associates highly variable drug targets with lower drug effectiveness and safety

Alignment of metabolic pathways

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks

ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts

The TissueNet v.3 Database: Protein-protein Interactions in Adult and Embryonic Human Tissue contexts

The Organ-Disease Annotations (ODiseA) Database of Hereditary Diseases and Inflicted Tissues

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