D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions

The role of TXNL1 in disease: treatment strategies for cancer and diseases with oxidative stress

(2021) Jin-Ming Zhao et al.   MOLECULAR BIOLOGY REPORTS

Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

(2021) Anna G. Green et al.   Nature Communications

Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell

(2021) Michelle M. Halstead et al.   Frontiers in Genetics

Learning the protein language: Evolution, structure, and function

(2021) Tristan Bepler et al.   Cell Systems

Mouse S100G protein exhibits properties characteristic of a calcium sensor

(2020) Sergei E. Permyakov et al.   CELL CALCIUM

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

More Than a Metabolic Enzyme: MTHFD2 as a Novel Target for Anticancer Therapy?

(2020) Zhiyuan Zhu et al.   Frontiers in Oncology

GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks

(2020) Kapil Devkota et al.   BIOINFORMATICS

Leveraging Uncertainty in Machine Learning Accelerates Biological Discovery and Design

(2020) Brian Hie et al.   Cell Systems

Network-based prediction of protein interactions

(2019) István A. Kovács et al.   Nature Communications

Genome-wide association study identifies QTLs for displacement of abomasum in Chinese Holstein cattle1

(2019) Hetian Huang et al.   JOURNAL OF ANIMAL SCIENCE

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

Multifaceted protein–protein interaction prediction based on Siamese residual RCNN

(2019) Muhao Chen et al.   BIOINFORMATICS

Assessment of network module identification across complex diseases

(2019) Sarvenaz Choobdar et al.   NATURE METHODS

COA6 Is Structurally Tuned to Function as a Thiol-Disulfide Oxidoreductase in Copper Delivery to Mitochondrial Cytochrome c Oxidase

(2019) Shivatheja Soma et al.   Cell Reports

Do metabolic HAD phosphatases moonlight as protein phosphatases?

(2018) Antje Gohla   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

OUP accepted manuscript

(2018)   BIOINFORMATICS

Genetic diversity of NDUFV1-dependent mitochondrial complex I deficiency

(2018) Anshika Srivastava et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A threonyl-tRNA synthetase-like protein has tRNA aminoacylation and editing activities

(2018) Yun Chen et al.   NUCLEIC ACIDS RESEARCH

ComplexContact: a web server for inter-protein contact prediction using deep learning

(2018) Hong Zeng et al.   NUCLEIC ACIDS RESEARCH

GeneMANIA update 2018

(2018) Max Franz et al.   NUCLEIC ACIDS RESEARCH

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks

(2018) Yang Liu et al.   Cell Systems

Network enhancement as a general method to denoise weighted biological networks

(2018) Bo Wang et al.   Nature Communications

GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms

(2018) Chenguang Zhao et al.   Scientific Reports

S100 proteins: Diagnostic and prognostic biomarkers in laboratory medicine

(2018) Claus W. Heizmann   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Computational discovery of direct associations between GO terms and protein domains

(2018) Seyed Ziaeddin Alborzi et al.   BMC BIOINFORMATICS

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

FlyBase 2.0: the next generation

(2018) Jim Thurmond et al.   NUCLEIC ACIDS RESEARCH

Smad nuclear interacting protein 1 (SNIP1) inhibits intestinal inflammation through regulation of epithelial barrier function

(2017) Y Shi et al.   Mucosal Immunology

Network propagation: a universal amplifier of genetic associations

(2017) Lenore Cowen et al.   NATURE REVIEWS GENETICS

A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle

(2016) Hermann Schwarzenbacher et al.   BMC GENOMICS

FAP Promotes Immunosuppression by Cancer-Associated Fibroblasts in the Tumor Microenvironment via STAT3–CCL2 Signaling

(2016) Xuguang Yang et al.   CANCER RESEARCH

Characteristics of dairy cows with a greater or lower risk of subacute ruminal acidosis: Volatile fatty acid absorption, rumen digestion, and expression of genes in rumen epithelial cells

(2016) X. Gao et al.   JOURNAL OF DAIRY SCIENCE

Glucose Availability and AMP-Activated Protein Kinase Link Energy Metabolism and Innate Immunity in the Bovine Endometrium

(2016) Matthew L. Turner et al.   PLoS One

A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL

(2016) Prudence Mutowo et al.   Journal of Biomedical Semantics

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

(2016) Hyunghoon Cho et al.   Cell Systems

A note on associations between polymorphism within the 2,4-dienoyl-CoA reductase gene (DECR1) and growth rate of Polish Landrace boars

(2016) S. Kamiński et al.   JOURNAL OF ANIMAL AND FEED SCIENCES

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

The GABA Transaminase, ABAT, Is Essential for Mitochondrial Nucleoside Metabolism

(2015) Arnaud Besse et al.   Cell Metabolism

The extended human PTPome: a growing tyrosine phosphatase family

(2015) Andrés Alonso et al.   FEBS Journal

Kinetics of lipogenic genes expression in milk purified mammary epithelial cells (MEC) across lactation and their correlation with milk and fat yield in buffalo

(2015) Poonam Yadav et al.   RESEARCH IN VETERINARY SCIENCE

New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence

(2014) Mengfei Cao et al.   BIOINFORMATICS

A Quantitative Chaperone Interaction Network Reveals the Architecture of Cellular Protein Homeostasis Pathways

(2014) Mikko Taipale et al.   CELL

Hyperketonemia during lipopolysaccharide-induced mastitis affects systemic and local intramammary metabolism in dairy cows

(2014) M. Zarrin et al.   JOURNAL OF DAIRY SCIENCE

PRRX1 promotes epithelial–mesenchymal transition through the Wnt/β-catenin pathway in gastric cancer

(2014) Jinbao Guo et al.   MEDICAL ONCOLOGY

Revealing Missing Parts of the Interactome via Link Prediction

(2014) Yuriy Hulovatyy et al.   PLoS One

The sheep genome illuminates biology of the rumen and lipid metabolism

(2014) Y. Jiang et al.   SCIENCE

AGXT2: a promiscuous aminotransferase

(2014) Roman N. Rodionov et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

Structure and catalytic mechanism of human protein tyrosine phosphatome

(2013) Seung Jun Kim et al.   BMB Reports

Microarray-based gene expression profiling of peripheral blood mononuclear cells in dairy cows with experimental hypocalcemia and milk fever

(2013) K. Sasaki et al.   JOURNAL OF DAIRY SCIENCE

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Correction: Going the Distance for Protein Function Prediction: A New Distance Metric for Protein Interaction Networks

(2013) Mengfei Cao et al.   PLoS One

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation of Protein Structure over Four Billion Years

(2013) Alvaro Ingles-Prieto et al.   STRUCTURE

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

(2013) Raghavendra Hosur et al.   GENOME BIOLOGY

Mutations of the Mitochondrial-tRNA Modifier MTO1 Cause Hypertrophic Cardiomyopathy and Lactic Acidosis

(2012) Daniele Ghezzi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A novel link prediction algorithm for reconstructing protein–protein interaction networks by topological similarity

(2012) Chengwei Lei et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

A novel Acetyl-CoA synthetase short-chain subfamily member 1 (Acss1) gene indicates a dynamic history of paralogue retention and loss in vertebrates

(2012) L. Filipe C. Castro et al.   GENE

Lipid metabolism, adipocyte depot physiology and utilization of meat animals as experimental models for metabolic research

(2012) Michael V. Dodson et al.   International Journal of Biological Sciences

The CDK5 repressor CDK5RAP1 is a methylthiotransferase acting on nuclear and mitochondrial RNA

(2012) Veronika Reiter et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

The power of protein interaction networks for associating genes with diseases

(2010) Saket Navlakha et al.   BIOINFORMATICS

FOXRED1, encoding an FAD-dependent oxidoreductase complex-I-specific molecular chaperone, is mutated in infantile-onset mitochondrial encephalopathy

(2010) Elisa Fassone et al.   HUMAN MOLECULAR GENETICS

Gluconeogenesis in dairy cows: The secret of making sweet milk from sour dough

(2010) Jörg R. Aschenbach et al.   IUBMB LIFE

iWRAP: An Interface Threading Approach with Application to Prediction of Cancer-Related Protein–Protein Interactions

(2010) Raghavendra Hosur et al.   JOURNAL OF MOLECULAR BIOLOGY

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach

(2010) R. Singh et al.   NUCLEIC ACIDS RESEARCH

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Serine/threonine kinase Stk33 exhibits autophosphorylation and phosphorylates the intermediate filament protein Vimentin

(2008) Bastienne Brauksiepe et al.   BMC BIOCHEMISTRY