I. Letunic

发表

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Colin N. Dewey, Paul E. Boardman, David D. Shteynberg, 2004, Nature.

Initial sequencing and comparative analysis of the mouse genome.

Colin N. Dewey, Simon C. Potter, James A. Cuff, 2002 .

A side effect resource to capture phenotypic effects of drugs

P. Bork, L. Jensen, M. Campillos, 2010, Molecular systems biology.

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites

Alex Bateman, Rolf Apweiler, Henning Hermjakob, 2002, Briefings Bioinform..

Protein domain analysis in the era of complete genomes

P. Bork, R. Copley, T. Doerks, 2002, FEBS letters.

iPath: interactive exploration of biochemical pathways and networks.

P. Bork, M. Kanehisa, Takuji Yamada, 2008, Trends in biochemical sciences.

Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

K. Büssow, I. Letunic, C. Scheich, 2004, BMC Structural Biology.

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

P. Bork, I. Letunic, I. Letunić, 2019, Nucleic Acids Res..

Pan-cancer analysis of whole genomes

Steven J. M. Jones, Nuno A. Fonseca, Icgc, 2020, Nature.

Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

P. Bork, E. Raineri, Takuji Yamada, 2009, Science.

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

Nicholas H. Putnam, P. Bork, D. Pincus, 2008, Nature.

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

P. Bork, J. Raes, Takuji Yamada, 2011, Molecular systems biology.

E. Birney, P. Bork, S. Meister, 2002, Science.

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

Gunnar Rätsch, Mark Gerstein, Li Ding, 2017, bioRxiv.

Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster

Peer Bork, Ewan Birney, Ivica Letunic, 2002, Science.

Insights into social insects from the genome of the honeybee Apis mellifera

Ying Wang, Michal Linial, Andrew G. Clark, 2006, Nature.

Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes

Peer Bork, Ivica Letunic, Jeroen Raes, 2008, Journal of bacteriology.

The genome of the choanoflagellate Monosiga brevicollis and the origins of metazoan multicellularity

Nichols, Nicholas H. Putnam, P. Bork, 2008 .

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

Jian Wang, Eugene W. Myers, Andrew G. Clark, 2002, Science.

Quantifying environmental adaptation of metabolic pathways in metagenomics

Jan O. Korbel, Peer Bork, Ivica Letunic, 2009, Proceedings of the National Academy of Sciences.

PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Peer Bork, Pablo Minguez, Ivica Letunic, 2012, Nucleic Acids Res..

Metagenomic analysis of gut microbial communities from a Central Asian population

P. Bork, S. Sunagawa, A. Voigt, 2018, BMJ Open.

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

Luis Pedro Coelho, P. Bork, S. Sunagawa, 2019, Nucleic Acids Res..

The InterPro protein families and domains database: 20 years on

Silvio C. E. Tosatto, Cathy H. Wu, Gustavo A. Salazar, 2020, Nucleic Acids Res..

Microbiome and Metabolome Features of the Cardiometabolic Disease 2 Spectrum 3 4

Isnard, Luis Pedro Coelho, Judith, 2022 .

George MW, Gene ER. Insights into social insects from the genome of the honeybee Apis mellifera. Nature

Ying Wang, Michal Linial, Peer Bork, 2006 .

The SIDER database of drugs and side effects

Peer Bork, Ivica Letunic, Lars Juhl Jensen, 2015, Nucleic Acids Res..

SMART 5: domains in the context of genomes and networks

Peer Bork, Ivica Letunic, Jörg Schultz, 2005, Nucleic Acids Res..

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins

Leszek Rychlewski, Peer Bork, Allegra Via, 2003, Nucleic Acids Res..

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

P. Bork, I. Letunic, I. Letunić, 2021, Nucleic Acids Res..

The InterPro protein families database: the classification resource after 15 years

Huaiyu Mi, Robert D. Finn, Matthew Fraser, 2014, Nucleic Acids Res..

InterPro in 2022

Silvio C. E. Tosatto, Cathy H. Wu, Gustavo A. Salazar, 2022, Nucleic Acids Res..

SMART: recent updates, new developments and status in 2020

Peer Bork, Ivica Letunic, Supriya Khedkar, 2020, Nucleic Acids Res..

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Davide Heller, Damian Szklarczyk, Christian von Mering, 2018, Nucleic Acids Res..

20 years of the SMART protein domain annotation resource

Peer Bork, Ivica Letunic, P. Bork, 2017, Nucleic Acids Res..

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Peer Bork, Ivica Letunic, P. Bork, 2016, Nucleic Acids Res..

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Silvio C. E. Tosatto, Neil D. Rawlings, Robert D. Finn, 2018, Nucleic Acids Res..

InterPro, progress and status in 2005

Cathy H. Wu, Alex Bateman, Rolf Apweiler, 2004, Nucleic Acids Res..

SMART 6: recent updates and new developments

Peer Bork, Ivica Letunic, Tobias Doerks, 2008, Nucleic Acids Res..

InterPro: the integrative protein signature database

Robert D. Finn, Cathy H. Wu, Alex Bateman, 2008, Nucleic Acids Res..

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

P. Bork, I. Letunic, J. Huerta-Cepas, 2021, bioRxiv.

Microbiome and metabolome features of the cardiometabolic disease spectrum

Luis Pedro Coelho, P. Bork, V. Tremaroli, 2022, Nature Medicine.

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Peer Bork, Ivica Letunic, P. Bork, 2007, Bioinform..

SMART 7: recent updates to the protein domain annotation resource

Peer Bork, Ivica Letunic, Tobias Doerks, 2011, Nucleic Acids Res..

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

P. Bork, S. Sunagawa, D. Mende, 2022, Nucleic Acids Res..

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

Damian Szklarczyk, Christian von Mering, Peer Bork, 2009, Nucleic Acids Res..

SMART 4.0: towards genomic data integration

Peer Bork, Francesca D. Ciccarelli, Ivica Letunic, 2004, Nucleic Acids Res..

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

Peer Bork, Ivica Letunic, P. Bork, 2011, Nucleic Acids Res..

Consistency of genome‐based methods in measuring Metazoan evolution

Peer Bork, Ivica Letunic, Christian von Mering, 2005, FEBS letters.

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

Luis Pedro Coelho, P. Bork, V. Tremaroli, 2020, Nature.

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

Luis Pedro Coelho, P. Bork, V. Tremaroli, 2020, Nature.

InterPro in 2011: new developments in the family and domain prediction database

Robert D. Finn, Matthew Fraser, Cathy H. Wu, 2011, Nucleic acids research.

Combinatorial, additive and dose-dependent drug–microbiome associations

Luis Pedro Coelho, P. Bork, V. Tremaroli, 2021, Nature.

Repository of the Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association

Karen, Lajos, P. Bork, 2023 .

Computational Analysis of Modular Protein Architectures

Peer Bork, Ivica Letunic, Toby J. Gibson, 2008 .

SMART: recent updates, new developments and status in 2015

Peer Bork, Ivica Letunic, Tobias Doerks, 2014, Nucleic Acids Res..

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Damian Szklarczyk, Christian von Mering, Peer Bork, 2011, Nucleic Acids Res..

Patterns of somatic structural variation in human cancer genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

InterPro in 2017—beyond protein family and domain annotations

Silvio C. E. Tosatto, Neil D. Rawlings, Huaiyu Mi, 2016, Nucleic Acids Res..

iPath2.0: interactive pathway explorer

Peer Bork, Minoru Kanehisa, Shujiro Okuda, 2011, Nucleic Acids Res..

C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants

Wasiu A. Akanni, P. Bork, Pamela Ferretti, 2022, bioRxiv.

Comprehensive molecular characterization of mitochondrial genomes in human cancers

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2017, bioRxiv.

New developments in the InterPro database

Robert D. Finn, Robert Petryszak, Cathy H. Wu, 2007, Nucleic Acids Res..

iPath3.0: interactive pathways explorer v3

Peer Bork, Ivica Letunic, Takuji Yamada, 2018, Nucleic Acids Res..

Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

P. Bork, J. Raes, I. Letunic, 2005, RNA.

Alternative splicing and evolution.

Peer Bork, Ivica Letunic, Stephanie Boue, 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

Common exon duplication in animals and its role in alternative splicing.

Peer Bork, Ivica Letunic, Richard R Copley, 2002, Human molecular genetics.

Sex differences in oncogenic mutational processes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2019, Nature Communications.

Recent improvements to the SMART domain-based sequence annotation resource

Peer Bork, Francesca D. Ciccarelli, Ivica Letunic, 2002, Nucleic Acids Res..

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Nuno A. Fonseca, Benjamin J. Raphael, Allison P. Heath, 2020, Nature Communications.

Visualization of multiple alignments, phylogenies and gene family evolution

Ivica Letunic, Julie Thompson, Geoffrey J Barton, 2010, Nature Methods.

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature Communications.

The InterPro Database, 2003 brings increased coverage and new features

Alex Bateman, Rolf Apweiler, Nicola J. Mulder, 2003, Nucleic Acids Res..

InterPro in 2011: new developments in the family and domain prediction database

C. Orengo, M. Madera, David Binns, 2012, Nucleic Acids Res..

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

P. Bork, D. Pincus, W. Lim, 2008, Proceedings of the National Academy of Sciences.

Towards the biogeography of prokaryotic genes

Luis Pedro Coelho, P. Bork, Pamela Ferretti, 2021, Nature.

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

Luis Pedro Coelho, P. Bork, V. Tremaroli, 2022, Gut.

eggNOG 6.0: enabling comparative genomics across 12 535 organisms

P. Bork, D. Mende, L. Jensen, 2022, Nucleic Acids Res..

Novel function in light-mediated microbial processes

P. Bork, J. Raes, T. Doerks, 2008 .

4DXpress: a database for cross-species expression pattern comparisons

Thorsten Henrich, Joachim Wittbrodt, Peer Bork, 2007, Nucleic Acids Res..

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

Joaquín Dopazo, Peer Bork, Jaime Huerta-Cepas, 2014, Nucleic Acids Res..

metaTIGER: a metabolic evolution resource

Ivica Letunic, David R. Westhead, John W. Whitaker, 2008, Nucleic Acids Res..