M. Tress

发表

GENCODE: The reference human genome annotation for The ENCODE Project

Bronwen L. Aken, Michael F. Lin, D. Haussler, 2012, Genome research.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure

D. T. Jones, M. Tress, K. Bryson, 1999, Proteins.

Sequence-based feature prediction and annotation of proteins

M. Tress, A. Valencia, P. Bork, 2009, Genome Biology.

Predicted residue–residue contacts can help the scoring of 3D models

M. Tress, A. Valencia, 2010, Proteins.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2011, PLoS biology.

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

M. Tress, A. Valencia, R. Aebersold, 2008, Genome Biology.

STRUCTURAL BIOLOGY AND BIOCOMPUTING PROGRAMME

M. Tress, Martin Krallinger, N. Dölker, 2016 .

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

M. Tress, J. Rodriguez, A. Valencia, 2016, Genome Biology.

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

M. Tress, I. Ezkurdia, A. Valencia, 2012, Genome research.

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2012, PloS one.

Analyzing the First Drafts of the Human Proteome

M. Tress, I. Ezkurdia, A. Valencia, 2014, Journal of proteome research.

Alternative Splicing May Not Be the Key to Proteome Complexity.

M. Tress, A. Valencia, F. Abascal, 2017, Trends in biochemical sciences.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation

Jonathan M. Mudge, M. Tress, Manolis Kellis, 2019, NAR genomics and bioinformatics.

1 SQANTI : extensive characterization of long read transcript sequences for quality control in 1 full-length transcriptome identification and quantification 2 3

Lennart Martens, Ana Conesa, Manuel Tardaguila, 2017 .

The potential clinical impact of the release of two drafts of the human proteome

Alfonso Valencia, Michael L. Tress, Iakes Ezkurdia, 2015, Expert review of proteomics.

Sequence analysis Alternative splicing and co-option of transposable elements : the case of TMPO / LAP 2 a and ZNF 451 in mammals

M. Tress, A. Valencia, F. Abascal, 2015 .

Predicting reliable regions in protein alignments from sequence profiles.

Alfonso Valencia, David T. Jones, Michael L Tress, 2003, Journal of molecular biology.

Scoring docking models with evolutionary information

J. Gonzalez, M. Tress, A. Valencia, 2005, Proteins.

An analysis of tissue-specific alternative splicing at the protein level

M. Tress, J. Rodriguez, Jesús Vázquez, 2020, PLoS Comput. Biol..

APPRIS: selecting functionally important isoforms

M. Tress, J. Rodriguez, Jesús Vázquez, 2021, Nucleic Acids Res..

Alternative Splicing in the ENCODE Protein complement

Gabrielle A. Reeves, G. A. Reeves, Peter F. Hallin, 2008 .

From Structure to Function

C. Orengo, J. Thornton, M. Tress, 2021, Models of the Mind.

chimeric RNA transcripts Chimeras taking shape : Potential functions of proteins encoded by P < P

M. Tress, I. Ezkurdia, A. Valencia, 2012 .

The implications of alternative splicing in the ENCODE protein complement

Hagen Blankenburg, Fidel Ramírez, Thomas Lengauer, 2007, Proceedings of the National Academy of Sciences.

Genome analysis Determination and validation of principal gene products

J. Harrow, A. Frankish, M. Tress, 2007 .

Nearly all new protein-coding predictions in the CHESS database are not protein-coding

Jonathan M. Mudge, M. Gerstein, A. Frankish, 2018, bioRxiv.

Assessment of predictions submitted for the CASP7 function prediction category

M. Tress, A. Valencia, A. Rojas, 2007, Proteins.

Genomic and phenotypic characterization of 404 individuals with neurodevelopmental disorders caused by CTNNB1 variants.

Ethan M. Goldberg, J. Gécz, M. Tress, 2022, Genetics in medicine : official journal of the American College of Medical Genetics.

Clinical variant interpretation and biologically relevant reference transcripts

M. Tress, J. Rodriguez, Jesús Vázquez, 2022, npj Genomic Medicine.

APPRIS principal isoforms and MANE Select transcripts define reference splice variants

M. Tress, J. Rodriguez, Jesús Vázquez, 2022, Bioinformatics.

From identification to validation to gene count

Bronwen L. Aken, J. Harrow, A. Frankish, 2010, Genome Biology.

Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

M. Tress, I. Ezkurdia, A. Mortazavi, 2018, Genome research.

GENCODE: reference annotation for the human and mouse genomes in 2023

James C. Wright, Jonathan M. Mudge, Andrew D. Yates, 2022, Nucleic Acids Res..

Origins and Evolution of Human Tandem Duplicated Exon Substitution Events

M. Tress, F. Abascal, Laura Martinez-Gomez, 2022, Genome biology and evolution.

Correction to "Analyzing the first drafts of the human proteome".

M. Tress, I. Ezkurdia, A. Valencia, 2015, Journal of proteome research.

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level

Alfonso Valencia, Michael L. Tress, Jose Manuel Rodriguez, 2015, PLoS Comput. Biol..

Protein Tertiary Structures: Prediction from Amino Acid Sequences

Michael Tress, M. Tress, 2013 .

GENCODE reference annotation for the human and mouse genomes

Mark Gerstein, Tomás Di Domenico, Jane Loveland, 2018, Nucleic Acids Res..

chimeric RNA transcripts Chimeras taking shape : Potential functions of proteins encoded by Material Supplemental

M. Tress, I. Ezkurdia, A. Valencia, 2012 .

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

J. Harrow, A. Frankish, M. Diekhans, 2014, Human molecular genetics.

Protein Structural Domains: Definition and Prediction

Iakes Ezkurdia, Michael L Tress, M. Tress, 2011, Current protocols in protein science.

GENCODE 2021

James C. Wright, Jonathan M. Mudge, Andrew D. Yates, 2020, Nucleic Acids Res..

Assessing the functional relevance of splice isoforms

M. Tress, J. Rodriguez, F. Abascal, 2021, NAR genomics and bioinformatics.

Most Alternative Isoforms Are Not Functionally Important.

M. Tress, A. Valencia, F. Abascal, 2017, Trends in biochemical sciences.

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

Alfonso Valencia, Jennifer Harrow, Michael L. Tress, 2012, Molecular biology and evolution.

Most highly expressed protein-coding genes have a single dominant isoform.

Alfonso Valencia, Jose Manuel Rodriguez, Iakes Ezkurdia, 2015, Journal of proteome research.

An analysis of the Sargasso Sea resource and the consequences for database composition

Anna Tramontano, Alfonso Valencia, Michael L. Tress, 2006, BMC Bioinformatics.

CASP6 assessment of contact prediction

Jens Meiler, Alfonso Valencia, Marco Punta, 2005, Proteins.

APPRIS: annotation of principal and alternative splice isoforms

Alfonso Valencia, Michael L. Tress, Gonzalo López, 2012, Nucleic Acids Res..

From Structure to Function

C. Orengo, J. Thornton, M. Tress, 2021, Models of the Mind.

APPRIS principal isoforms and MANE Select transcripts in clinical variant interpretation

M. Tress, J. Rodriguez, Jesús Vázquez, 2021, bioRxiv.

The Evolutionary Fate of Alternatively Spliced Homologous Exons after Gene Duplication

M. Tress, A. Valencia, F. Abascal, 2015, Genome biology and evolution.

The shrinking human protein coding complement: are there now fewer than 20,000 genes?

Alfonso Valencia, Mark Diekhans, Jennifer Harrow, 2013, bioRxiv.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals

Alfonso Valencia, Michael L. Tress, Federico Abascal, 2015, Bioinform..

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Tapio Salakoski, Paolo Fontana, Silvio C. E. Tosatto, 2016, Genome Biology.

Determination and validation of principal gene products

Alfonso Valencia, Jennifer L. Harrow, Michael L. Tress, 2008, Bioinform..

Progress and challenges in predicting protein-protein interaction sites

Alfonso Valencia, Piero Fariselli, Rita Casadio, 2008, Briefings Bioinform..

Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance

David G. Pisano, Luis Manso, Gonzalo Gómez-López, 2016, PloS one.

APPRIS 2017: principal isoforms for multiple gene sets

Alfonso Valencia, Tomás Di Domenico, Michael L. Tress, 2017, Nucleic Acids Res..

firestar—prediction of functionally important residues using structural templates and alignment reliability

Alfonso Valencia, Gonzalo López, Michael L Tress, 2007, Nucleic Acids Res..

The clinical importance of tandem exon duplication-derived substitutions

M. Tress, F. Abascal, Thomas A. Walsh, 2021, Nucleic acids research.

APPRIS WebServer and WebServices

Alfonso Valencia, Michael L. Tress, Jose Manuel Rodriguez, 2015, Nucleic Acids Res..

Assessment of predictions submitted for the CASP6 comparative modeling category

Alfonso Valencia, Gonzalo López, Osvaldo Graña, 2005, Proteins.

TreeDet: a web server to explore sequence space

Alfonso Valencia, Florencio Pazos, Michael L. Tress, 2006, Nucleic Acids Res..

Loose ends: almost one in five human genes still have unresolved coding status

Laura Martinez, Jose Manuel Rodriguez, David Juan, 2018, Nucleic acids research.

firestar—advances in the prediction of functionally important residues

Alfonso Valencia, Michael L. Tress, Gonzalo López, 2011, Nucleic Acids Res..

Alternative Splicing

M. Tress, I. Ezkurdia, A. Valencia, 2019, Encyclopedia of Biophysics.

The GENCODE human gene set

T Derrien, M Gerstein, T Hunt, 2010, Genome Biology.

Assessment of ligand binding residue predictions in CASP8

Gonzalo López, Iakes Ezkurdia, Michael L Tress, 2009, Proteins.

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8

Osvaldo Graña, Iakes Ezkurdia, Michael L Tress, 2009, Proteins.

Assessment of intramolecular contact predictions for CASP7

Alfonso Valencia, Osvaldo Graña, Michael L Tress, 2007, Proteins.

Assessment of predictions submitted for the CASP7 function prediction category.

Alfonso Valencia, Gonzalo López, Michael Tress, 2007, Proteins.

Assessment of predictions submitted for the CASP7 domain prediction category

David Kim, Keehyoung Joo, Jinwoo Lee, 2007, Proteins.

FireDB—a database of functionally important residues from proteins of known structure

Alfonso Valencia, Michael L. Tress, Gonzalo López, 2006, Nucleic Acids Res..

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2012, PloS one.

Automated Function Prediction Featuring a Critical Assessment of Function Annotations

M. Tress, S. Kasif, Guy Nimrod, 2011 .

Evidence for transcript networks composed of chimeric RNAs in human cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2017 .

Evidence for transcript networks composed of chimeric RNAs in human cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2014 .

Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure

M. Tress, K. Bryson, C. Hadley, 1999, Proteins: Structure, Function, and Bioinformatics.

Assessment of predictions submitted for the CASP7 domain prediction category

M. Tress, K. Joo, D. Chivian, 2007, Proteins.

firestar—prediction of functionally important residues using structural templates and alignment reliability

M. Tress, A. Valencia, Gonzalo López, 1996, Nucleic Acids Res..

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

Lennart Martens, Ana Conesa, Manuel Tardaguila, 2017, bioRxiv.

FireDB: a compendium of biological and pharmacologically relevant ligands

Alfonso Valencia, Michael L. Tress, Gonzalo López, 2013, Nucleic Acids Res..

SQUARE-determining reliable regions in sequence alignments

Alfonso Valencia, Michael L. Tress, Osvaldo Graña, 2004, Bioinform..

The Aquila Digital Community The Aquila Digital Community

Silvio C. E. Tosatto, Karin M. Verspoor, David A. Lee, 2022 .

Determination and validation of principal gene products

J. Harrow, A. Frankish, M. Tress, 2008, Bioinform..