Toni Gabaldon

Toni Gabaldon

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Toni Gabaldon

Publications by authors named "Toni Gabaldon"

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CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies.

Bioinformatics 2020 Feb;36(3):925-927

Centre for Genomic Regulation, Department of Bioinformatics and Genomics, The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btz626DOI Listing
February 2020

EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes.

Bioinformatics 2020 Feb;36(4):1265-1266

Centre for Genomic Regulation (CRG), Bioinformatics and Genomics department, The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btz706DOI Listing
February 2020

Gene gain and loss across the metazoan tree of life.

Nat Ecol Evol 2020 Jan 28. Epub 2020 Jan 28.

Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1038/s41559-019-1069-xDOI Listing
January 2020

Commercial Formulates of Induce Systemic Plant Resistance to in Tomato and the Effect Is Additive to That of the Resistance Gene.

Front Microbiol 2019 31;10:3042. Epub 2020 Jan 31.

Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Barcelona, Spain.

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http://dx.doi.org/10.3389/fmicb.2019.03042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006539PMC
January 2020

Evolutionary and functional patterns of shared gene neighbourhood in fungi.

Nat Microbiol 2019 12 16;4(12):2383-2392. Epub 2019 Sep 16.

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1038/s41564-019-0552-0DOI Listing
December 2019

Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: (syn. ) and (syn. ).

G3 (Bethesda) 2019 12 3;9(12):3921-3927. Epub 2019 Dec 3.

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain,

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http://dx.doi.org/10.1534/g3.119.400762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893180PMC
December 2019

Fungal evolution: diversity, taxonomy and phylogeny of the Fungi.

Biol Rev Camb Philos Soc 2019 12;94(6):2101-2137

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1111/brv.12550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6899921PMC
December 2019

Parental origin of the allotetraploid tobacco Nicotiana benthamiana.

Plant J 2019 Dec 12. Epub 2019 Dec 12.

Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria.

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http://dx.doi.org/10.1111/tpj.14648DOI Listing
December 2019

HaploTypo: a variant-calling pipeline for phased genomes.

Bioinformatics 2019 Dec 13. Epub 2019 Dec 13.

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btz933DOI Listing
December 2019

Microbiome and colorectal cancer: Roles in carcinogenesis and clinical potential.

Mol Aspects Med 2019 Oct 24;69:93-106. Epub 2019 May 24.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain; Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.mam.2019.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856719PMC
October 2019

Molecular Typing of Candida glabrata.

Mycopathologia 2019 Oct 15. Epub 2019 Oct 15.

Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, 37075, Göttingen, Germany.

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http://dx.doi.org/10.1007/s11046-019-00388-xDOI Listing
October 2019

Transcriptome Sequencing Approaches to Elucidate Host-Microbe Interactions in Opportunistic Human Fungal Pathogens.

Curr Top Microbiol Immunol 2019 ;422:193-235

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1007/82_2018_122DOI Listing
September 2019

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS.

Authors:
Toni Gabaldón

FEMS Microbiol Rev 2019 Sep;43(5):517-547

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain.

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http://dx.doi.org/10.1093/femsre/fuz015DOI Listing
September 2019

Fungal evolution: major ecological adaptations and evolutionary transitions.

Biol Rev Camb Philos Soc 2019 08 25;94(4):1443-1476. Epub 2019 Apr 25.

Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1111/brv.12510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850671PMC
August 2019

Induces Plant-Dependent Systemic Resistance to .

Front Plant Sci 2019 13;10:945. Epub 2019 Aug 13.

Departament d'Enginyeria Agroalimentària i Biotecnologia, Universitat Politècnica de Catalunya, Barcelona, Spain.

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http://dx.doi.org/10.3389/fpls.2019.00945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700505PMC
August 2019

Evolution of the Peroxisomal Proteome.

Authors:
Toni Gabaldón

Subcell Biochem 2018;89:221-233

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader, 88, 08003, Barcelona, Spain.

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http://link.springer.com/10.1007/978-981-13-2233-4_9
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http://dx.doi.org/10.1007/978-981-13-2233-4_9DOI Listing
June 2019

Utilization of selenocysteine in early-branching fungal phyla.

Nat Microbiol 2019 05 11;4(5):759-765. Epub 2019 Feb 11.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41564-018-0354-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6551623PMC
May 2019

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Uncovers Its Hybrid Origin.

Front Genet 2019 25;10:383. Epub 2019 Apr 25.

Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.3389/fgene.2019.00383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6494940PMC
April 2019

Candida parapsilosis: from Genes to the Bedside.

Clin Microbiol Rev 2019 03 27;32(2). Epub 2019 Feb 27.

Department of Microbiology, University of Szeged Interdisciplinary Excellence Centre, Szeged, Hungary

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http://dx.doi.org/10.1128/CMR.00111-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431126PMC
March 2019

Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal.

Curr Genet 2019 Feb 19;65(1):93-98. Epub 2018 Jul 19.

GQE-Le Moulon, INRA-Université Paris-Sud-CNRS-AgroParisTech, 91400, Orsay, France.

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http://dx.doi.org/10.1007/s00294-018-0867-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342864PMC
February 2019

Genome Comparisons of Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations.

Front Microbiol 2019 12;10:112. Epub 2019 Feb 12.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.3389/fmicb.2019.00112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6379656PMC
February 2019

Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes.

mBio 2019 01 22;10(1). Epub 2019 Jan 22.

Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Barcelona, Spain

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http://mbio.asm.org/lookup/doi/10.1128/mBio.02494-18
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http://dx.doi.org/10.1128/mBio.02494-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343036PMC
January 2019

Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis.

Authors:
Toni Gabaldón

IUBMB Life 2018 12 25;70(12):1188-1196. Epub 2018 Oct 25.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://doi.wiley.com/10.1002/iub.1950
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http://dx.doi.org/10.1002/iub.1950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6282991PMC
December 2018

MICU1 Confers Protection from MCU-Dependent Manganese Toxicity.

Cell Rep 2018 11;25(6):1425-1435.e7

Institute for Diabetes and Obesity, Helmholtz Diabetes Center (HDC), Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Biochemistry, Gene Center Munich, Ludwig-Maximilians Universität München, 81377 Munich, Germany; Munich Cluster for Systems Neurology, 81377 Munich, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183161
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http://dx.doi.org/10.1016/j.celrep.2018.10.037DOI Listing
November 2018

Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens.

Genes (Basel) 2018 Sep 19;9(9). Epub 2018 Sep 19.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.

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http://dx.doi.org/10.3390/genes9090461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162425PMC
September 2018

Genome Variation in the Model Halophilic Bacterium .

Front Microbiol 2018 19;9:1499. Epub 2018 Jul 19.

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.3389/fmicb.2018.01499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060240PMC
July 2018

Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications.

Yeast 2018 06 22;35(6):425-429. Epub 2018 Feb 22.

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1002/yea.3303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001429PMC
June 2018

nextPARS: parallel probing of RNA structures in Illumina.

RNA 2018 04 22;24(4):609-619. Epub 2018 Jan 22.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.

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http://dx.doi.org/10.1261/rna.063073.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855959PMC
April 2018

Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa.

Genome Announc 2018 Apr 26;6(17). Epub 2018 Apr 26.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain

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http://dx.doi.org/10.1128/genomeA.00214-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5920163PMC
April 2018

Hybridization and emergence of virulence in opportunistic human yeast pathogens.

Yeast 2018 01 14;35(1):5-20. Epub 2017 Sep 14.

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1002/yea.3242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813172PMC
January 2018

Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans.

Curr Biol 2018 01 14;28(1):15-27.e7. Epub 2017 Dec 14.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2017.11.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772174PMC
January 2018

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events.

BMC Biol 2018 01 25;16(1):15. Epub 2018 Jan 25.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1186/s12915-018-0482-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5785856PMC
January 2018

Peroxisomes in parasitic protists.

Mol Biochem Parasitol 2016 Sep - Oct;209(1-2):35-45. Epub 2016 Feb 16.

Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, UK; Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, UK; Laboratorio de Enzimología de Parásitos, Departamento de Biología, Universidad de Los Andes, Mérida, Venezuela. Electronic address:

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http://dx.doi.org/10.1016/j.molbiopara.2016.02.005DOI Listing
November 2017

Distinct roles of the polarity factors Boi1 and Boi2 in the control of exocytosis and abscission in budding yeast.

Mol Biol Cell 2017 Nov 13;28(22):3082-3094. Epub 2017 Sep 13.

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain

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http://dx.doi.org/10.1091/mbc.E17-06-0404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662264PMC
November 2017

Regulatory Mechanisms of a Highly Pectinolytic Mutant of and Functional Analysis of a Candidate Gene in the Plant Pathogen .

Front Microbiol 2017 8;8:1627. Epub 2017 Sep 8.

Departamento de Genetica, Universidad de Cordoba and Campus de Excelencia Agroalimentario (ceiA3)Cordoba, Spain.

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http://dx.doi.org/10.3389/fmicb.2017.01627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599776PMC
September 2017

Eukaryotic transporters for hydroxyderivatives of benzoic acid.

Sci Rep 2017 08 21;7(1):8998. Epub 2017 Aug 21.

Departments of Biochemistry and Genetics, Comenius University in Bratislava, Faculty of Natural Sciences, Ilkovičova 6, 842 15, Bratislava, Slovak Republic.

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http://dx.doi.org/10.1038/s41598-017-09408-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5566891PMC
August 2017

Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host.

PLoS Genet 2017 May 24;13(5):e1006816. Epub 2017 May 24.

Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain.

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http://dx.doi.org/10.1371/journal.pgen.1006816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5464674PMC
May 2017

The Case of the Missing Ancient Fungal Polyploids.

Am Nat 2016 Dec 26;188(6):602-614. Epub 2016 Sep 26.

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http://dx.doi.org/10.1086/688763DOI Listing
December 2016

Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes.

Front Microbiol 2016 20;7:2001. Epub 2016 Dec 20.

Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain.

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http://dx.doi.org/10.3389/fmicb.2016.02001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5169069PMC
December 2016

High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation.

Dev Cell 2016 10 13;39(2):186-197. Epub 2016 Oct 13.

Proteomics Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2016.09.019DOI Listing
October 2016

Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems.

Mol Biol Evol 2016 09 12;33(9):2441-53. Epub 2016 Jul 12.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA

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http://dx.doi.org/10.1093/molbev/msw122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989117PMC
September 2016

Evolutionary genomics of yeast pathogens in the Saccharomycotina.

FEMS Yeast Res 2016 09 3;16(6). Epub 2016 Aug 3.

Department of Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/femsyr/fow064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5815160PMC
September 2016

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

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

Redundans: an assembly pipeline for highly heterozygous genomes.

Nucleic Acids Res 2016 07 29;44(12):e113. Epub 2016 Apr 29.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gkw294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937319PMC
July 2016

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.

Nucleic Acids Res 2016 07 19;44(W1):W176-80. Epub 2016 May 19.

Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain Microbiology and Cell Science, IFAS, University of Florida, Gainesville, USA

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http://dx.doi.org/10.1093/nar/gkw443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987953PMC
July 2016

Secondary structure impacts patterns of selection in human lncRNAs.

BMC Biol 2016 07 25;14:60. Epub 2016 Jul 25.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1186/s12915-016-0283-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4960838PMC
July 2016

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.

Curr Biol 2016 06 26;26(12):1577-1584. Epub 2016 May 26.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089372PMC
http://dx.doi.org/10.1016/j.cub.2016.04.038DOI Listing
June 2016

Long Non-Coding RNAs As Potential Novel Prognostic Biomarkers in Colorectal Cancer.

Front Genet 2016 12;7:54. Epub 2016 Apr 12.

Department of Oncology Research, Parc Taulí Foundation, Corporació Sanitària Parc Taulí - University Institute - UAB BarcelonaSabadell, Spain; Oncology Service, Hospital de Sabadell, Corporació Sanitària Parc Taulí - University Institute - UAB BarcelonaSabadell, Spain.

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http://dx.doi.org/10.3389/fgene.2016.00054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828582PMC
May 2016

The birth of a deadly yeast: tracing the evolutionary emergence of virulence traits in Candida glabrata.

FEMS Yeast Res 2016 Mar 17;16(2):fov110. Epub 2015 Dec 17.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/femsyr/fov110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5815135PMC
March 2016

Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry.

Nature 2016 Mar 3;531(7592):101-4. Epub 2016 Feb 3.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Carrer del Dr Aiguader, 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1038/nature16941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780264PMC
March 2016

Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes.

Genome Biol Evol 2016 Feb 9;8(3):470-80. Epub 2016 Feb 9.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biochemistry, Mississippi State University

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http://dx.doi.org/10.1093/gbe/evw013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4825420PMC
February 2016

Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi.

Fungal Genet Biol 2016 Jan 10;86:71-80. Epub 2015 Dec 10.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.fgb.2015.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712825PMC
January 2016

Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum.

BMC Genomics 2016 Jan 5;17:19. Epub 2016 Jan 5.

DiSAFA - Dept. Agricultural, Forestry and Food Sciences and AGROINNOVA - Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, Torino, Italy.

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http://dx.doi.org/10.1186/s12864-015-2347-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700700PMC
January 2016

Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes.

Biochimie 2015 Dec 11;119:262-8. Epub 2015 Apr 11.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1016/j.biochi.2015.03.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678951PMC
December 2015

Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing.

Appl Environ Microbiol 2015 Dec 2;81(24):8445-56. Epub 2015 Oct 2.

Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain Multidisciplinary Institute of Environmental Studies Ramon Margalef, University of Alicante, Alicante, Spain

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http://dx.doi.org/10.1128/AEM.02690-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644643PMC
December 2015

Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum.

Genome Biol Evol 2015 Dec 14;8(1):218-27. Epub 2015 Dec 14.

Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana De Recerca I Estudis Avançats (ICREA), Barcelona, Spain

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http://dx.doi.org/10.1093/gbe/evv252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758248PMC
December 2015

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis.

PLoS Genet 2015 Oct 30;11(10):e1005626. Epub 2015 Oct 30.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pgen.1005626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627764PMC
October 2015

The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships.

BMC Genomics 2015 Oct 30;16:887. Epub 2015 Oct 30.

Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Presidente Antonio Carlos, 6627 - Pampulha, Belo Horizonte, MG, 31270-901, Brazil.

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http://dx.doi.org/10.1186/s12864-015-2091-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4628237PMC
October 2015

Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization.

Genome Res 2015 Sep 20;25(9):1256-67. Epub 2015 Jul 20.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain; Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain;

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http://dx.doi.org/10.1101/gr.190538.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561486PMC
September 2015

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage.

PLoS Biol 2015 Aug 7;13(8):e1002220. Epub 2015 Aug 7.

Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pbio.1002220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529251PMC
August 2015

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Genome Biol Evol 2015 Jul 1;7(7):1988-99. Epub 2015 Jul 1.

Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain Universitat Pompeu Fabra, Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats, Barcelona, Spain.

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http://dx.doi.org/10.1093/gbe/evv121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524488PMC
July 2015

Origin, diversification and substrate specificity in the family of NCS1/FUR transporters.

Mol Microbiol 2015 Jun 7;96(5):927-50. Epub 2015 Apr 7.

Faculty of Biology, University of Athens, Panepistimioupolis, Athens, 15784, Greece.

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http://dx.doi.org/10.1111/mmi.12982DOI Listing
June 2015

Metabolic gene clusters encoding the enzymes of two branches of the 3-oxoadipate pathway in the pathogenic yeast Candida albicans.

FEMS Yeast Res 2015 May 4;15(3). Epub 2015 Mar 4.

Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius University, Mlynska dolina CH-1 and B-1, 842 15 Bratislava, Slovakia

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http://dx.doi.org/10.1093/femsyr/fov006DOI Listing
May 2015

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Science 2014 Dec 11;346(6215):1254449. Epub 2014 Dec 11.

Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.

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http://dx.doi.org/10.1126/science.1254449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386873PMC
December 2014