Javier Herrero - Publications

Affiliations: 
2000-2004 CNIO (Spanish National Cancer Research Center) 
 2004-2014 European Bioinformatics Institute, Hinxton, England, United Kingdom 
 2014-2015 The Genome Analysis Centre 
 2015- UCL Cancer Institute University College London 

55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Ghorani E, Reading JL, Henry JY, de Massy MR, Rosenthal R, Turati V, Joshi K, Furness AJS, Aissa AB, Saini SK, Ramskov S, Georgiou A, Sunderland MW, Wong YNS, De Mucha MV, ... ... Herrero J, et al. The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nature Cancer. 1: 546-561. PMID 32803172 DOI: 10.1038/s43018-020-0066-y  1
2020 Alrasheed N, Lee L, Ghorani E, Henry JY, Conde L, Chin M, Galas-Filipowicz D, Furness AJS, Chavda SJ, Richards H, De-Silva D, Cohen OC, Patel D, Brooks A, Rodriguez-Justo M, ... ... Herrero J, et al. Marrow infiltrating regulatory T cells correlate with the presence of dysfunctional CD4+PD-1+ cells and inferior survival in patients with newly diagnosed multiple myeloma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 32220887 DOI: 10.1158/1078-0432.CCR-19-1714  1
2019 Chervova O, Conde L, Guerra-Assunção JA, Moghul I, Webster AP, Berner A, Larose Cadieux E, Tian Y, Voloshin V, Jesus TF, Hamoudi R, Herrero J, Beck S. The Personal Genome Project-UK, an open access resource of human multi-omics data. Scientific Data. 6: 257. PMID 31672996 DOI: 10.1038/s41597-019-0205-4  1
2018 Tie CH, Fernandes L, Conde L, Robbez-Masson L, Sumner RP, Peacock T, Rodriguez-Plata MT, Mickute G, Gifford R, Towers GJ, Herrero J, Rowe HM. KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control. Embo Reports. PMID 30061100 DOI: 10.15252/embr.201745000  1
2018 Robbez-Masson L, Tie CHC, Conde L, Tunbak H, Husovsky C, Tchasovnikarova IA, Timms RT, Herrero J, Lehner PJ, Rowe HM. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Research. PMID 29728366 DOI: 10.1101/gr.228171.117  1
2017 Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes I, Armstrong J, Laayouni H, Gordon D, Huddleston J, Perez RG, Povolotskaya I, Armero AS, Garrido JG, Ho D, Ribeca P, ... ... Herrero J, et al. A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0). Gigascience. PMID 29092041 DOI: 10.1093/gigascience/gix098  1
2016 Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, ... ... Herrero J, et al. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Reports. 17: 2137-2150. PMID 27851974 DOI: 10.1016/j.celrep.2016.10.059  1
2016 Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Ensembl comparative genomics resources. Database : the Journal of Biological Databases and Curation. 2016. PMID 27141089 DOI: 10.1093/database/baw053  1
2016 Pignatelli M, Vilella AJ, Muffato M, Gordon L, White S, Flicek P, Herrero J. ncRNA orthologies in the vertebrate lineage. Database : the Journal of Biological Databases and Curation. 2016. PMID 26980512 DOI: 10.1093/database/bav127  1
2016 Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Ensembl comparative genomics resources. Database : the Journal of Biological Databases and Curation. 2016. PMID 26896847 DOI: 10.1093/database/bav096  1
2015 Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J, Loveland JE, Dunn M, Louzada S, Fu B, Chow W, Gilbert J, Austin-Guest S, Beal K, Carvalho-Silva D, Cheng W, et al. The pig X and Y Chromosomes: structure, sequence and evolution. Genome Research. PMID 26560630 DOI: 10.1101/gr.188839.114  1
2015 Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference. Systematic Biology. PMID 26031838 DOI: 10.1093/sysbio/syv033  1
2015 Denas O, Sandstrom R, Cheng Y, Beal K, Herrero J, Hardison RC, Taylor J. Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution. Bmc Genomics. 16: 87. PMID 25765714 DOI: 10.1186/s12864-015-1245-6  1
2015 Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P. Extending reference assembly models. Genome Biology. 16: 13. PMID 25651527 DOI: 10.1186/s13059-015-0587-3  1
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Herrero J, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/nature13992  1
2014 Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, ... ... Herrero J, et al. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Research. 24: 2077-89. PMID 25273068 DOI: 10.1101/gr.174920.114  1
2014 Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 513: 195-201. PMID 25209798 DOI: 10.1038/nature13679  1
2014 . The common marmoset genome provides insight into primate biology and evolution. Nature Genetics. 46: 850-7. PMID 25038751 DOI: 10.1038/ng.3042  1
2014 Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, ... ... Herrero J, et al. Ensembl 2014. Nucleic Acids Research. 42: D749-55. PMID 24316576 DOI: 10.1093/nar/gkt1196  1
2013 Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, ... ... Herrero J, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science (New York, N.Y.). 342: 1235587. PMID 24092746 DOI: 10.1126/science.1235587  1
2013 Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, ... ... Herrero J, et al. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nature Genetics. 45: 776-83. PMID 23749191 DOI: 10.1038/ng.2657  1
2013 Wang Z, Pascual-Anaya J, Zadissa A, Li W, Niimura Y, Huang Z, Li C, White S, Xiong Z, Fang D, Wang B, Ming Y, Chen Y, Zheng Y, Kuraku S, ... ... Herrero J, et al. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nature Genetics. 45: 701-6. PMID 23624526 DOI: 10.1038/ng.2615  1
2013 Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, ... ... Herrero J, et al. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature Genetics. 45: 415-21, 421e1-2. PMID 23435085 DOI: 10.1038/ng.2568  1
2013 Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, ... ... Herrero J, et al. Ensembl 2013. Nucleic Acids Research. 41: D48-55. PMID 23203987 DOI: 10.1093/nar/gks1236  1
2012 Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biology. 13: R49. PMID 22950968 DOI: 10.1186/gb-2012-13-9-r49  1
2012 Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, et al. Insights into hominid evolution from the gorilla genome sequence. Nature. 483: 169-75. PMID 22398555 DOI: 10.1038/nature10842  1
2012 Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J. Toward community standards in the quest for orthologs. Bioinformatics (Oxford, England). 28: 900-4. PMID 22332236 DOI: 10.1093/bioinformatics/bts050  1
2012 Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, ... ... Herrero J, et al. Ensembl 2012. Nucleic Acids Research. 40: D84-90. PMID 22086963 DOI: 10.1093/nar/gkr991  1
2011 Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Herrero J, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/nature10530  1
2011 Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, et al. RNAcentral: A vision for an international database of RNA sequences. Rna (New York, N.Y.). 17: 1941-6. PMID 21940779 DOI: 10.1261/rna.2750811  1
2011 Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, ... ... Herrero J, et al. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biology. 12: R81. PMID 21854559 DOI: 10.1186/gb-2011-12-8-r81  1
2011 Vilella AJ, Birney E, Flicek P, Herrero J. Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. Genome Biology. 12: 401. PMID 21320298 DOI: 10.1186/gb-2011-12-2-401  1
2011 Locke DP, Hillier LW, Warren WC, Worley KC, Nazareth LV, Muzny DM, Yang SP, Wang Z, Chinwalla AT, Minx P, Mitreva M, Cook L, Delehaunty KD, Fronick C, Schmidt H, ... ... Herrero J, et al. Comparative and demographic analysis of orang-utan genomes. Nature. 469: 529-33. PMID 21270892 DOI: 10.1038/nature09687  1
2011 Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, ... ... Herrero J, et al. Ensembl 2011. Nucleic Acids Research. 39: D800-6. PMID 21045057 DOI: 10.1093/nar/gkq1064  1
2010 Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, ... ... Herrero J, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/journal.pbio.1000475  1
2010 Severin J, Beal K, Vilella AJ, Fitzgerald S, Schuster M, Gordon L, Ureta-Vidal A, Flicek P, Herrero J. eHive: an artificial intelligence workflow system for genomic analysis. Bmc Bioinformatics. 11: 240. PMID 20459813 DOI: 10.1186/1471-2105-11-240  1
2010 Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, ... ... Herrero J, et al. Ensembl's 10th year. Nucleic Acids Research. 38: D557-62. PMID 19906699 DOI: 10.1093/nar/gkp972  1
2009 Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics (Oxford, England). 25: 295-301. PMID 19056777 DOI: 10.1093/bioinformatics/btn630  1
2008 Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research. 18: 1829-43. PMID 18849525 DOI: 10.1101/gr.076521.108  1
2008 Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research. 18: 1814-28. PMID 18849524 DOI: 10.1101/gr.076554.108  1
2008 Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nature Biotechnology. 26: 779-85. PMID 18612301 DOI: 10.1038/nbt1414  1
2006 Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J, Van Der Weyden L, Bradley A, Birney E, Adams DJ. TranscriptSNPView: A genome-wide catalog of mouse coding variation [1] Nature Genetics. 38: 853. PMID 16874317 DOI: 10.1038/ng0806-853a  1
2006 Montaner D, Tárraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MA, Alloza E, Herrero J, Al-Shahrour F, Dopazo J. Next station in microarray data analysis: GEPAS. Nucleic Acids Research. 34: W486-91. PMID 16845056 DOI: 10.1093/nar/gkl197  1
2005 Vaquerizas JM, Conde L, Yankilevich P, Cabezón A, Minguez P, Díaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Research. 33: W616-20. PMID 15980548 DOI: 10.1093/nar/gki500  1
2004 Herrero J, Vaquerizas JM, Al-Shahrour F, Conde L, Mateos A, Díaz-Uriarte JS, Dopazo J. New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Research. 32: W485-91. PMID 15215434 DOI: 10.1093/nar/gkh421  1
2003 Herrero J, Díaz-Uriarte R, Dopazo J. An approach to inferring transcriptional regulation among genes from large-scale expression data. Comparative and Functional Genomics. 4: 148-54. PMID 18629097 DOI: 10.1002/cfg.237  1
2003 Herrero J, Al-Shahrour F, Díaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J. GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Research. 31: 3461-7. PMID 12824345  1
2003 Martin MJ, Herrero J, Mateos A, Dopazo J. Comparing bacterial genomes through conservation profiles. Genome Research. 13: 991-8. PMID 12695324 DOI: 10.1101/gr.678303  1
2003 Herrero J, Díaz-Uriarte R, Dopazo J. Gene expression data preprocessing. Bioinformatics (Oxford, England). 19: 655-6. PMID 12651726  1
2002 Herrero J, Dopazo J. Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns. Journal of Proteome Research. 1: 467-70. PMID 12645919 DOI: 10.1021/pr025521v  1
2002 Tracey L, Villuendas R, Ortiz P, Dopazo A, Spiteri I, Lombardia L, Rodríguez-Peralto JL, Fernández-Herrera J, Hernández A, Fraga J, Dominguez O, Herrero J, Alonso MA, Dopazo J, Piris MA. Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma. The American Journal of Pathology. 161: 1825-37. PMID 12414529  1
2002 Tamames J, Clark D, Herrero J, Dopazo J, Blaschke C, Fernández JM, Oliveros JC, Valencia A. Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction. Journal of Biotechnology. 98: 269-83. PMID 12141992 DOI: 10.1016/s0168-1656(02)00137-2  1
2001 Dopazo J, Mendoza A, Herrero J, Caldara F, Humbert Y, Friedli L, Guerrier M, Grand-Schenk E, Gandin C, de Francesco M, Polissi A, Buell G, Feger G, García E, Peitsch M, et al. Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate. Microbial Drug Resistance (Larchmont, N.Y.). 7: 99-125. PMID 11442348 DOI: 10.1089/10766290152044995  1
2001 Herrero J, Valencia A, Dopazo J. A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics (Oxford, England). 17: 126-36. PMID 11238068 DOI: 10.1093/bioinformatics/17.2.126  1
2000 Oliveros JC, Blaschke C, Herrero J, Dopazo J, Valencia A. Expression profiles and biological function. Genome Informatics. Workshop On Genome Informatics. 11: 106-17. PMID 11700592  1
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