| Year |
Citation |
Score |
| 2017 |
Martínez M, Sorzano COS, Pascual-Montano A, Carazo JM. Gene signature associated with benign neurofibroma transformation to malignant peripheral nerve sheath tumors. Plos One. 12: e0178316. PMID 28542306 DOI: 10.1371/Journal.Pone.0178316 |
0.676 |
|
| 2016 |
Manesia JK, Franch M, Tabas-Madrid D, Nogales-Cadenas R, Vanwelden T, Van Den Bosch E, Xu Z, Pascual-Montano A, Khurana S, Verfaillie C. Distinct molecular signature of murine fetal liver and adult hematopoietic stem cells identifies novel regulators of hematopoietic stem cell function. Stem Cells and Development. PMID 27958775 DOI: 10.1089/Scd.2016.0294 |
0.344 |
|
| 2015 |
Tabas-Madrid D, Alves-Cruzeiro J, Segura V, Guruceaga E, Vialas V, Prieto G, Garcia C, Corrales FJ, Albar JP, Pascual-Montano A. Proteogenomics Dashboard for the Human Proteome Project. Journal of Proteome Research. PMID 26144527 DOI: 10.1021/Acs.Jproteome.5B00466 |
0.385 |
|
| 2015 |
Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, ... ... Pascual-Montano A, et al. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. Journal of Proteome Research. PMID 26076068 DOI: 10.1021/Pr5013009 |
0.337 |
|
| 2015 |
Setoain J, Franch M, Martínez M, Tabas-Madrid D, Sorzano CO, Bakker A, Gonzalez-Couto E, Elvira J, Pascual-Montano A. NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning. Nucleic Acids Research. 43: W193-9. PMID 25940629 DOI: 10.1093/Nar/Gkv445 |
0.536 |
|
| 2014 |
Alves-Cruzeiro JM, Nogales-Cadenas R, Pascual-Montano AD. CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster. Nucleic Acids Research. 42: D430-6. PMID 24270791 DOI: 10.1093/nar/gkt1126 |
0.323 |
|
| 2014 |
Segura V, Medina-Aunon JA, Mora MI, MartÃnez-Bartolomé S, Abian J, Aloria K, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Beaskoetxea J, Bech-Serra JJ, Blanco F, Monteiro MB, Cáceres D, ... ... Pascual-Montano A, et al. Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome. Journal of Proteome Research. 13: 158-72. PMID 24138474 DOI: 10.1021/Pr400721R |
0.328 |
|
| 2013 |
Aranguren XL, Agirre X, Beerens M, Coppiello G, Uriz M, Vandersmissen I, Benkheil M, Panadero J, Aguado N, Pascual-Montano A, Segura V, Prósper F, Luttun A. Unraveling a novel transcription factor code determining the human arterial-specific endothelial cell signature. Blood. 122: 3982-92. PMID 24108462 DOI: 10.1182/Blood-2013-02-483255 |
0.316 |
|
| 2012 |
Tabas-Madrid D, Nogales-Cadenas R, Pascual-Montano A. GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. Nucleic Acids Research. 40: W478-83. PMID 22573175 DOI: 10.1093/nar/gks402 |
0.351 |
|
| 2011 |
Rebholz-Schuhmann D, Jimeno Yepes A, Li C, Kafkas S, Lewin I, Kang N, Corbett P, Milward D, Buyko E, Beisswanger E, Hornbostel K, Kouznetsov A, Witte R, Laurila JB, Baker CJ, ... ... Pascual-Montano A, et al. Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. Journal of Biomedical Semantics. 2: S11. PMID 22166494 DOI: 10.1186/2041-1480-2-S5-S11 |
0.318 |
|
| 2011 |
Fontanillo C, Nogales-Cadenas R, Pascual-Montano A, De las Rivas J. Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. Plos One. 6: e24289. PMID 21949701 DOI: 10.1371/Journal.Pone.0024289 |
0.452 |
|
| 2011 |
Pascual-Montano A. Gene expression modular analysis: an overview from the data mining perspective Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery. 1: 381-396. DOI: 10.1002/Widm.29 |
0.454 |
|
| 2010 |
Vazquez M, Nogales-Cadenas R, Arroyo J, Botías P, García R, Carazo JM, Tirado F, Pascual-Montano A, Carmona-Saez P. MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures. Nucleic Acids Research. 38: W228-32. PMID 20513648 DOI: 10.1093/Nar/Gkq476 |
0.576 |
|
| 2010 |
Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J, García F, Marbà M, Montaner D, Dopazo J. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research. 38: W210-3. PMID 20478823 DOI: 10.1093/Nar/Gkq388 |
0.446 |
|
| 2010 |
Neves ML, Carazo JM, Pascual-Montano A. Moara: a Java library for extracting and normalizing gene and protein mentions. Bmc Bioinformatics. 11: 157. PMID 20346105 DOI: 10.1186/1471-2105-11-157 |
0.51 |
|
| 2010 |
Pascual-Montano A, Carazo JM. Efficient functional bioinformatics tools: towards understanding biological processes Embnet.Journal. 16: 31. DOI: 10.14806/Ej.16.1.184 |
0.613 |
|
| 2009 |
Vialás V, Nogales-Cadenas R, Nombela C, Pascual-Montano A, Gil C. Proteopathogen, a protein database for studying Candida albicans--host interaction. Proteomics. 9: 4664-8. PMID 19743419 DOI: 10.1002/Pmic.200900023 |
0.352 |
|
| 2009 |
Nogales-Cadenas R, Carmona-Saez P, Vazquez M, Vicente C, Yang X, Tirado F, Carazo JM, Pascual-Montano A. GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Research. 37: W317-22. PMID 19465387 DOI: 10.1093/Nar/Gkp416 |
0.563 |
|
| 2009 |
Vazquez M, Carmona-Saez P, Nogales-Cadenas R, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A. SENT: semantic features in text. Nucleic Acids Research. 37: W153-9. PMID 19458159 DOI: 10.1093/Nar/Gkp392 |
0.544 |
|
| 2009 |
Nogales-Cadenas R, Abascal F, Díez-Pérez J, Carazo JM, Pascual-Montano A. CentrosomeDB: a human centrosomal proteins database. Nucleic Acids Research. 37: D175-80. PMID 18971254 DOI: 10.1093/Nar/Gkn815 |
0.553 |
|
| 2008 |
Chagoyen M, Carazo JM, Pascual-Montano A. Assessment of protein set coherence using functional annotations. Bmc Bioinformatics. 9: 444. PMID 18937846 DOI: 10.1186/1471-2105-9-444 |
0.53 |
|
| 2008 |
Abascal F, Carmona-Saez P, Carazo JM, Pascual-Montano A. ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data. Bioinformatics (Oxford, England). 24: 1208-9. PMID 18339638 DOI: 10.1093/Bioinformatics/Btn094 |
0.556 |
|
| 2008 |
Anton MA, Gorostiaga D, Guruceaga E, Segura V, Carmona-Saez P, Pascual-Montano A, Pio R, Montuenga LM, Rubio A. SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays. Genome Biology. 9: R46. PMID 18312629 DOI: 10.1186/Gb-2008-9-2-R46 |
0.311 |
|
| 2007 |
Liang W, Pascual-Montano A, Silva AJ, Benitez JA. The cyclic AMP receptor protein modulates quorum sensing, motility and multiple genes that affect intestinal colonization in Vibrio cholerae. Microbiology (Reading, England). 153: 2964-75. PMID 17768239 DOI: 10.1099/Mic.0.2007/006668-0 |
0.333 |
|
| 2007 |
Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A. GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biology. 8: R3. PMID 17204154 DOI: 10.1186/Gb-2007-8-1-R3 |
0.623 |
|
| 2006 |
Pascual-Montano A, Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Marqui RD. bioNMF: a versatile tool for non-negative matrix factorization in biology. Bmc Bioinformatics. 7: 366. PMID 16875499 DOI: 10.1186/1471-2105-7-366 |
0.581 |
|
| 2006 |
Chagoyen M, Carmona-Saez P, Gil C, Carazo JM, Pascual-Montano A. A literature-based similarity metric for biological processes. Bmc Bioinformatics. 7: 363. PMID 16872502 DOI: 10.1186/1471-2105-7-363 |
0.498 |
|
| 2006 |
Pascual-Montano A, Carazo JM, Kochi K, Lehmann D, Pascual-Marqui RD. Nonsmooth nonnegative matrix factorization (nsNMF). Ieee Transactions On Pattern Analysis and Machine Intelligence. 28: 403-15. PMID 16526426 DOI: 10.1109/Tpami.2006.60 |
0.551 |
|
| 2006 |
Carmona-Saez P, Pascual-Marqui RD, Tirado F, Carazo JM, Pascual-Montano A. Biclustering of gene expression data by Non-smooth Non-negative Matrix Factorization. Bmc Bioinformatics. 7: 78. PMID 16503973 DOI: 10.1186/1471-2105-7-78 |
0.562 |
|
| 2006 |
Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A. Integrated analysis of gene expression by Association Rules Discovery. Bmc Bioinformatics. 7: 54. PMID 16464256 DOI: 10.1186/1471-2105-7-54 |
0.624 |
|
| 2006 |
Chagoyen M, Carmona-Saez P, Shatkay H, Carazo JM, Pascual-Montano A. Discovering semantic features in the literature: a foundation for building functional associations. Bmc Bioinformatics. 7: 41. PMID 16438716 DOI: 10.1186/1471-2105-7-41 |
0.592 |
|
| 2006 |
Guerra S, López-Fernández LA, Pascual-Montano A, Nájera JL, Zaballos A, Esteban M. Host response to the attenuated poxvirus vector NYVAC: upregulation of apoptotic genes and NF-kappaB-responsive genes in infected HeLa cells. Journal of Virology. 80: 985-98. PMID 16379000 DOI: 10.1128/Jvi.80.2.985-998.2006 |
0.334 |
|
| 2006 |
Sorzano COS, Marabini R, Pascual-Montano A, Scheres SHW, Carazo JM. Optimization problems in electron microscopy of single particles Annals of Operations Research. 148: 133-165. DOI: 10.1007/S10479-006-0078-8 |
0.701 |
|
| 2004 |
Sorzano CO, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SH, Carazo JM, Pascual-Montano A. XMIPP: a new generation of an open-source image processing package for electron microscopy. Journal of Structural Biology. 148: 194-204. PMID 15477099 DOI: 10.1016/J.Jsb.2004.06.006 |
0.711 |
|
| 2004 |
Guerra S, López-Fernández LA, Conde R, Pascual-Montano A, Harshman K, Esteban M. Microarray analysis reveals characteristic changes of host cell gene expression in response to attenuated modified vaccinia virus Ankara infection of human HeLa cells. Journal of Virology. 78: 5820-34. PMID 15140980 DOI: 10.1128/Jvi.78.11.5820-5834.2004 |
0.318 |
|
| 2003 |
Guerra S, López-Fernández LA, Pascual-Montano A, Muñoz M, Harshman K, Esteban M. Cellular gene expression survey of vaccinia virus infection of human HeLa cells. Journal of Virology. 77: 6493-506. PMID 12743306 DOI: 10.1128/Jvi.77.11.6493-6506.2003 |
0.314 |
|
| 2003 |
García de la Nava J, Santaella DF, Cuenca Alba J, María Carazo J, Trelles O, Pascual-Montano A. Engene: the processing and exploratory analysis of gene expression data. Bioinformatics (Oxford, England). 19: 657-8. PMID 12651727 DOI: 10.1093/Bioinformatics/Btg028 |
0.309 |
|
| 2002 |
Pascual-Montano A, Taylor KA, Winkler H, Pascual-Marqui RD, Carazo JM. Quantitative self-organizing maps for clustering electron tomograms. Journal of Structural Biology. 138: 114-22. PMID 12160707 DOI: 10.1016/S1047-8477(02)00008-4 |
0.389 |
|
| 2002 |
De-Alarcón PA, Pascual-Montano A, Gupta A, Carazo JM. Modeling shape and topology of low-resolution density maps of biological macromolecules. Biophysical Journal. 83: 619-32. PMID 12124252 DOI: 10.1016/S0006-3495(02)75196-5 |
0.549 |
|
| 2001 |
Pascual-Montano A, Donate LE, Valle M, Bárcena M, Pascual-Marqui RD, Carazo JM. A novel neural network technique for analysis and classification of EM single-particle images. Journal of Structural Biology. 133: 233-45. PMID 11472094 DOI: 10.1006/Jsbi.2001.4369 |
0.704 |
|
| 2001 |
Pascual-Marqui R, Pascual-Montano A, Kochi K, Carazo J. Smoothly distributed fuzzy c-means: a new self-organizing map Pattern Recognition. 34: 2395-2402. DOI: 10.1016/S0031-3203(00)00167-9 |
0.419 |
|
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