Publications by authors named "Fatima Al-Shahrour"

83Publications

Metatax: Metataxonomics with a Compi-Based Pipeline for Precision Medicine.

Interdiscip Sci 2020 Sep 30;12(3):252-257. Epub 2020 Apr 30.

Department of Computer Science, University of Vigo, ESEI, Campus As Lagoas, 32004, Ourense, Spain.

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http://dx.doi.org/10.1007/s12539-020-00368-6DOI Listing
September 2020

Global Transcriptomic Profiling of the Bone Marrow Stromal Microenvironment during Postnatal Development, Aging, and Inflammation.

Cell Rep 2019 12;29(10):3313-3330.e4

Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.11.004DOI Listing
December 2019

In Silico Drug Prescription for Targeting Cancer Patient Heterogeneity and Prediction of Clinical Outcome.

Cancers (Basel) 2019 Sep 13;11(9). Epub 2019 Sep 13.

Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.

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http://dx.doi.org/10.3390/cancers11091361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769767PMC
September 2019

Precision medicine needs pioneering clinical bioinformaticians.

Brief Bioinform 2019 05;20(3):752-766

Spanish National Cancer Research Centre.

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http://dx.doi.org/10.1093/bib/bbx144DOI Listing
May 2019

Pancreas Cancer Precision Treatment Using Avatar Mice from a Bioinformatics Perspective.

Public Health Genomics 2017 1;20(2):81-91. Epub 2017 Sep 1.

Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.

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http://dx.doi.org/10.1159/000479812DOI Listing
April 2018

Treatment of Pancreatic Cancer Patient-Derived Xenograft Panel with Metabolic Inhibitors Reveals Efficacy of Phenformin.

Clin Cancer Res 2017 Sep 13;23(18):5639-5647. Epub 2017 Jun 13.

Abramson Cancer Center, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1158/1078-0432.CCR-17-1115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6540110PMC
September 2017

Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML.

Cell 2016 Apr;165(2):303-16

Department of Medicine, Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.03.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4826477PMC
April 2016

Mutant Calreticulin Requires Both Its Mutant C-terminus and the Thrombopoietin Receptor for Oncogenic Transformation.

Cancer Discov 2016 Apr 7;6(4):368-81. Epub 2016 Mar 7.

Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Broad Institute, Cambridge, Massachusetts. Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1158/2159-8290.CD-15-1434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851866PMC
April 2016

MicroRNA deep-sequencing reveals master regulators of follicular and papillary thyroid tumors.

Mod Pathol 2015 Jun 27;28(6):748-57. Epub 2015 Feb 27.

1] Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain [2] ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain.

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http://dx.doi.org/10.1038/modpathol.2015.44DOI Listing
June 2015

Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment.

Clin Cancer Res 2014 May 14;20(9):2476-84. Epub 2014 Mar 14.

Authors' Affiliations: Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Champions Oncology, Baltimore, Maryland; Personal Genome Diagnostics, Inc., Baltimore, Maryland; Laboratorio Dianas Terapéuticas, Hospital Universitario Madrid-Sanchinarro, Madrid, Spain; Centro Integral Oncológico Clara Campal, Hospital Universitario Madrid-Sanchinarro, Madrid, Spain; Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322867PMC
http://dx.doi.org/10.1158/1078-0432.CCR-13-3047DOI Listing
May 2014

Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs.

J Exp Med 2014 Jan 6;211(1):71-87. Epub 2014 Jan 6.

Molecular Pharmacology and Chemistry Program, 2 Center for Cell Engineering, and 3 Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065.

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http://www.jem.org/lookup/doi/10.1084/jem.20130736
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http://dx.doi.org/10.1084/jem.20130736DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892968PMC
January 2014

Distinct roles for long-term hematopoietic stem cells and erythroid precursor cells in a murine model of Jak2V617F-mediated polycythemia vera.

Blood 2012 Jul 24;120(1):166-72. Epub 2012 May 24.

Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1182/blood-2012-01-402396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390954PMC
July 2012

Selection upon genome architecture: conservation of functional neighborhoods with changing genes.

PLoS Comput Biol 2010 Oct 7;6(10):e1000953. Epub 2010 Oct 7.

Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1000953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951340PMC
October 2010

SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.

Nucleic Acids Res 2009 Jul 19;37(Web Server issue):W109-14. Epub 2009 May 19.

Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkp402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703972PMC
July 2009

Gene set internal coherence in the context of functional profiling.

BMC Genomics 2009 Apr 27;10:197. Epub 2009 Apr 27.

Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.

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http://dx.doi.org/10.1186/1471-2164-10-197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680416PMC
April 2009

Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli.

Microbiology (Reading) 2009 Mar;155(Pt 3):813-824

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal.

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http://dx.doi.org/10.1099/mic.0.023911-0DOI Listing
March 2009

Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution.

Bioinformatics 2009 Apr 19;25(8):1078-9. Epub 2009 Feb 19.

Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp091DOI Listing
April 2009

Expression and microarrays.

Methods Mol Biol 2008 ;453:245-55

Department of Bioinformatics, Centro de Investigación Príncipe Felipe, Valencia, Spain.

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http://dx.doi.org/10.1007/978-1-60327-429-6_12DOI Listing
October 2008

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Nucleic Acids Res 2008 Jul 31;36(Web Server issue):W341-6. Epub 2008 May 31.

Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Autopista del Saler 16, E46013 Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkn318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447758PMC
July 2008

Functional profiling of microarray experiments using text-mining derived bioentities.

Bioinformatics 2007 Nov 13;23(22):3098-9. Epub 2007 Sep 13.

Department of Bioinformatics and Functional Genomics Node, (INB), Centro de Investigación Príncipe Felipe (CIPF), Valencia, E46013, Spain.

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http://bioinformatics.oxfordjournals.org/content/23/22/3098.
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btm445DOI Listing
November 2007

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.

BMC Bioinformatics 2007 May 22;8 Suppl 4:S4. Epub 2007 May 22.

Structural Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain.

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http://dx.doi.org/10.1186/1471-2105-8-S4-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892083PMC
May 2007

Functional profiling and gene expression analysis of chromosomal copy number alterations.

Bioinformation 2007 Apr 10;1(10):432-5. Epub 2007 Apr 10.

Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, E-46013, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1896059PMC
http://dx.doi.org/10.6026/97320630001432DOI Listing
April 2007

Evidence for systems-level molecular mechanisms of tumorigenesis.

BMC Genomics 2007 Jun 20;8:185. Epub 2007 Jun 20.

Bioinformatics and Biostatistics Unit, and Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Barcelona, Spain.

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http://dx.doi.org/10.1186/1471-2164-8-185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929080PMC
June 2007

A function-centric approach to the biological interpretation of microarray time-series.

Genome Inform 2006 ;17(2):57-66

Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Autopista del Saler 16, E46013, Valencia, Spain.

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June 2007

DBAli tools: mining the protein structure space.

Nucleic Acids Res 2007 Jul 3;35(Web Server issue):W393-7. Epub 2007 May 3.

Structural Genomics Unit, and California Institute for Quantitative Biomedical Research, University of California at San Francisco, San Francisco, CA 94158-2330, USA.

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http://dx.doi.org/10.1093/nar/gkm236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933139PMC
July 2007

ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.

Nucleic Acids Res 2007 Jul 27;35(Web Server issue):W81-5. Epub 2007 Apr 27.

Bioinformatics Department, Centro de Investigación Príncipe Felipe, INB, CIPF, Valencia 46013, Spain.

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http://dx.doi.org/10.1093/nar/gkm257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933149PMC
July 2007

Next station in microarray data analysis: GEPAS.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W486-91

Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, E46013, Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkl197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538867PMC
July 2006

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W472-6

Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, E-46013, Valencia, Spain.

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http://dx.doi.org/10.1093/nar/gkl172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538844PMC
July 2006

Ontology-driven approaches to analyzing data in functional genomics.

Methods Mol Biol 2006 ;316:67-86

Computer Science Research Institute, University of Ulster, Northern Ireland, UK.

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http://dx.doi.org/10.1385/1-59259-964-8:67DOI Listing
June 2006

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W616-20

Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO) Melchor Fernández Almagro 3, 28029 Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gki500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160260PMC
July 2005

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W460-4

Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO) Melchor Fernández Almagro 3, 28029, Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gki456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160217PMC
July 2005

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.

Bioinformatics 2005 Jul 19;21(13):2988-93. Epub 2005 Apr 19.

Department of Bioinformatics, and Functional Genomics Node (INB), Centro de Investigación Príncipe Felipe Autopista del Saler 16, 46013 Valencia, Spain.

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http://dx.doi.org/10.1093/bioinformatics/bti457DOI Listing
July 2005

New challenges in gene expression data analysis and the extended GEPAS.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W485-91

Bioinformatics Unit, Biotechnology Programme, Centro Nacional de Investigaciones Oncológicas, Melchor Fernández Almagro, 3, E-28029 Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkh421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441559PMC
July 2004

PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W242-8

Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain.

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http://dx.doi.org/10.1093/nar/gkh438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441576PMC
July 2004

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes.

Bioinformatics 2004 Mar 22;20(4):578-80. Epub 2004 Jan 22.

Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btg455DOI Listing
March 2004

GEPAS: A web-based resource for microarray gene expression data analysis.

Nucleic Acids Res 2003 Jul;31(13):3461-7

Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas, c/Melchor Fernández Almagro 3, 28029, Madrid, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168997PMC
http://dx.doi.org/10.1093/nar/gkg591DOI Listing
July 2003