Marilyn Safran

Summary

Affiliation: Weizmann Institute of Science
Country: Israel

Publications

  1. ncbi request reprint GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes
    Vered Chalifa-Caspi
    Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 20:1457-8. 2004
  2. pmc Novel definition files for human GeneChips based on GeneAnnot
    Francesco Ferrari
    Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G Campi 287, 41100, Modena, Italy
    BMC Bioinformatics 8:446. 2007
  3. pmc GeneCards Version 3: the human gene integrator
    Marilyn Safran
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Database (Oxford) 2010:baq020. 2010
  4. ncbi request reprint GeneCards 2002: towards a complete, object-oriented, human gene compendium
    Marilyn Safran
    Departments of Molecular Genetics Biological Services Bioinformatics Unit Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 18:1542-3. 2002
  5. pmc Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE
    Marilyn Safran
    Department of Biological Services Bioinformatics Unit, The Weizmann Institute of Science, 76100 Rehovot, Israel
    Nucleic Acids Res 31:142-6. 2003
  6. ncbi request reprint Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
    Itai Yanai
    Department of Molecular Genetics, Weizmann Institute of Science 76100 Rehovot, Israel
    Bioinformatics 21:650-9. 2005
  7. doi request reprint Non-redundant compendium of human ncRNA genes in GeneCards
    Frida Belinky
    Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 29:255-61. 2013
  8. pmc GIFtS: annotation landscape analysis with GeneCards
    Arye Harel
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    BMC Bioinformatics 10:348. 2009
  9. ncbi request reprint GeneLoc: exon-based integration of human genome maps
    Naomi Rosen
    Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 19:i222-4. 2003
  10. pmc GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases
    Maxim Shklar
    Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
    Nucleic Acids Res 33:D556-61. 2005

Collaborators

Detail Information

Publications16

  1. ncbi request reprint GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes
    Vered Chalifa-Caspi
    Department of Biological Services, Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 20:1457-8. 2004
    ..Moreover, a gene is often represented by more than one probeset, and analyzing probe matches at the mRNA level can help one deduce whether these probesets are derived from the same or different splice variants...
  2. pmc Novel definition files for human GeneChips based on GeneAnnot
    Francesco Ferrari
    Department of Biomedical Sciences, University of Modena and Reggio Emilia, via G Campi 287, 41100, Modena, Italy
    BMC Bioinformatics 8:446. 2007
    ..In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence...
  3. pmc GeneCards Version 3: the human gene integrator
    Marilyn Safran
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Database (Oxford) 2010:baq020. 2010
    ..Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite. Database URL: www.genecards.org...
  4. ncbi request reprint GeneCards 2002: towards a complete, object-oriented, human gene compendium
    Marilyn Safran
    Departments of Molecular Genetics Biological Services Bioinformatics Unit Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 18:1542-3. 2002
    ..In the post-genomic era, functional analysis of genes requires a sophisticated interdisciplinary arsenal. Comprehensive resources are challenged to provide consistently improving, state-of-the-art tools...
  5. pmc Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE
    Marilyn Safran
    Department of Biological Services Bioinformatics Unit, The Weizmann Institute of Science, 76100 Rehovot, Israel
    Nucleic Acids Res 31:142-6. 2003
    ..weizmann.ac.il/HORDE). The synergistic relationships amongst these efforts have positively impacted the quality, quantity and usefulness of the GeneCards gene compendium...
  6. ncbi request reprint Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
    Itai Yanai
    Department of Molecular Genetics, Weizmann Institute of Science 76100 Rehovot, Israel
    Bioinformatics 21:650-9. 2005
    ..Genes are often characterized dichotomously as either housekeeping or single-tissue specific. We conjectured that crucial functional information resides in genes with midrange profiles of expression...
  7. doi request reprint Non-redundant compendium of human ncRNA genes in GeneCards
    Frida Belinky
    Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
    Bioinformatics 29:255-61. 2013
    ..Non-coding RNA (ncRNA) genes are increasingly acknowledged for their importance in the human genome. However, there is no comprehensive non-redundant database for all such human genes...
  8. pmc GIFtS: annotation landscape analysis with GeneCards
    Arye Harel
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    BMC Bioinformatics 10:348. 2009
    ..GeneCards is a gene-centric compendium of rich annotative information for over 50,000 human gene entries, building upon 68 data sources, including Gene Ontology (GO), pathways, interactions, phenotypes, publications and many more...
  9. ncbi request reprint GeneLoc: exon-based integration of human genome maps
    Naomi Rosen
    Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 19:i222-4. 2003
    ..Despite the numerous available whole-genome mapping resources, no comprehensive, integrated map of the human genome yet exists...
  10. pmc GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases
    Maxim Shklar
    Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
    Nucleic Acids Res 33:D556-61. 2005
    ..3 of GeneTide, are further annotated with various parameters, including splicing evidence and expression data extracted from the GeneNote database, to determine their validity as possible de novo genes...
  11. doi request reprint GeneDecks: paralog hunting and gene-set distillation with GeneCards annotation
    Gil Stelzer
    Departments of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    OMICS 13:477-87. 2009
    ..GeneDecks enables the elucidation of unsuspected putative functional paralogs, and a refined scrutiny of various gene-sets (e.g., from high-throughput experiments) for discovering relevant biological patterns...
  12. pmc In-silico human genomics with GeneCards
    Gil Stelzer
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
    Hum Genomics 5:709-17. 2011
    ....
  13. pmc MalaCards: an integrated compendium for diseases and their annotation
    Noa Rappaport
    Department of Molecular Genetics, Weizmann Institute of Science, 234 Hertzel St Rehovot, 76100, Israel
    Database (Oxford) 2013:bat018. 2013
    ..Work in progress includes hierarchical malady classification, ontological mapping and disease set analyses, striving to make MalaCards an even more effective tool for biomedical research. Database URL: http://www.malacards.org/..
  14. ncbi request reprint GeneNote: whole genome expression profiles in normal human tissues
    Orit Shmueli
    Department of Molecular Genetics, The Weizmann Institute of Science, 76100 Rehovot, Israel
    C R Biol 326:1067-72. 2003
    ..The data is posted in GeneNote (http://genecards.weizmann.ac.il/genenote/), a widely used compendium of human genes (http://bioinfo.weizmann.ac.il/genecards)...
  15. doi request reprint Omics data management and annotation
    Arye Harel
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Methods Mol Biol 719:71-96. 2011
    ....
  16. ncbi request reprint GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia
    Vered Chalifa-Caspi
    Bioinformatics Support Unit, Life Sciences Dept, Ben Gurion University of the Negev, Beer Sheva, Israel
    Brief Bioinform 4:349-60. 2003
    ....