Our Publications

Select PathCards Publications

  1. PathCards - Human Biological Pathway Unification (pathcards.genecards.org)
    PathCards: multi-source consolidation of human biological pathways (PubMedId: 25725062, Citations: 334)
    Belinky F, Nativ N, Stelzer G, Zimmerman S, Iny Stein T, Safran M, and Lancet, D
    Database (2015) Vol. 2015: article ID bav006; DOI: 10.1093/database/bav006
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Complete list of our publications and presentations

  1. Expanding and Enriching the LncRNA Gene–Disease Landscape Using the GeneCaRNA Database (Citations: 4)
    Aggarwal S., Rosenblum C., Gould M., Ziman S., Barshir R., Zelig O., Guan-Golan Y., Iny-Stein T., Safran M., Pietrokovski S., Lancet D.
    Biomedicines 2024, 12(6), 1305
    [PDF]
  2. The GeneCards Suite (Citations: 311)
    Safran M, Rosen N, Twik M, BarShir R, Iny Stein T, Dahary D, Fishilevich S, and Lancet D. Chapter
    Practical Guide to Life Science Databases (2022) pp 27-56
    [PDF]
  3. GeneCaRNA: a comprehensive gene-centric database of human non-coding RNAs in the GeneCards Suite (PubMedId: 33676929, Citations: 109)
    Barshir R, Fishilevich F, Iny-Stein T, Zelig O, Mazor Y, Guan-Golan Y, Safran M, Lancet D
    Journal of Molecular Biology (2021), 433 (11), p.166913, DOI: 10.1016/j.jmb.2021.166913
    [PDF]
  4. Disease interpretation of non-coding genomic elements with the GeneCards Suite (Citations: 1)
    Fishilevich S, Barshir R, Iny-Stein T, Zelig O, Guan-Golan Y, Safran M and Lancet D
    Molecular Genetics and Metabolism (2021) Vol.132, eP189, pp S123-S123
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  5. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (PubMedId: 33106848, Citations: 295)
    RNAcentral Consortium
    Nucleic Acids Res. 2021. DOI: 10.1093/nar/gkaa921
    [PDF]
  6. Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene (PubMedId: 33264630, Citations: 30)
    Cooper-Knock J, Zhang S, Kenna KP, Moll T, Franklin JP, Allen S, Nezhad HG, Iacoangeli A, Yacovzada NY, Eitan C, Hornstein E, Ehilak E, Celadova P, Bose D, Farhan S, Fishilevich S, Lancet D, Morrison KE, Shaw CE, Al-Chalabi A; Project MinE ALS Sequencing Consortium, Veldink JH, Kirby J, Snyder MP, Shaw PJ
    Cell Rep. 2020 Dec 1;33(9):108456. DOI: 10.1016/j.celrep.2020.108456
    [PDF]
  7. Genome-wide association study identifies 16 genomic regions associated with circulating cytokines at birth (PubMedId: 33227023, Citations: 17)
    Wang Y, Nudel R, Benros ME, Skogstrand K, Fishilevich S, iPSYCH-BROAD, Lancet D, Sun J, Hougaard DM, Andreassen OA, Mortensen PB, Buil A, Hansen TF, Thompson WK and Werge T
    PLoS Genet 16(11): e1009163. doi: 10.1371/journal.pgen.1009163
    [PDF]
  8. Genome analysis and knowledge-driven variant interpretation with TGex (PubMedId: 31888639, Citations: 55)
    Dahary D, Golan Y, Mazor Y, Zelig O, Barshir R, Twik M, Iny Stein T, Rosner G, Kariv R, Chen F, Zhang Q, Shen Y, Safran M, Lancet D and Fishilevich S
    BMC Med Genomics 12, 200 (2019) doi:10.1186/s12920-019-0647-8
    [PDF]
  9. Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect (PubMedId: 28830434, Citations: 98)
    Rappaport S, Fishilevich S, Nudel R, Twik M, Belinky F, Plaschkes I, Iny Stein T, Cohen D, Oz-Levi D, Safran M, and Lancet D
    BioMed Eng OnLine 2017, 16(Suppl 1):72, DOI: 10.1186/s12938-017-0359-2
    [PDF]
  10. GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (PubMedId: 28605766, Citations: 1305)
    Fishilevich S, Nudel R, Rappaport N, Hadar R, Plaschkes I, Iny Stein T, Rosen N, Kohn A, Twik M, Safran M, Lancet D, and Cohen D
    Database(Oxford)(2017), DOI: 10.1093/database/bax028
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  11. MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search (PubMedId: 27899610, Citations: 598)
    Rappaport N, Twik M, Plaschkes I, Nudel R, Iny Stein T, Levitt J, Gershoni M, Morrey CP, Safran M, and Lancet D
    Nucleic Acids Research(2016), DOI: 10.1093/nar/gkw1012
    [PDF]
  12. VarElect: the phenotype-based variation prioritizer of the GeneCards Suite (PubMedId: 27357693, Citations: 247)
    Stelzer G, Plaschkes I, Oz - Levi D, Alkelai A, Olender T, Zimmerman S, Twik M., Belinky F, Fishilevich S, Nudel R, Guan - Golan Y, Warshawsky D, Dahary D, Kohn A, Mazor Y, Kaplan S, Iny Stein T, Baris H, Rappaport N, Safran M, and Lancet D
    BMC Genomics(2016), 17(Suppl 2):444; DOI: 10.1186/s12864-016-2722-2
    [PDF]
  13. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses (PubMedId: 27322403, Citations: 4633)
    Stelzer G, Rosen R, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Iny Stein T, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary, D, Warshawsky D, Guan - Golan Y, Kohn A, Rappaport N, Safran M, and Lancet D
    Current Protocols in Bioinformatics(2016), 54:1.30.1 - 1.30.33.doi: 10.1002 / cpbi.5
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  14. Genic Insights From Integrated Human Proteomics in GeneCards (PubMedId: 27048349, Citations: 190)
    Fishilevich S, Zimmerman S, Kohn A, Iny Stein T, Safran M, and Lancet D
    Database (2016); doi: 10.1093/database/baw030
    [PDF]
  15. GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data (PubMedId: 26983021, Citations: 253)
    Ben-Ari Fuchs S, Lieder I, Stelzer G, Mazor Y, Buzhor E, Kaplan S, Bogoch Y, Plaschkes I, Shitrit A, Rappaport N, Kohn A, Edgar R, Shenhav L, Safran M, Lancet D, Guan-Golan Y, Warshawsky D, and Strichman R
    OMICS(2016) Volume 20, Number 3; DOI: 10.1089/omi.2015.0168
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  16. PathCards: multi-source consolidation of human biological pathways (PubMedId: 25725062, Citations: 334)
    Belinky F, Nativ N, Stelzer G, Zimmerman S, Iny Stein T, Safran M, and Lancet, D
    Database (2015) Vol. 2015: article ID bav006; DOI: 10.1093/database/bav006
    [PDF]
  17. MalaCards: A Comprehensive Automatically‐Mined Database of Human Diseases (PubMedId: 25199789, Citations: 104)
    Rappaport N, Twik M, Nativ N, Stelzer G, Bahir I, Iny Stein T, Safran M and Lancet D
    Curr. Protoc. Bioinform. 47:1.24:1.24.11.24.19. (Sept 2014)
    [PDF]
  18. Gene Trends: On Muscle, Fat, and Brain
    Lancet D, Stelzer G, Golan Y, and Rinon A
    Genetic Engineering & Biotechnology News, Dec 16, 2013
  19. Gene Trends: Eye-Openers for Unusual Gene Variations
    Lancet D, Golan Y, Leshansky L, and Stelzer G
    Genetic Engineering & Biotechnology News, Oct 24, 2013
  20. Gene Trends: Which Ones Should You Be Studying Now?
    Lancet D, Golan Y, and Stelzer G
    Genetic Engineering & Biotechnology News, Oct 3, 2013
  21. An Overview of Synergistic Data Tools for Biological Scrutiny (Citations: 5)
    Olender T, Safran M, Edgar R, Stelzer G, Nativ N, Rosen N, Shtrichman R, Mazor Y, West M D, Keydar I, Rappaport N, Belinky F, Warshawsky D, and Lancet D
    Israel Journal of Chemistry, Volume 53, Issue 3-4, pages 185-198, April 2013
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  22. MalaCards: an integrated compendium for diseases and their annotation (PubMedId: 23584832, Citations: 320)
    Rappaport N, Nativ N, Stelzer G, Twik M, Guan-Golan Y, Iny Stein T, Bahir I, Belinky F, Morrey CP, Safran M and Lancet D
    Database 2013; doi: 10.1093/database/bat018
    [PDF]
  23. Non-redundant compendium of human ncRNA genes in GeneCards (PubMedId: 23172862, Citations: 56)
    Belinky F, Bahir I, Stelzer G, Zimmerman S, Rosen N, Nativ N, Dalah I, Iny Stein T, Rappaport N, Mituyama M, Safran M and Lancet D. , 29, 2: 255-61 (2013)
    Bioinformatics
    [PDF]
  24. MalaCards – the integrated Human Malady Compendium
    Safran M, Nativ N, Golan Y, Dalah I, Iny Stein T, Stelzer G, and Lancet D. , ISMB 2012
    [PDF]
  25. In-silico Human Genomics with GeneCards (PubMedId: 22155609, Citations: 255)
    Stelzer G, Dalah I, Iny Stein T, Satanower Y, Rosen N, Nativ N, Oz-Levi D, Olender T, Belinky F, Bahir I, Krug H, Perco P, Mayer B, Kolker E, Safran M and Lancet, D. , , 2011 Oct;5(6):709-17
    Human Genomics
    [PDF]
  26. Omics Data Management and Annotation (PubMedId: 21370079, Citations: 23)
    Harel A, Dalah I, Pietrokovski M, Safran M and Lancet D. , Chapter 3 Series: Methods in Molecular Biology, Vol. 719, ISBN: 978-1-61779-026-3, Mayer, Bernd (Ed.), Humana Press, March, 2011
    Bioinformatics for Omics Data: Methods and Protocols
  27. GeneCards Version 3: the human gene integrator (PubMedId: 20689021, Citations: 2027)
    Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I, Doniger T, Krug H, Sirota-Madi A, Olender T, Golan Y, Stelzer G, Harel A and Lancet D
    Database 2010; doi: 10.1093/database/baq020
    [PDF]
  28. GeneDecks: Paralog Hunting and Gene-Set Distillation with GeneCards Annotation (PubMedId: 20001862, Citations: 85)
    Stelzer G, Inger A, Olender T, Iny Stein T, Dalah I, Harel A, Safran M and Lancet D
    OMICS, 2009, 13(6): 477-487
    [PDF]
  29. GIFtS: annotation landscape analysis with GeneCards (PubMedId: 19852797, Citations: 63)
    Harel A, Inger A, Stelzer G, Strichman-Almashanu L, Dalah I, Safran M and Lancet D
    BMC Bioinformatics 2009, 10:348
    [PDF]
  30. GeneDecks: GeneCards-based paralog hunting and gene set distillation
    Stelzer G, Harel A, Inger A, Olender T, Dalah I, Shmoish M, Ron S, Safran M and Lancet D. CSB2008 Aug, 2008
    CSB2008 Aug, 2008
  31. GeneCards tools for combinatorial annotation and dissemination of human genome information
    Lancet D, Safran M, Olender T, Dalah I, Iny-Stein T, Inger A, Harel A and Stelzer G. April, 2008
    GIACS Conference on Data in Complex Systems
  32. GeneCards: One stop site for human gene research
    Stelzer G, Harel A, Dalah A, Rosen N, Shmoish M, Iny Stein T, Sirota A, Madi A, Safran M and Lancet D
    FISEB (ILANIT) , Jan, 2008
  33. Novel definition files for human GeneChips based on GeneAnnot (PubMedId: 18005434, Citations: 146)
    Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli G A, and Bicciato S
    BMC Bioinformatics 2007, 8:446 (15 NOV 2007)
    [PDF]
  34. GeneDecks annotation combinatorics and unification for human genes
    Safran M, Dalah I, Ron S, Shmoish M, Iny-Stein T, Rosen N, Madi A, Sirota A, Stelzer G and Lancet D
    ISMB ECCB 2007
  35. GeneDecks: Gene-Set Analyses of GeneCards Annotations
    Ron S, Strichman-Almashanu L, Shmoish M, Greenshpan O, Sirota A, Madi A, Iny-Stein T, Rosen N, Dalah I, Shmueli O, Safran M, Aumann Y, and Lancet D
    ECCB 2006
  36. GeneDecks: A Systems Biology Facilitator with Combinatorial GeneCards Display
    Lancet D, Ron S, Shmoish M, Madi A, Sirota A, Noy K, Rosen N, Greenshpan O, Shmueli O, Safran M, Aumann Y, and Strichman-Almashanu L. Transcriptome 2005
    [PDF]
  37. GeneDecks: A Systems Biology Facilitator With Combinatorial GeneCards Outlook
    Ron S, Strichman-Almashanu L, Shmoish M, Madi A, Sirota A, Noy K, Rosen N, Shmueli O, Safran M, and Lancet D. Poster and abstract at
    ISMB 2005
    [PDF]
  38. GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases (PubMedId: 15608261, Citations: 17)
    Shklar M, Strichman-Almashanu L, Shmueli O, Shmoish M, Safran M, and Lancet D
    Nucleic Acids Res. 33: D556 - D561 (2005)
    [PDF]
  39. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification (PubMedId: 15388519, Citations: 1211)
    Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, Lancet D, Shmueli O
    Bioinformatics 21, 5: 650-659 (2005)
    [PDF]
  40. TIDE--Terra Incognita Discovery Endeavor: Comprehensive EST assignment to GeneCards genes
    Shklar, M., Shmueli, O., Strichman-Almashanu, L., Shmoish, M., Iny-Stein, T., Safran, M. and Lancet, D. Short paper and talk at
    ISMB/ECCB 2004
    [PDF]
  41. GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes (PubMedId: 14962929, Citations: 69)
    Chalifa-Caspi, V., Yanai, I., Ophir, R., Rosen, N., Shmoish, M., Benjamin-Rodrig, H., Iny Stein, T., Shmueli, O., Safran, M. and Lancet, D
    Bioinformatics 20, 9: 1457-1458 (2004)
    [PDF]
  42. GeneAnnot: Interfacing GeneCards with high-throughput gene expression compendia (PubMedId: 14725348, Citations: 24)
    Chalifa-Caspi, V., Shmueli, O., Benjamin-Rodrig, H., Rosen, N., Shmoish, M., Yanai, I., Ophir, R., Kats, P., Safran, M. and Lancet, D
    Briefings in Bioinformatics 4, 4: 349-360 (2003)
    [PDF]
  43. The GeneCards Family of Databases: GeneCards, GeneLoc, GeneNote and GeneAnnot
    Safran, M., Chalifa-Caspi, V., Shmueli, O., Rosen, N., Benjamin-Rodrig, H., Ophir, R., Yanai, I., Shmoish, M., and Lancet, D. Proceedings of the IEEE Computer Science Bioinformatics Conference CSB2003,(2003) ()
    Poster Abstract at CSB2003
  44. GeneNote: whole genome expression profiles in normal human tissues (PubMedId: 14744114, Citations: 236)
    Shmueli, O., Horn-Saban, S., Chalifa-Caspi, V., Shmoish, M., Ophir, R., Benjamin-Rodrig, H., Safran, M., Domany, E., and Lancet, D
    Comptes Rendus Biologies: 326, 10-11:1067-1072 (2003)
    [PDF]
  45. GeneAnnot: Annotation of high-density oligunocleotide arrays and their linking with GeneCards
    Chalifa-Caspi, V., Yanai, I., Ophir, R., Shmoish,M., Benjamin-Rodrig, H., Rosen, N., Kats, P., Safran, M., Shmueli, O., and Lancet, D
    Poster Abstract at ISMB 2003
  46. GeneLoc: Exon-based integration of human genome maps (PubMedId: 12855462, Citations: 49)
    Rosen, N., Chalifa-Caspi, V., Shmueli, O., Adato, A., Lapidot, M., Stampnitzky, J., Safran, M., and Lancet, D
    Bioinformatics: 19,S1: 222-224 (2003)
    [PDF]
  47. Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE (PubMedId: 12519968, Citations: 254)
    Safran, M., Chalifa-Caspi, V., Shmueli, O., Olender, T., Lapidot, M., Rosen, N., Shmoish, M., Peter, Y., Glusman, G., Feldmesser, E., Adato, A., Peter, I., Khen, M., Atarot, T., Groner, Y., and Lancet, D
    Nucleic Acids Research 31,1:142-146 (2003)
    [PDF]
  48. GeneCards™ 2002: towards a complete, object-oriented, human gene compendium (PubMedId: 12424129, Citations: 1826)
    Safran, M., Solomon, I., Shmueli, O., Lapidot, M., Shen-Orr, S., Adato, A., Ben-Dor, U., Esterman, N., Rosen, N., Peter, I., Olender, T., Chalifa-Caspi, V., and Lancet, D
    Bioinformatics: 18,11: 1542-1543 (2002)
    [PDF]
  49. GeneCards 2002: An Evolving Human Gene Compendium (Citations: 1)
    Safran, M., Solomon, I., Shmueli, O., Lapidot, M., Shen-Orr, S., Adato, A., Ben-Dor, U., Esterman, N., Rosen, N., Peter, I., Olender, T., Chalifa-Caspi, V., and Lancet, D
    Proceedings of the IEEE Computer Science Bioinformatics Conference CSB2002, p. 339 (2002)
  50. GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support. (PubMedId: 9789091, Citations: 547)
    Rebhan, M., Chalifa-Caspi, V., Prilusky, J., and Lancet, D
    Bioinformatics: 14: 656-664 (1998)
    [PDF]
  51. Rapid access to biomedical knowledge with GeneCards and HotMolecBase: Implications for the electrophoretic analysis of large sets of gene products (PubMedId: 9504809, Citations: 13)
    Rebhan, M., Prilusky, J
    Electrophoresis, special issue on 'Biomedicine and Biocomputing' , vol. 18: 2774-80 (1997)
  52. GeneCards: integrating information about genes, proteins and diseases (PubMedId: 9097728, Citations: 738)
    Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D
    Trends in Genetics 13: 163 (1997)
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