| Year |
Citation |
Score |
| 2022 |
Geffen Y, Ofran Y, Unger R. DistilProtBert: a distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts. Bioinformatics (Oxford, England). 38: ii95-ii98. PMID 36124789 DOI: 10.1093/bioinformatics/btac474 |
0.321 |
|
| 2020 |
Peled S, Leiderman O, Charar R, Efroni G, Shav-Tal Y, Ofran Y. Function Prediction: Predicting whether a proteins binds DNA from sequence F1000research. 8. DOI: 10.7490/F1000Research.1117793.1 |
0.464 |
|
| 2018 |
Nimrod G, Fischman S, Austin M, Herman A, Keyes F, Leiderman O, Hargreaves D, Strajbl M, Breed J, Klompus S, Minton K, Spooner J, Buchanan A, Vaughan TJ, Ofran Y. Computational Design of Epitope-Specific Functional Antibodies. Cell Reports. 25: 2121-2131.e5. PMID 30463010 DOI: 10.1016/J.Celrep.2018.10.081 |
0.356 |
|
| 2018 |
Fischman S, Ofran Y. Computational design of antibodies. Current Opinion in Structural Biology. 51: 156-162. PMID 29791878 DOI: 10.1016/J.Sbi.2018.04.007 |
0.344 |
|
| 2017 |
Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat R, Li X, Pal LR, ... ... Ofran Y, et al. Working towards precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation. PMID 28634997 DOI: 10.1002/Humu.23280 |
0.629 |
|
| 2016 |
Peled S, Leiderman O, Charar R, Efroni G, Shav-Tal Y, Ofran Y. De-novo protein function prediction using DNA binding and RNA binding proteins as a test case. Nature Communications. 7: 13424. PMID 27869118 DOI: 10.1038/Ncomms13424 |
0.484 |
|
| 2016 |
Burkovitz A, Ofran Y. Understanding differences between synthetic and natural antibodies can help improve antibody engineering. Mabs. 8: 278-87. PMID 26652053 DOI: 10.1080/19420862.2015.1123365 |
0.346 |
|
| 2015 |
Sela-Culang I, Ofran Y, Peters B. Antibody specific epitope prediction-emergence of a new paradigm. Current Opinion in Virology. 11: 98-102. PMID 25837466 DOI: 10.1016/J.Coviro.2015.03.012 |
0.427 |
|
| 2015 |
Sela-Culang I, Ashkenazi S, Peters B, Ofran Y. PEASE: predicting B-cell epitopes utilizing antibody sequence. Bioinformatics (Oxford, England). 31: 1313-5. PMID 25432167 DOI: 10.1093/Bioinformatics/Btu790 |
0.419 |
|
| 2014 |
Kaever T, Meng X, Matho MH, Schlossman A, Li S, Sela-Culang I, Ofran Y, Buller M, Crump RW, Parker S, Frazier A, Crotty S, Zajonc DM, Peters B, Xiang Y. Potent neutralization of vaccinia virus by divergent murine antibodies targeting a common site of vulnerability in L1 protein. Journal of Virology. 88: 11339-55. PMID 25031354 DOI: 10.1128/Jvi.01491-14 |
0.334 |
|
| 2014 |
Sela-Culang I, Benhnia MR, Matho MH, Kaever T, Maybeno M, Schlossman A, Nimrod G, Li S, Xiang Y, Zajonc D, Crotty S, Ofran Y, Peters B. Using a combined computational-experimental approach to predict antibody-specific B cell epitopes. Structure (London, England : 1993). 22: 646-57. PMID 24631463 DOI: 10.1016/J.Str.2014.02.003 |
0.401 |
|
| 2014 |
Feiglin A, Ashkenazi S, Schlessinger A, Rost B, Ofran Y. Co-expression and co-localization of hub proteins and their partners are encoded in protein sequence. Molecular Biosystems. 10: 787-94. PMID 24457447 DOI: 10.1039/C3Mb70411D |
0.719 |
|
| 2014 |
Burkovitz A, Sela-Culang I, Ofran Y. Large-scale analysis of somatic hypermutations in antibodies reveals which structural regions, positions and amino acids are modified to improve affinity. The Febs Journal. 281: 306-19. PMID 24279419 DOI: 10.1111/Febs.12597 |
0.359 |
|
| 2013 |
Sela-Culang I, Kunik V, Ofran Y. The structural basis of antibody-antigen recognition. Frontiers in Immunology. 4: 302. PMID 24115948 DOI: 10.3389/Fimmu.2013.00302 |
0.359 |
|
| 2013 |
Kunik V, Ofran Y. The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops. Protein Engineering, Design & Selection : Peds. 26: 599-609. PMID 23754530 DOI: 10.1093/Protein/Gzt027 |
0.403 |
|
| 2013 |
Burkovitz A, Leiderman O, Sela-Culang I, Byk G, Ofran Y. Computational identification of antigen-binding antibody fragments. Journal of Immunology (Baltimore, Md. : 1950). 190: 2327-34. PMID 23359499 DOI: 10.4049/Jimmunol.1200757 |
0.331 |
|
| 2013 |
Noivirt-Brik O, Hazan G, Unger R, Ofran Y. Non-local residue-residue contacts in proteins are more conserved than local ones. Bioinformatics (Oxford, England). 29: 331-7. PMID 23202807 DOI: 10.1093/Bioinformatics/Bts694 |
0.426 |
|
| 2012 |
Ashkenazi S, Snir R, Ofran Y. Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins Bioinformatics. 28: 3203-3210. PMID 23080118 DOI: 10.1093/Bioinformatics/Bts608 |
0.48 |
|
| 2012 |
Feiglin A, Hacohen A, Sarusi A, Fisher J, Unger R, Ofran Y. Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks. Bioinformatics (Oxford, England). 28: 2811-8. PMID 22923292 DOI: 10.1093/Bioinformatics/Bts517 |
0.356 |
|
| 2012 |
Feiglin A, Moult J, Lee B, Ofran Y, Unger R. Neighbor Overlap is enriched in the yeast interaction network: Analysis and implications Plos One. 7. PMID 22761860 DOI: 10.1371/Journal.Pone.0039662 |
0.467 |
|
| 2012 |
Kunik V, Ashkenazi S, Ofran Y. Paratome: An online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure Nucleic Acids Research. 40. PMID 22675071 DOI: 10.1093/Nar/Gks480 |
0.403 |
|
| 2012 |
Kunik V, Peters B, Ofran Y. Structural consensus among antibodies defines the antigen binding site. Plos Computational Biology. 8: e1002388. PMID 22383868 DOI: 10.1371/Journal.Pcbi.1002388 |
0.374 |
|
| 2012 |
Kunik V, Ofran Y. Identifying antigen binding sites from Ab sequence F1000research. 3. DOI: 10.7490/F1000Research.1092131.1 |
0.341 |
|
| 2011 |
Sendiña-Nadal I, Ofran Y, Almendral JA, Buldú JM, Leyva I, Li D, Havlin S, Boccaletti S. Unveiling protein functions through the dynamics of the interaction network. Plos One. 6: e17679. PMID 21408013 DOI: 10.1371/Journal.Pone.0017679 |
0.483 |
|
| 2011 |
Gophna U, Ofran Y. Lateral acquisition of genes is affected by the friendliness of their products. Proceedings of the National Academy of Sciences of the United States of America. 108: 343-8. PMID 21149709 DOI: 10.1073/Pnas.1009775108 |
0.458 |
|
| 2010 |
Aran A, Weiner K, Lin L, Finn LA, Greco MA, Peppard P, Young T, Ofran Y, Mignot E. Post-streptococcal auto-antibodies inhibit protein disulfide isomerase and are associated with insulin resistance. Plos One. 5: e12875. PMID 20886095 DOI: 10.1371/Journal.Pone.0012875 |
0.32 |
|
| 2010 |
Dan A, Ofran Y, Kliger Y. Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins. Proteins. 78: 236-48. PMID 19676113 DOI: 10.1002/Prot.22531 |
0.351 |
|
| 2009 |
Bromberg Y, Yachdav G, Ofran Y, Schneider R, Rost B. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'. Current Opinion in Drug Discovery & Development. 12: 408-19. PMID 19396742 |
0.732 |
|
| 2008 |
Punta M, Ofran Y. The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. Plos Computational Biology. 4: e1000160. PMID 18974821 DOI: 10.1371/Journal.Pcbi.1000160 |
0.525 |
|
| 2008 |
Ofran Y, Schlessinger A, Rost B. Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes. Journal of Immunology (Baltimore, Md. : 1950). 181: 6230-5. PMID 18941213 DOI: 10.4049/Jimmunol.181.9.6230 |
0.69 |
|
| 2008 |
Rost B, Liu J, Przybylski D, Nair R, Wrzeszczynski KO, Bigelow H, Ofran Y. Prediction of Protein Structure Through Evolution Handbook of Chemoinformatics. 4: 1789-1811. DOI: 10.1002/9783527618279.ch45b |
0.747 |
|
| 2007 |
Ofran Y, Mysore V, Rost B. Prediction of DNA-binding residues from sequence Bioinformatics. 23: i347-i353. PMID 17646316 DOI: 10.1093/bioinformatics/btm174 |
0.486 |
|
| 2007 |
Ofran Y, Rost B. Protein-protein interaction hotspots carved into sequences Plos Computational Biology. 3: e119. PMID 17630824 DOI: 10.1371/Journal.Pcbi.0030119 |
0.675 |
|
| 2007 |
Ofran Y, Rost B. ISIS: Interaction sites identified from sequence Bioinformatics. 23: e13-e16. PMID 17237081 DOI: 10.1093/Bioinformatics/Btl303 |
0.622 |
|
| 2007 |
Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, et al. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. Journal of Molecular Recognition : Jmr. 20: 75-82. PMID 17205610 DOI: 10.1002/Jmr.815 |
0.626 |
|
| 2006 |
Ofran Y, Yachdav G, Mozes E, Soong TT, Nair R, Rost B. Create and assess protein networks through molecular characteristics of individual proteins Bioinformatics. 22: e402-e407. PMID 16873500 DOI: 10.1093/Bioinformatics/Btl258 |
0.706 |
|
| 2006 |
Ofran Y, Margalit H. Proteins of the same fold and unrelated sequences have similar amino acid composition. Proteins. 64: 275-9. PMID 16565950 DOI: 10.1002/Prot.20964 |
0.407 |
|
| 2006 |
Schlessinger A, Ofran Y, Yachdav G, Rost B. Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Research. 34: D777-80. PMID 16381978 DOI: 10.1093/Nar/Gkj053 |
0.703 |
|
| 2005 |
Ofran Y, Punta M, Schneider R, Rost B. Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discovery Today. 10: 1475-82. PMID 16243268 DOI: 10.1016/S1359-6446(05)03621-4 |
0.595 |
|
| 2004 |
Rost B, Liu J, Nair R, Wrzeszczynski KO, Ofran Y. Automatic prediction of protein function. Cellular and Molecular Life Sciences : Cmls. 60: 2637-50. PMID 14685688 DOI: 10.1007/S00018-003-3114-8 |
0.763 |
|
| 2003 |
Ofran Y, Rost B. Predicted protein-protein interaction sites from local sequence information. Febs Letters. 544: 236-9. PMID 12782323 DOI: 10.1016/S0014-5793(03)00456-3 |
0.67 |
|
| 2003 |
Ofran Y, Rost B. Analysing six types of protein-protein interfaces. Journal of Molecular Biology. 325: 377-87. PMID 12488102 DOI: 10.1016/S0022-2836(02)01223-8 |
0.579 |
|
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