Works matching AU Ofran, Yanay

Results: 31

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools.

Published in:

Journal of Molecular Recognition, 2007, v. 20, n. 2, p. 75, doi. 10.1002/jmr.815

By:

Greenbaum, Jason A.;
Andersen, Pernille Haste;
Blythe, Martin;
Bui, Huynh-Hoa;
Cachau, Raul E.;
Crowe, James;
Davies, Matthew;
Kolaskar, A. S.;
Lund, Ole;
Morrison, Sherrie;
Mumey, Brendan;
Ofran, Yanay;
Pellequer, Jean-Luc;
Pinilla, Clemencia;
Ponomarenko, Julia V.;
Raghava, G. P. S.;
van Regenmortel, Marc H. V.;
Roggen, Erwin L.;
Sette, Alessandro;
Schlessinger, Avner

Publication type:

Article

DistilProtBert: a distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts.

Published in:

Bioinformatics, 2022, v. 38, p. ii95, doi. 10.1093/bioinformatics/btac474

By:

Geffen, Yaron;
Ofran, Yanay;
Unger, Ron

Publication type:

Article

The structural basis of antibody-antigen recognition.

Published in:

Frontiers in Immunology, 2013, v. 4, p. 1, doi. 10.3389/fimmu.2013.00302

By:

Sela-Culang, Inbal;
Kunik, Vered;
Ofran, Yanay

Publication type:

Article

Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure.

Published in:

Nucleic Acids Research, 2012, v. 40, p. W521, doi. 10.1093/nar/gks480

By:

Kunik, Vered;
Ashkenazi, Shaul;
Ofran, Yanay

Publication type:

Article

Epitome: database of structure-inferred antigenic epitopes.

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d777, doi. 10.1093/nar/gkj053

By:

Schlessinger, Avner;
Ofran, Yanay;
Yachdav, Guy;
Rost, Burkhard

Publication type:

Article

Targeting the actin nucleation promoting factor WASp provides a therapeutic approach for hematopoietic malignancies.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25842-7

By:

Biber, Guy;
Ben-Shmuel, Aviad;
Noy, Elad;
Joseph, Noah;
Puthenveetil, Abhishek;
Reiss, Neria;
Levy, Omer;
Lazar, Itay;
Feiglin, Ariel;
Ofran, Yanay;
Kedmi, Meirav;
Avigdor, Abraham;
Fried, Sophia;
Barda-Saad, Mira

Publication type:

Article

Proteins of the same fold and unrelated sequences have similar amino acid composition.

Published in:

Proteins, 2006, v. 64, n. 1, p. 275, doi. 10.1002/prot.20964

By:

Ofran, Yanay;
Margalit, Hanah

Publication type:

Article

Large-scale analysis of somatic hypermutations in antibodies reveals which structural regions, positions and amino acids are modified to improve affinity.

Published in:

FEBS Journal, 2014, v. 281, n. 1, p. 306, doi. 10.1111/febs.12597

By:

Burkovitz, Anat;
Sela‐Culang, Inbal;
Ofran, Yanay

Publication type:

Article

Prediction of DNA-binding residues from sequence.

Published in:

Bioinformatics, 2007, v. 23, n. 13, p. i347, doi. 10.1093/bioinformatics/btm174

By:

Yanay Ofran;
Venkatesh Mysore;
Burkhard Rost

Publication type:

Article

ISIS: interaction sites identified from sequence.

Published in:

Bioinformatics, 2007, v. 23, n. 2, p. e13, doi. 10.1093/bioinformatics/btl303

By:

Yanay Ofran;
Burkhard Rost

Publication type:

Article

Protein-Protein Interaction Hotspots Carved into Sequences.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 7, p. e119, doi. 10.1371/journal.pcbi.0030119

By:

Ofran, Yanay;
Rost, Burkhard

Publication type:

Article

Integrating genomic data from high-throughput studies with computational modeling reveals differences in the molecular basis of hyposalivation between type 1 and type 2 diabetes.

Published in:

Clinical Oral Investigations, 2018, v. 22, n. 1, p. 151, doi. 10.1007/s00784-017-2094-2

By:

Tickotsky, Nili;
Ofran, Yanay

Publication type:

Article

PEASE: predicting B-cell epitopes utilizing antibody sequence.

Published in:

Bioinformatics, 2015, v. 31, n. 8, p. 1313, doi. 10.1093/bioinformatics/btu790

By:

Sela-Culang, Inbal;
Ashkenazi, Shaul;
Peters, Bjoern;
Ofran, Yanay

Publication type:

Article

PEASE: predicting B-cell epitopes utilizing antibody sequence.

Published in:

2015

By:

Sela-Culang, Inbal;
Ashkenazi, Shaul;
Peters, Bjoern;
Ofran, Yanay

Publication type:

Product Review

Non-local residue–residue contacts in proteins are more conserved than local ones.

Published in:

Bioinformatics, 2013, v. 29, n. 3, p. 331, doi. 10.1093/bioinformatics/bts694

By:

Noivirt-Brik, Orly;
Hazan, Gershon;
Unger, Ron;
Ofran, Yanay

Publication type:

Article

Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins.

Published in:

Bioinformatics, 2012, v. 28, n. 24, p. 3203, doi. 10.1093/bioinformatics/bts608

By:

Ashkenazi, Shaul;
Snir, Rotem;
Ofran, Yanay

Publication type:

Article

Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks.

Published in:

Bioinformatics, 2012, v. 28, n. 21, p. 2811, doi. 10.1093/bioinformatics/bts517

By:

Feiglin, Ariel;
Hacohen, Adar;
Sarusi, Avital;
Fisher, Jasmin;
Unger, Ron;
Ofran, Yanay

Publication type:

Article

Predicted protein–protein interaction sites from local sequence information

Published in:

FEBS Letters, 2003, v. 544, n. 1-3, p. 236, doi. 10.1016/S0014-5793(03)00456-3

By:

Ofran, Yanay;
Rost, Burkhard

Publication type:

Article

Large-scale analysis of secondary structure changes in proteins suggests a role for disorder-to-order transitions in nucleotide binding proteins.

Published in:

Proteins, 2010, v. 78, n. 2, p. 236, doi. 10.1002/prot.22531

By:

Dan, Adi;
Ofran, Yanay;
Kliger, Yossef

Publication type:

Article

De-novo protein function prediction using DNA binding and RNA binding proteins as a test case.

Published in:

Nature Communications, 2016, v. 7, n. 11, p. 13424, doi. 10.1038/ncomms13424

By:

Peled, Sapir;
Leiderman, Olga;
Charar, Rotem;
Efroni, Gilat;
Shav-Tal, Yaron;
Ofran, Yanay

Publication type:

Article

Structural Consensus among Antibodies Defines the Antigen Binding Site.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 2, p. 1, doi. 10.1371/journal.pcbi.1002388

By:

Kunik, Vered;
Peters, Bjoern;
Ofran, Yanay

Publication type:

Article

Accurate profiling of full-length Fv in highly homologous antibody libraries using UMI tagged short reads.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 11, p. e61, doi. 10.1093/nar/gkad235

By:

Levin, Itay;
Štrajbl, Marek;
Fastman, Yair;
Baran, Dror;
Twito, Shir;
Mioduser, Jessica;
Keren, Adi;
Fischman, Sharon;
Zhenin, Michael;
Nimrod, Guy;
Levitin, Natalie;
Mayor, May Ben;
Gadrich, Meital;
Ofran, Yanay

Publication type:

Article

How far from the SNP may the causative genes be?

Published in:

Nucleic Acids Research, 2016, v. 44, n. 13, p. 6046, doi. 10.1093/nar/gkw500

By:

Brodie, Aharon;
Azaria, Johnathan Roy;
Ofran, Yanay

Publication type:

Article

A novel Fer/FerT targeting compound selectively evokes metabolic stress and necrotic death in malignant cells.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-00832-w

By:

Elkis, Yoav;
Cohen, Moshe;
Yaffe, Etai;
Satmary-Tusk, Shirly;
Feldman, Tal;
Hikri, Elad;
Nyska, Abraham;
Feiglin, Ariel;
Ofran, Yanay;
Shpungin, Sally;
Nir, Uri

Publication type:

Article

Large Scale Analysis of Phenotype-Pathway Relationships Based on GWAS Results.

Published in:

PLoS ONE, 2014, v. 9, n. 7, p. 1, doi. 10.1371/journal.pone.0100887

By:

Brodie, Aharon;
Tovia-Brodie, Oholi;
Ofran, Yanay

Publication type:

Article

Neighbor Overlap Is Enriched in the Yeast Interaction Network: Analysis and Implications.

Published in:

PLoS ONE, 2012, v. 7, n. 6, p. 1, doi. 10.1371/journal.pone.0039662

By:

Feiglin, Ariel;
Moult, John;
Byungkook Lee;
Ofran, Yanay;
Unger, Ron

Publication type:

Article

Unveiling Protein Functions through the Dynamics of the Interaction Network.

Published in:

PLoS ONE, 2011, v. 6, n. 3, p. 1, doi. 10.1371/journal.pone.0017679

By:

Sendiñ a-Nadal, Irene;
Ofran, Yanay;
Almendral, Juan A.;
Buldú, Javier M.;
Leyva, Inmaculada;
Li, Daqing;
Havlin, Shlomo;
Boccaletti, Stefano

Publication type:

Article

Post-Streptococcal Auto-Antibodies Inhibit Protein Disulfide Isomerase and Are Associated with Insulin Resistance.

Published in:

PLoS ONE, 2010, v. 5, n. 9, p. 1, doi. 10.1371/journal.pone.0012875

By:

Aran, Adi;
Weiner, Karin;
Ling Lin;
Finn, Laurel Ann;
Greco, Mary Ann;
Peppard, Paul;
Young, Terry;
Ofran, Yanay;
Mignot, Emmanuel

Publication type:

Article

The Two Cultures and Systems Biology: How Philosophy Starts Where Science Ends.

Published in:

European Legacy, 2008, v. 13, n. 5, p. 589, doi. 10.1080/10848770802268766

By:

Ofran, Yanay

Publication type:

Article

The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops.

Published in:

PEDS: Protein Engineering, Design & Selection, 2013, v. 26, n. 10, p. 599, doi. 10.1093/protein/gzt027

By:

Kunik, Vered;
Ofran, Yanay

Publication type:

Article

Understanding differences between synthetic and natural antibodies can help improve antibody engineering.

Published in:

mAbs (1942-0862), 2016, v. 8, n. 2, p. 278, doi. 10.1080/19420862.2015.1123365

By:

Burkovitz, Anat;
Ofran, Yanay

Publication type:

Article