Y. Ofran

发表

Computational Identification of Antigen-Binding Antibody Fragments

Anat Burkovitz, Olga Leiderman, Inbal Sela-Culang, 2013, The Journal of Immunology.

The Structural Basis of Antibody-Antigen Recognition

Inbal Sela-Culang, Y. Ofran, Vered Kunik, 2013, Front. Immunol..

Automated Identification of Complementarity Determining Regions (CDRs) Reveals Peculiar Characteristics of CDRs and B Cell Epitopes1

B. Rost, A. Schlessinger, Y. Ofran, 2008, The Journal of Immunology.

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

Y. Ofran, Vered Kunik, Yanay Ofran, 2013, Protein engineering, design & selection : PEDS.

Automatic prediction of protein function

B. Rost, Jinfeng Liu, K. Wrzeszczynski, 2003, Cellular and Molecular Life Sciences CMLS.

Analysing six types of protein-protein interfaces.

B. Rost, Y. Ofran, Yanay Ofran, 2003, Journal of molecular biology.

Predicted protein–protein interaction sites from local sequence information

B. Rost, Y. Ofran, Yanay Ofran, 2003, FEBS letters.

Using a combined computational-experimental approach to predict antibody-specific B cell epitopes.

Yanay Ofran, Bjoern Peters, Yan Xiang, 2014, Structure.

Structure Resource Using a Combined Computational-Experimental Approach to Predict Antibody-Specific B Cell Epitopes

Guy Nimrod, B. Peters, Inbal Sela-Culang, 2014 .

A Systematic Comparison of Free and Bound Antibodies Reveals Binding-Related Conformational Changes

Yanay Ofran, Shahar Alon, Inbal Sela-Culang, 2012, The Journal of Immunology.

Antibody specific epitope prediction-emergence of a new paradigm.

Yanay Ofran, Bjoern Peters, Inbal Sela-Culang, 2015, Current opinion in virology.

How far from the SNP may the causative genes be?

Y. Ofran, Aharon Brodie, J. R. Azaria, 2016, Nucleic acids research.

Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.

Marco Punta, Yanay Ofran, Burkhard Rost, 2005, Drug discovery today.

Prediction of Protein Structure Through Evolution

Yanay Ofran, Burkhard Rost, Henry R. Bigelow, 2008 .

Land degradation is not a necessary outcome of communal pastoralism in arid Namibia

Yanay Ofran, David Ward, D. Ward, 1998 .

Antibody Modeling, Engineering, and Design

Y. Ofran, Sharon Fischman, Yanay Ofran, 2018 .

ScienceDirect Computational design of antibod ies

Y. Ofran, Sharon Fischman, Yanay Ofran, 2018 .

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

R. Unger, Y. Ofran, Yaron Geffen, 2022, bioRxiv.

Co-expression and co-localization of hub proteins and their partners are encoded in protein sequence.

B. Rost, A. Schlessinger, Y. Ofran, 2014, Molecular bioSystems.

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Alexander A. Morgan, Yanay Ofran, Predrag Radivojac, 2017, Human mutation.

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

R. Unger, J. Moult, Y. Ofran, 2012, PloS one.

Conformational Changes Antibodies Reveals Binding-Related A Systematic Comparison of Free and Bound

Inbal Sela-Culang, Y. Ofran, Yanay Ofran, 2012 .

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

Y. Ofran, U. Nir, A. Nyska, 2017, Nature Communications.

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

Yanay Ofran, Jasmin Fisher, Ron Unger, 2012, Bioinform..

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

Yanay Ofran, Y. Ofran, Aharon Brodie, 2014, PloS one.

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

Yanay Ofran, Inbal Sela-Culang, Anat Burkovitz, 2014, The FEBS journal.

New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.

Burkhard Rost, Yanay Ofran, Reinhard Schneider, 2009, Current opinion in drug discovery & development.

Correction: The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

M. Punta, Y. Ofran, Yanay Ofran, 2008, PLoS computational biology.

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

Marco Punta, Yanay Ofran, M. Punta, 2008, PLoS Comput. Biol..

PROTEIN INTERACTIONS AND DISEASE

Marco Punta, Yanay Ofran, Predrag Radivojac, 2007 .

ISIS: interaction sites identified from sequence

Burkhard Rost, Yanay Ofran, B. Rost, 2007, Bioinform..

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

Avner Schlessinger, Jean-Luc Pellequer, Yanay Ofran, 2007, Journal of molecular recognition : JMR.

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

Omer Levy, Y. Ofran, M. Barda-Saad, 2021, Nature Communications.

Protein–Protein Interaction Hotspots Carved into Sequences

Burkhard Rost, Yanay Ofran, B. Rost, 2007, PLoS Comput. Biol..

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

Y. Ofran, U. Nir, A. Nyska, 2017, Nature Communications.

PEASE: predicting B-cell epitopes utilizing antibody sequence

Yanay Ofran, Björn Peters, Shaul Ashkenazi, 2014, Bioinform..

Potent Neutralization of Vaccinia Virus by Divergent Murine Antibodies Targeting a Common Site of Vulnerability in L1 Protein

Bjoern Peters, Inbal Sela-Culang, Y. Ofran, 2014, Journal of Virology.

Prediction of DNA-binding residues from sequence

Burkhard Rost, Yanay Ofran, Venkatesh Mysore, 2007, ISMB/ECCB.

Create and assess protein networks through molecular characteristics of individual proteins

Burkhard Rost, Yanay Ofran, Guy Yachdav, 2006, ISMB.

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

Yanay Ofran, Vered Kunik, Shaul Ashkenazi, 2012, Nucleic Acids Res..

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

Yanay Ofran, Yossef Kliger, Y. Ofran, 2010, Proteins.

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

T. Young, E. Mignot, L. Finn, 2010, PloS one.

Antigen-Binding Antibody Fragments Computational Identification of

Yanay Ofran, Inbal Sela-Culang, Gerardo Byk, 2013 .

Structural Consensus among Antibodies Defines the Antigen Binding Site

Yanay Ofran, Björn Peters, Vered Kunik, 2012, PLoS Comput. Biol..

Epitome: database of structure-inferred antigenic epitopes

Avner Schlessinger, Burkhard Rost, Yanay Ofran, 2005, Nucleic Acids Res..

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

Yanay Ofran, Shaul Ashkenazi, Rotem Snir, 2012, Bioinform..

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

Yanay Ofran, Anat Burkovitz, Anat Burkovitz, 2016, mAbs.

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

Yanay Ofran, Ron Unger, Orly Noivirt-Brik, 2013, Bioinform..

Computational Design of Epitope-Specific Functional Antibodies.

Yanay Ofran, Guy Nimrod, Sharon Fischman, 2018, Cell reports.

Computational design of antibodies.

Yanay Ofran, Sharon Fischman, Y. Ofran, 2018, Current opinion in structural biology.

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

Guy Nimrod, Y. Ofran, Dror Baran, 2023, Nucleic acids research.

Unveiling Protein Functions through the Dynamics of the Interaction Network

Yanay Ofran, Javier M. Buldú, Daqing Li, 2011, PloS one.

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

Y. Ofran, 2008 .