H. Margalit

发表

How reliable are experimental protein-protein interaction data?

Shmuel Sattath, E. Sprinzak, H. Margalit, 2003, Journal of molecular biology.

Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.

C. DeLisi, H. Margalit, J. Cornette, 1987, Journal of molecular biology.

Evaluation of PSI‐BLAST alignment accuracy in comparison to structural alignments

H. Margalit, I. Friedberg, T. Kaplan, 2000, Protein science : a publication of the Protein Society.

Sequence signals for generation of antigenic peptides by the proteasome: implications for proteasomal cleavage mechanism.

H. Margalit, Y. Altuvia, 2000, Journal of molecular biology.

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

H. Margalit, G. Bejerano, J. Vogel, 2001, Current Biology.

Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications.

H. Margalit, E. Nadir, T. Gallily, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.

R. Milo, U. Alon, Shmuel Sattath, 2004, Proceedings of the National Academy of Sciences of the United States of America.

E. Sprinzak, H. Margalit, Einat Sprinzak, 2001, Journal of molecular biology.

Towards an Integrated Protein-Protein Interaction Network

Nir Friedman, Hanah Margalit, Gal Elidan, 2005, RECOMB.

Ranking potential binding peptides to MHC molecules by a computational threading approach.

H. Margalit, Y. Altuvia, O. Schueler, 1995, Journal of molecular biology.

Hierarchy of sequence-dependent features associated with prokaryotic translation.

H. Margalit, G. Lithwick, 2003, Genome research.

Built-in loops allow versatility in domain–domain interactions: Lessons from self-interacting domains

H. Margalit, E. Akiva, Zohar Itzhaki, 2008, Proceedings of the National Academy of Sciences.

A survey of small RNA-encoding genes in Escherichia coli.

H. Margalit, Ruth Hershberg, S. Altuvia, 2003, Nucleic acids research.

Conserved sequence elements associated with exon skipping.

H. Margalit, E. Miriami, R. Sperling, 2003, Nucleic acids research.

Regulation of gene expression by small non-coding RNAs: a quantitative view

G. Friedlander, H. Margalit, O. Biham, 2007, Molecular systems biology.

A role for CH...O interactions in protein-DNA recognition.

H. Margalit, V. Zhurkin, R. Jernigan, 1998, Journal of molecular biology.

Reduced Polymorphism in Domains Involved in Protein-Protein Interactions

H. Margalit, Zohar Itzhaki, 2012, PloS one.

Conservation of salt bridges in protein families.

H. Margalit, O. Schueler, H Margalit, 1995, Journal of molecular biology.

Stochastic analysis of bistability in coherent mixed feedback loops combining transcriptional and posttranscriptional regulations.

H. Margalit, O. Biham, Y. Shimoni, 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.

Stochastic Analysis of the SOS Response in Escherichia coli

H. Margalit, O. Biham, S. Altuvia, 2009, PloS one.

Initiation of DNA replication in bacteria: analysis of an autorepressor control model.

H. Margalit, N. Grover, R. Rosenberger, 1984, Journal of theoretical biology.

Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation.

Hanah Margalit, Esti Yeger-Lotem, H. Margalit, 2003, Nucleic acids research.

Comparative Functional Genomics of the Fission Yeasts

Manolis Kellis, Nir Friedman, Hanah Margalit, 2011, Science.

Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions

H. Margalit, A. Peer, 2011, Journal of bacteriology.

Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles.

H. Margalit, Y. Mandel-Gutfreund, O. Schueler, 1995, Journal of molecular biology.

Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites.

H. Margalit, Y. Mandel-Gutfreund, 1998, Nucleic acids research.

Structure‐based prediction of binding peptides to MHC class I molecules: Application to a broad range of MHC alleles

O. Schueler‐Furman, H. Margalit, A. Sette, 2000, Protein science : a publication of the Protein Society.

Evolutionary conservation of domain-domain interactions

Zohar Itzhaki, Eyal Akiva, Hanah Margalit, 2006, Genome Biology.

Co-evolution of transcription factors and their targets depends on mode of regulation

Hanah Margalit, Ruth Hershberg, H. Margalit, 2006, Genome Biology.

A structure-based algorithm to predict potential binding peptides to MHC molecules with hydrophobic binding pockets.

A Sette, J Sidney, H. Margalit, 1997, Human immunology.

A structure-based approach for prediction of MHC-binding peptides.

Hanah Margalit, Yael Altuvia, H. Margalit, 2004, Methods.

Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes.

R Elber, O. Schueler‐Furman, H. Margalit, 1998, Folding & design.

Clustering and conservation patterns of human microRNAs

Hanah Margalit, Thomas Tuschl, Pablo Landgraf, 2005, Nucleic acids research.

Chromosomal organization is shaped by the transcription regulatory network.

Hanah Margalit, Esti Yeger-Lotem, Ruth Hershberg, 2005, Trends in genetics : TIG.

Assessing the functional association of intronic miRNAs with their host genes

H. Margalit, Avital Steiman-Shimony, Orr Shtrikman, 2018, RNA.

Compilation of E. coli mRNA promoter sequences.

H. Margalit, S Lisser, H Margalit, 1993, Nucleic acids research.

Initiation of chromosome replication in bacteria: analysis of an inhibitor control model

H. Margalit, N. Grover, N B Grover, 1987, Journal of bacteriology.

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

H. Margalit, Maya Botzman, 2011, Genome Biology.

Global Mapping of Small RNA-Target Interactions in Bacteria

H. Margalit, Y. Altuvia, L. Argaman, 2016, Molecular cell.

Hierarchy in Hfq Chaperon Occupancy of Small RNA Targets Plays a Major Role in Their Regulation

H. Margalit, L. Argaman, Raya Faigenbaum-Romm, 2020, Cell reports.

Global regulation of transcription by a small RNA: a quantitative view.

H. Margalit, K. Wassarman, O. Biham, 2014, Biophysical journal.

Comparative analysis of structurally defined heparin binding sequences reveals a distinct spatial distribution of basic residues.

H. Margalit, S. Ben‐Sasson, N. Fischer, 1993, The Journal of biological chemistry.

Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics

H. Margalit, Naama Wald, 2014, Nucleic acids research.

Helper T-cell antigenic site identification in the acquired immunodeficiency syndrome virus gp120 envelope protein and induction of immunity in mice to the native protein using a 16-residue synthetic peptide.

C. DeLisi, H. Margalit, J. Cornette, 1987, Proceedings of the National Academy of Sciences of the United States of America.

T cell multideterminant regions in the human immunodeficiency virus envelope: toward overcoming the problem of major histocompatibility complex restriction.

C. DeLisi, H. Margalit, J. Cornette, 1989, International immunology.

Legionella pneumophila 6S RNA optimizes intracellular multiplication

G. Friedlander, H. Margalit, J. Livny, 2010, Proceedings of the National Academy of Sciences.

Protein Antigenic Structures Recognized by T Cells; Potential Applications to Vaccine Design

C. DeLisi, H. Margalit, J. Cornette, 1987, Immunological reviews.

Insights from MHC-bound peptides.

H. Margalit, Y. Altuvia, 2003, Novartis Foundation symposium.

Repeated determinants within the retinal interphotoreceptor retinoid-binding protein (IRBP): immunological properties of the repeats of an immunodominant determinant.

H. Margalit, J. Berzofsky, G. Chader, 1990, Cellular immunology.

Identification of an immunodominant and highly immunopathogenic determinant in the retinal interphotoreceptor retinoid-binding protein (IRBP)

H. Margalit, J. Berzofsky, G. Chader, 1989, The Journal of experimental medicine.

SURVEY A survey of small RNA-encoding genes in Escherichia coli

H. Margalit, Ruth Hershberg, S. Altuvia, 2022 .

Construction of synthetic immunogen: use of new T-helper epitope on malaria circumsporozoite protein.

H. Margalit, J. Cornette, J. Berzofsky, 1987, Science.

Immune responses to peptides derived from the retinal protein IRBP: immunopathogenic determinants are not necessarily immunodominant.

H. Margalit, J. Berzofsky, G. Chader, 1989, Clinical immunology and immunopathology.

Synthetic peptides derived from IRBP induce EAU and EAP in Lewis rats.

H. Margalit, J. Cornette, G. Chader, 1988, Current eye research.

Correction: A Dynamic View of Domain-Motif Interactions

G. Friedlander, H. Margalit, E. Akiva, 2012, PLoS Computational Biology.

A Ubiquitous Platform for Bacterial Nanotube Biogenesis

H. Margalit, S. Ben-Yehuda, S. Bhattacharya, 2019, Cell reports.

A complete Alu element within the coding sequence of a central gene

H. Margalit, E. Nadir, S. Ben‐Sasson, 1994, Cell.

Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence

Hanah Margalit, Ruth Hershberg, H. Margalit, 2008, Nucleic acids research.

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

Nir Friedman, Hanah Margalit, Aviv Regev, 2012 .

Relative predicted protein levels of functionally associated proteins are conserved across organisms

Hanah Margalit, H. Margalit, G. Lithwick, 2005, Nucleic acids research.

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval

Nir Friedman, Hanah Margalit, Tommy Kaplan, 2008, PLoS Comput. Biol..

Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity.

H. Margalit, J. Vogel, Y. Altuvia, 2022, Molecular cell.

Prediction of Novel Bacterial Small RNAs From RIL-Seq RNA–RNA Interaction Data

H. Margalit, Y. Altuvia, L. Argaman, 2021, Frontiers in Microbiology.

Integration of Bacterial Small RNAs in Regulatory Networks.

Hanah Margalit, Mor Nitzan, H. Margalit, 2017, Annual review of biophysics.

10 – The Role of MHC and Amphipathic Structures in T Cell Recognition: Features Determining Immunodominance

C. DeLisi, H. Margalit, J. Cornette, 1988 .

Immunodominance of Amphipathic Peptides and Their Localization on the Cell Surface for Antigen Presentation to Helper T Cells

C. DeLisi, H. Margalit, J. Cornette, 1986 .

Molecular features of class II MHC-restricted T-cell recognition of protein and peptide antigens: the importance of amphipathic structures.

C. DeLisi, H. Margalit, J. Cornette, 1986, Current topics in microbiology and immunology.

Host Immune System Gene Targeting by a Viral miRNA

Hanah Margalit, Albert Zimmermann, Simcha Yagel, 2007, Science.

A wide repertoire of miRNA binding sites: prediction and functional implications

Hanah Margalit, Naama Elefant, Yael Altuvia, 2011, Bioinform..

Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens

H. Margalit, Y. E. Gatt, Yair E. Gatt, 2020, Molecular biology and evolution.

IntAct: an open source molecular interaction database

Martin Vingron, David James Sherman, Alfonso Valencia, 2004, Nucleic Acids Res..

Molecular Basis for Expression of Common and Rare Fragile Sites

S. Scherer, B. Kerem, H. Margalit, 2003, Molecular and Cellular Biology.

Common fragile sites: G-band characteristics within an R-band.

B. Kerem, H. Margalit, Y. Mandel-Gutfreund, 1999, American journal of human genetics.

Examination of possible structural constraints of MHC‐binding peptides by assessment of their native structure within their source proteins

O. Schueler‐Furman, H. Margalit, Y. Altuvia, 2001, Proteins.

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

H. Margalit, L. Argaman, M. Berger, 2017, Nature Communications.

RepTar: a database of predicted cellular targets of host and viral miRNAs

Hanah Margalit, Matan Hofree, Naama Elefant, 2010, Nucleic Acids Res..

A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs.

Hanah Margalit, Thomas Tuschl, Pavel Morozov, 2012, RNA.

Degradation of Ndd1 by APC/CCdh1 generates a feed forward loop that times mitotic protein accumulation

Hanah Margalit, Mor Nitzan, Tommer Ravid, 2015, Nature Communications.

Inferring the contribution of small RNAs to changes in gene expression in response to stress

H. Margalit, Shira Fisher, Meshi Barsheshet, 2022, NAR genomics and bioinformatics.

The impact of Hfq-mediated sRNA-mRNA interactome on the virulence of enteropathogenic Escherichia coli

H. Margalit, Y. Altuvia, L. Argaman, 2021, Science advances.

Mapping the small RNA interactome in bacteria using RIL-seq

H. Margalit, Y. Altuvia, L. Argaman, 2017, Nature Protocols.

Approaches and developments in studying the human microbiome network

H. Margalit, M. Nitzan, S. Mintzer, 2015 .

Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge

Nir Friedman, Hanah Margalit, Tommy Kaplan, 2005, PLoS Comput. Biol..

Predicting Transcription Factor Binding Sites Using Structural Knowledge

Nir Friedman, Hanah Margalit, Tommy Kaplan, 2005, RECOMB.

Interactions between Distant ceRNAs in Regulatory Networks

Hanah Margalit, Mor Nitzan, Ofer Biham, 2014, Biophysical journal.

Sequence features that correlate with MHC restriction.

H. Margalit, J. Berzofsky, Y. Altuvia, 1994, Molecular immunology.

Characterization and prediction of protein–protein interactions within and between complexes

Hanah Margalit, Einat Sprinzak, Yael Altuvia, 2006, Proceedings of the National Academy of Sciences.

Molecular characterization of a common fragile site (FRA7H) on human chromosome 7 by the cloning of a simian virus 40 integration site.

S. Scherer, L. Tsui, B. Kerem, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Prediction of immunodominant helper T cell antigenic sites from the primary sequence.

J L Cornette, C. DeLisi, H. Margalit, 1987, Journal of immunology.

Identification of T-cell epitopes and use in construction of synthetic vaccines.

C. DeLisi, H. Margalit, J. Cornette, 1989, Methods in enzymology.

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids

Hanah Margalit, H. Margalit, Naama Wald, 2012, Nucleic acids research.

Markovian domain fingerprinting: statistical segmentation of protein sequences

Naftali Tishby, Hanah Margalit, Yevgeny Seldin, 2001, Bioinform..

A Dynamic View of Domain-Motif Interactions

Zohar Itzhaki, Eyal Akiva, Hanah Margalit, 2012, PLoS Comput. Biol..

A Structure-Based Approach for Prediction of Protein Binding Sites in Gene-Upstream Regions

Hanah Margalit, Yael Mandel-Gutfreund, A. Baron, 2000, Pacific Symposium on Biocomputing.

Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions

H. Margalit, A. Peer, 2014, RNA.

Modularity and directionality in genetic interaction maps

Nir Friedman, Hanah Margalit, Ruty Rinott, 2010, Bioinform..

A defense-offense multi-layered regulatory switch in a pathogenic bacterium

H. Margalit, Y. Altuvia, O. Biham, 2015, Nucleic acids research.

Structure and function of the Pseudomonas putida integration host factor

H. Margalit, V. de Lorenzo, K. Timmis, 1996, Journal of bacteriology.

Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function

Hanah Margalit, Iddo Friedberg, H. Margalit, 2002, Protein science : a publication of the Protein Society.

Molecular analysis of HLA class II genes in primary Sjögren's syndrome. A study of Israeli Jewish and Greek non-Jewish patients.

H. Margalit, E. Ben-Chetrit, H. Moutsopoulos, 1993, Human immunology.

PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites

Hanah Margalit, Gill Bejerano, Alberto Santos-Zavaleta, 2001, Nucleic Acids Res..

Strong conformational propensities enhance T cell antigenicity.

C DeLisi, J L Cornette, H. Guy, 1987, Journal of immunology.

Zinc fingers: conserved properties that can distinguish between spurious and actual DNA-binding motifs.

H. Margalit, R. Rosenfeld, 1993, Journal of biomolecular structure & dynamics.

Competition between small RNAs: a quantitative view.

Hanah Margalit, Ofer Biham, Itamar Simon, 2012, Biophysical journal.

Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon

Hanah Margalit, Y. M. Fraenkel, Y. Mandel, 1995, Comput. Appl. Biosci..

Identification and characterization of E.coli ribosomal binding sites by free energy computation.

H. Margalit, E. Nadir, T. Schurr, 1993, Nucleic acids research.

Determination of common structural features in Escherichia coli promoters by computer analysis.

H. Margalit, S Lisser, H Margalit, 1994, European journal of biochemistry.

Nucleotide sequence, organization and characterization of the atp genes and the encoded subunits of Mycoplasma gallisepticum ATPase.

H. Margalit, O. Rasmussen, S. Rottem, 1992, The Biochemical journal.

Helix stability in prokaryotic promoter regions.

R Nussinov, B A Shapiro, R L Jernigan, 1988, Biochemistry.

In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III.

H. Margalit, Y. Altuvia, P. Romby, 2013, Methods.

Convergent Within-Host Adaptation of Pseudomonas aeruginosa through the Transcriptional Regulatory Network

H. Margalit, Yair E. Gatt, Dana Savion, 2023, mSystems.

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

H. Margalit, Y. Altuvia, L. Argaman, 2018, Nucleic acids research.

In vivo cleavage rules and target repertoire of RNase III in Escherichia coli

H. Margalit, Y. Altuvia, L. Argaman, 2018, Nucleic Acids Research.

Assigning functions to genes: identification of S-phase expressed genes in Leishmania major based on post-transcriptional control elements

H. Margalit, A. Zick, I. Onn, 2005, Nucleic acids research.

Towards an Integrated Protein-Protein Interaction Network: A Relational Markov Network Approach

Nir Friedman, Hanah Margalit, Gal Elidan, 2006, J. Comput. Biol..

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

H. Margalit, L. Argaman, M. Berger, 2017, Nature Communications.

Patched 1 Regulates Hedgehog Signaling at the Primary Cilium

H. Margalit, Naama Elefant, Noam Stern-Ginossar, 2007 .

Cytomegalovirus microRNAs Facilitate Persistent Virus Infection in Salivary Glands

H. Margalit, S. Pfeffer, Y. Altuvia, 2010, PLoS pathogens.

Assessing the functional association of intronic miRNAs with their host genes

H. Margalit, Avital Steiman-Shimony, Orr Shtrikman, 2018, RNA.

Patched 1 Regulates Hedgehog Signaling at the Primary Cilium

M. Scott, H. Margalit, Naama Elefant, 2022 .

Prolonged survival of a patient with active MDR-TB HIV co-morbidity: insights from a Mycobacterium tuberculosis strain with a unique genomic deletion

H. Margalit, D. Zeevi, Mor Rubinstein, 2023, medRxiv.

Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold

Hanah Margalit, Iddo Friedberg, Tommy Kaplan, 2000, ISMB.

Harnessing the cellular immune system to the gene-prediction cart.

H. Margalit, G. Lithwick, Y. Altuvia, 2001, Trends in genetics : TIG.

Patched 1 Regulates Hedgehog Signaling at the Primary Cilium

H. Margalit, Y. Altuvia, Naama Elefant, 2022 .

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.

R. Milo, U. Alon, Shmuel Sattath, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Comparative Functional Genomics of the Fission Yeasts

Ryan J. Yoder, Michael F. Lin, Carolin A. Müller, 2011 .

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

Yanay Ofran, Hanah Margalit, H. Margalit, 2006, Proteins.