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1

Integration of Bacterial Small RNAs in Regulatory Networks

Nitzan, Mor, Rehani, Rotem, Margalit, Hanah

Journal:

Annual Review of Biophysics

Year:

2017

Language:

english

File:

PDF, 9.99 MB

english, 2017

2

Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins

James L. Cornette, Kemp B. Cease, Hanah Margalit, John L. Spouge, Jay A. Berzofsky, Charles DeLisi

Journal:

Journal of Molecular Biology

Year:

1987

Language:

english

File:

PDF, 3.18 MB

english, 1987

3

Molecular Characterization of a Common Fragile Site (FRA7H) on Human Chromosome 7 by the Cloning of a Simian Virus 40 Integration Site

Dan Mishmar, Ayelet Rahat, Stephen W. Scherer, Gerald Nyakatura, Bernd Hinzmann, Yoshinori Kohwi, Yael Mandel-Gutfroind, Jeffrey R. Lee, Bernd Drescher, Dean E. Sas, Hanah Margalit, Mattias Platzer, A

Journal:

Proceedings of the National Academy of Sciences

Year:

1998

Language:

english

File:

PDF, 1.85 MB

english, 1998

4

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval

Habib, Naomi, Kaplan, Tommy, Margalit, Hanah, Friedman, Nir, Fraenkel, Ernest

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 789 KB

english, 2008

5

Mapping the small RNA interactome in bacteria using RIL-seq

Melamed, Sahar, Faigenbaum-Romm, Raya, Peer, Asaf, Reiss, Niv, Shechter, Omer, Bar, Amir, Altuvia, Yael, Argaman, Liron, Margalit, Hanah

Journal:

Nature Protocols

Year:

2017

Language:

english

File:

PDF, 1.27 MB

english, 2017

6

Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge

Kaplan, Tommy, Friedman, Nir, Margalit, Hanah

Journal:

PLoS Computational Biology

Year:

2005

Language:

english

File:

PDF, 465 KB

english, 2005

7

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

Ora Schueler-Furman, Yael Altuvia, Hanah Margalit

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 152 KB

english, 2001

8

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

Yanay Ofran, Hanah Margalit

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2006

Language:

english

File:

PDF, 398 KB

english, 2006

9

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

Jay A. Berzofsky, Kemp B. Cease, James L. Cornette, John L. Spouge, Hanah Margalit, Ira J. Berkower, Michael F. Good, Louis H. Miller, Charles Delisi

Journal:

Immunological Reviews

Year:

1987

Language:

english

File:

PDF, 14.19 MB

english, 1987

10

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

Ora Schueler-Furman, Yael Altuvia, Alessandro Sette, Hanah Margalit

Journal:

Protein Science

Year:

2000

Language:

english

File:

PDF, 235 KB

english, 2000

11

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

Iddo Friedberg, Hanah Margalit

Journal:

Protein Science

Year:

2002

Language:

english

File:

PDF, 302 KB

english, 2002

12

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

Iddo Friedberg, Tommy Kaplan, Hanah Margalit

Journal:

Protein Science

Year:

2000

Language:

english

File:

PDF, 308 KB

english, 2000

13

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

Satoshi Kotake, Barbara Wiggert, T.Michael Redmond, Diane E. Borst, John M. Nickerson, Hanah Margalit, Jay A. Berzofsky, Gerald J. Chader, Igal Gery

Journal:

Cellular Immunology

Year:

1990

Language:

english

File:

PDF, 2.20 MB

english, 1990

14

Chromosomal organization is shaped by the transcription regulatory network

Ruth Hershberg, Esti Yeger-Lotem, Hanah Margalit

Journal:

Trends in Genetics

Year:

2005

Language:

english

File:

PDF, 106 KB

english, 2005

15

Harnessing the cellular immune system to the gene-prediction cart

Yael Altuvia, Gila Lithwick, Hanah Margalit

Journal:

Trends in Genetics

Year:

2001

Language:

english

File:

PDF, 51 KB

english, 2001

16

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

Liron Argaman, Ruth Hershberg, Jörg Vogel, Gill Bejerano, E.Gerhart H Wagner, Hanah Margalit, Shoshy Altuvia

Journal:

Current Biology

Year:

2001

Language:

english

File:

PDF, 264 KB

english, 2001

17

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

Ora Schueler-Furman, Ron Elber, Hanah Margalit

Journal:

Folding and Design

Year:

1998

Language:

english

File:

PDF, 183 KB

english, 1998

18

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

Shlomit LISSER, Hanah MARGALIT

Journal:

Year:

1994

Language:

english

File:

PDF, 896 KB

english, 1994

19

Conservation of Salt Bridges in Protein Families

Ora Schueler, Hanah Margalit

Journal:

Journal of Molecular Biology

Year:

1995

Language:

english

File:

PDF, 634 KB

english, 1995

20

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

Yael Altuvia, Ora Schueler, Hanah Margalit

Journal:

Journal of Molecular Biology

Year:

1995

Language:

english

File:

PDF, 702 KB

english, 1995

21

Comprehensive Analysis of Hydrogen Bonds in Regulatory Protein DNA-Complexes: In Search of Common Principles

Yael Mandel-Gutfreund, Ora Schueler, Hanah Margalit

Journal:

Journal of Molecular Biology

Year:

1995

Language:

english

File:

PDF, 455 KB

english, 1995

22

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

Yael Mandel-Gutfreund, Hanah Margalit, Robert L Jernigan, Victor B Zhurkin

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 349 KB

english, 1998

23

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

Yael Altuvia, Hanah Margalit

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 286 KB

english, 2000

24

Correlated sequence-signatures as markers of protein-protein interaction

Einat Sprinzak, Hanah Margalit

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 297 KB

english, 2001

25

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

Yael Altuvia, Hanah Margalit

Journal:

Year:

2004

Language:

english

File:

PDF, 540 KB

english, 2004

26

How Reliable are Experimental Protein–Protein Interaction Data?

Einat Sprinzak, Shmuel Sattath, Hanah Margalit

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 337 KB

english, 2003

27

A Structure-Based Algorithm to Predict Potential Binding Peptides to MHC Molecules with Hydrophobic Binding Pockets

Yael Altuvia, Alessandro Sette, John Sidney, Scott Southwood, Hanah Margalit

Journal:

Human Immunology

Year:

1997

Language:

english

File:

PDF, 512 KB

english, 1997

28

Common Fragile Sites: G-Band Characteristics within an R-Band

Dan Mishmar, Yael Mandel-Gutfreund, Hanah Margalit, Ayelet Rahat, Batsheva Kerem

Journal:

The American Journal of Human Genetics

Year:

1999

Language:

english

File:

PDF, 58 KB

english, 1999

29

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

Schurr, Tamar, Nadir, Eyal, Margalit, Hanah

Journal:

Nucleic Acids Research

Year:

1993

Language:

english

File:

PDF, 485 KB

english, 1993

30

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

T.Michael Redmond, Hiroki Sanui, Li-Hong Hu, Barbara Wiggeri, Hanah Margalit, Jay A. Berzofsky, Gerald J. Chader, Igal Gery

Journal:

Clinical Immunology and Immunopathology

Year:

1989

Language:

english

File:

PDF, 895 KB

english, 1989

31

Sequence features that correlate with MHC restriction

Yael Altuvia, Jay A. Berzofsky, Rakefet Rosenfeld, Hanah Margalit

Journal:

Molecular Immunology

Year:

1994

Language:

english

File:

PDF, 2.15 MB

english, 1994

32

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

Hanah Margalit, Eyal Nadir, Shmuel A. Ben-Sasson

Journal:

Year:

1994

Language:

english

File:

PDF, 154 KB

english, 1994

33

Competition between Small RNAs: A Quantitative View

Loinger, Adiel, Shemla, Yael, Simon, Itamar, Margalit, Hanah, Biham, Ofer

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 650 KB

english, 2012

34

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

Habib, Naomi, Wapinski, Ilan, Margalit, Hanah, Regev, Aviv, Friedman, Nir

Journal:

Molecular Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.06 MB

english, 2012

35

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

Maya Botzman, Hanah Margalit

Journal:

Year:

2011

Language:

english

File:

PDF, 504 KB

english, 2011

36

Evolutionary conservation of domain-domain interactions

Zohar Itzhaki, Eyal Akiva, Yael Altuvia, Hanah Margalit

Journal:

Year:

2006

Language:

english

File:

PDF, 336 KB

english, 2006

37

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

Ruth Hershberg, Hanah Margalit

Journal:

Year:

2006

Language:

english

File:

PDF, 403 KB

english, 2006

38

Global Regulation of Transcription by a Small RNA: A Quantitative View

Nitzan, Mor, Wassarman, Karen M., Biham, Ofer, Margalit, Hanah

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 1.09 MB

english, 2014

39

Molecular analysis of HLA class II genes in primary sjo¨gren's syndrome

Roitberg-Tambur, Anat, Friedmann, Adam, Safirman, Cilly, Markitziu, Alice, Ben-Chetrit, Eldad, Rubinow, Alan, Moutsopoulos, Haralampos M., Stavropoulos, Efthymois, Skopouli, Fotini N., Margalit, Hanah

Journal:

Human Immunology

Year:

1993

Language:

english

File:

PDF, 642 KB

english, 1993

40

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

Lioliou, Efthimia, Sharma, Cynthia M., Altuvia, Yaël, Caldelari, Isabelle, Romilly, Cédric, Helfer, Anne-Catherine, Margalit, Hanah, Romby, Pascale

Journal:

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

41

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

Kemp B. Cease, Hanah Margalit, James L. Cornette, Scott D. Putney, W. Gerard Robey, Cecilia Ouyang, Howard Z. Streicher, Peter J. Fischinger, Robert C. Gallo, Charles DeLisi and Jay A. Berzofsky

Journal:

Proceedings of the National Academy of Sciences

Year:

1987

Language:

english

File:

PDF, 1.05 MB

english, 1987

42

Microsatellite Spreading in the Human Genome: Evolutionary Mechanisms and Structural Implications

Eyal Nadir, Hanah Margalit, Tamar Gallily and Shmuel A. Ben-Sasson

Journal:

Proceedings of the National Academy of Sciences

Year:

1996

Language:

english

File:

PDF, 1.25 MB

english, 1996

43

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

Shimoni, Yishai, Friedlander, Gilgi, Hetzroni, Guy, Niv, Gali, Altuvia, Shoshy, Biham, Ofer, Margalit, Hanah

Journal:

Molecular Systems Biology

Year:

2007

Language:

english

File:

PDF, 295 KB

english, 2007

44

Compilation of E.coli mRNA promoter sequences

Lisser, Shlomit, Margalit, Hanah

Journal:

Nucleic Acids Research

Year:

1993

Language:

english

File:

PDF, 992 KB

english, 1993

45

Helix stability in prokaryotic promoter regions

Margalit, Hanah, Shapiro, Bruce A., Nussinov, Ruth, Owens, John, Jernigan, Robert L.

Journal:

Year:

1988

Language:

english

File:

PDF, 1.17 MB

english, 1988

46

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

Sanui, Hiroki, Redmond, T. Michael, Hu, Li-Hong, Kuwabara, Toichiro, Margalit, Hanah, Cornette, James L., Wiggert, Barbara, Chader, Gerald J., Gery, Igal

Journal:

Current Eye Research

Year:

1988

Language:

english

File:

PDF, 790 KB

english, 1988

47

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

Jaimovich, Ariel, Elidan, Gal, Margalit, Hanah, Friedman, Nir

Journal:

Journal of Computational Biology

Year:

2006

Language:

english

File:

PDF, 638 KB

english, 2006

48

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

Sajman, Julia, Zenvirth, Drora, Nitzan, Mor, Margalit, Hanah, Simpson-Lavy, Kobi J., Reiss, Yuval, Cohen, Itamar, Ravid, Tommer, Brandeis, Michael

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 1.69 MB

english, 2015

49

Zinc Fingers: Conserved Properties that Can Distinguish Between Spurious and Actual DNA-Binding Motifs

Rosenfeld, Rakefet, Margalit, Hanah

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

1993

Language:

english

File:

PDF, 820 KB

english, 1993

50

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

Fraenkel, Yishai M., Mandel, Yael, Friedberg, Devorah, Margalit, Hanah

Journal:

Year:

1995

Language:

english

File:

PDF, 1.99 MB

english, 1995

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