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1

Efficient Methods for Parameter Estimation of Ordinary and Partial Differential Equation Models of Viral Hepatitis Kinetics

Churkin, Alexander, Lewkiewicz, Stephanie, Reinharz, Vladimir, Dahari, Harel, Barash, Danny

Journal:

Year:

2020

File:

PDF, 4.15 MB

2020

2

A common framework for nonlinear diffusion, adaptive smoothing, bilateral filtering and mean shift

Danny Barash, Dorin Comaniciu

Journal:

Image and Vision Computing

Year:

2004

Language:

english

File:

PDF, 301 KB

english, 2004

3

Nonlinear diffusion filtering on extended neighborhood

Journal:

Applied Numerical Mathematics

Year:

2005

Language:

english

File:

PDF, 450 KB

english, 2005

4

RiboD: A comprehensive database for prokaryotic riboswitches

Mukherjee, Sumit, Das Mandal, Sukhen, Gupta, Nikita, Drory-Retwitzer, Matan, Barash, Danny, Sengupta, Supratim, Wren, Jonathan

Journal:

Year:

2019

File:

PDF, 173 KB

2019

5

Sequence-dependent solution structure and motions of 13 TATA/TBP (TATA-box binding protein) complexes

Daniel Strahs, Danny Barash, Xiaoliang Qian, Tamar Schlick

Journal:

Year:

2003

Language:

english

File:

PDF, 5.16 MB

english, 2003

6

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms

Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 492 KB

english, 2003

7

RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences

Assaf Avihoo, Alexander Churkin, Danny Barash

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 608 KB

english, 2011

8

FASH: A web application for nucleotides sequence search

Isana Veksler-Lublinksy, Danny Barash, Chai Avisar, Einav Troim, Paul Chew, Klara Kedem

Journal:

Source Code for Biology and Medicine

Year:

2008

Language:

english

File:

PDF, 1.17 MB

english, 2008

9

Primordia Vita. Deconvolution from Modern Sequences.

Edward N. Trifonov, Idan Gabdank, Danny Barash, Yehoshua Sobolevsky

Journal:

Origins of Life and Evolution of Biospheres

Year:

2006

Language:

english

File:

PDF, 181 KB

english, 2006

10

RNAmute: RNA secondary structure mutation analysis tool

Alexander Churkin, Danny Barash

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.19 MB

english, 2006

11

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions

Alexander Churkin, Danny Barash

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.10 MB

english, 2008

12

In silicowhole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions

Abdel Aouacheria, Vincent Navratil, Ricardo López-Pérez, Norma C Gutiérrez, Alexander Churkin, Danny Barash, Dominique Mouchiroud, Christian Gautier

Journal:

Year:

2007

Language:

english

File:

PDF, 377 KB

english, 2007

13

On topological indices for small RNA graphs

Churkin, Alexander, Gabdank, Idan, Barash, Danny

Journal:

Computational Biology and Chemistry

Year:

2012

Language:

english

File:

PDF, 666 KB

english, 2012

14

RNA dot plots: an image representation for RNA secondary structure analysis and manipulations

Churkin, Alexander, Barash, Danny

Journal:

Wiley Interdisciplinary Reviews: RNA

Year:

2013

Language:

english

File:

PDF, 478 KB

english, 2013

15

Shape Similarity Measures for the Design of Small RNA Switches

Avihoo, Assaf, Barash, Danny

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2006

Language:

english

File:

PDF, 551 KB

english, 2006

16

Tracing Ancient mRNA Hairpins

Gabdank, Idan, Barash, Danny, Trifonov, Edward N.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2006

Language:

english

File:

PDF, 824 KB

english, 2006

17

Design of Small RNA Switches

Avihoo, Assaf, Gabdank, Idan, Shapira, Michal, Barash*, Danny

Journal:

IEEE Transactions on NanoBioscience

Year:

2007

Language:

english

File:

PDF, 910 KB

english, 2007

18

Spectral Decomposition for the Search and Analysis of RNA Secondary Structure

Journal:

Journal of Computational Biology

Year:

2004

Language:

english

File:

PDF, 71 KB

english, 2004

19

A Structure-Based Flexible Search Method for Motifs in RNA

Veksler-Lublinsky, Isana, Ziv-Ukelson, Michal, Barash, Danny, Kedem, Klara

Journal:

Journal of Computational Biology

Year:

2007

Language:

english

File:

PDF, 471 KB

english, 2007

20

Laser-induced resonance states as dynamic suppressors of ionization in high-frequency short pulses

Barash, Danny, Orel, Ann E., Baer, Roi

Journal:

Physical Review A

Year:

1999

Language:

english

File:

PDF, 65 KB

english, 1999

21

Adaptive Mutations In RNA-Based Regulatory Mechanisms: Computational and Experimental Investigations

Barash, Danny, Sikorski, Johannes, Perry, Elizabeth B., Nevo, Eviatar, Nudler, Evgeny

Journal:

Israel Journal of Ecology and Evolution

Year:

2006

Language:

english

File:

PDF, 1.44 MB

english, 2006

22

BIOINFORMATIC ANALYSIS OF THE NEUTRALITY OF RNA SECONDARY STRUCTURE ELEMENTS ACROSS GENOTYPES REVEALS EVIDENCE FOR DIRECT EVOLUTION OF GENETIC ROBUSTNESS IN HCV

CHURKIN, ALEXANDER, COHEN, MORIAH, SHEMER-AVNI, YONAT, BARASH, DANNY

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2010

Language:

english

File:

PDF, 1007 KB

english, 2010

23

Energy minimization methods applied to riboswitches: A perspective and challenges

Barash, Danny, Gabdank, Idan

Journal:

Year:

2010

Language:

english

File:

PDF, 654 KB

english, 2010

24

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

Drory Retwitzer, Matan, Polishchuk, Maya, Churkin, Elena, Kifer, Ilona, Yakhini, Zohar, Barash, Danny

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.95 MB

english, 2015

25

Intraobserver and Interobserver Variability of Renal Volume Measurements in Polycystic Kidney Disease Using a Semiautomated MR Segmentation Algorithm

Cohen, Benjamin A., Barash, Irina, Kim, Danny C., Sanger, Matthew D., Babb, James S., Chandarana, Hersh

Journal:

American Journal of Roentgenology

Year:

2012

Language:

english

File:

PDF, 799 KB

english, 2012

26

Structural Analysis of Single-Point Mutations Given an RNA Sequence: A Case Study with RNAMute

Churkin, Alexander, Barash, Danny

Journal:

EURASIP Journal on Advances in Signal Processing (Hindawi Publishing Corporation)

Year:

2006

Language:

english

File:

PDF, 1.12 MB

english, 2006

27

: a web server for the fragment-based design of RNA sequences

Drory Retwitzer, Matan, Reinharz, Vladimir, Ponty, Yann, Waldispühl, Jérôme, Barash, Danny

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 1.57 MB

english, 2016

28

Design of RNAs: comparing programs for inverse RNA folding

Churkin, Alexander, Retwitzer, Matan Drory, Reinharz, Vladimir, Ponty, Yann, Waldispühl, Jérôme, Barash, Danny

Journal:

Briefings in Bioinformatics

Year:

2017

Language:

english

File:

PDF, 456 KB

english, 2017

29

Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi

Mukherjee, Sumit, Retwitzer, Matan Drory, Barash, Danny, Sengupta, Supratim

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 3.98 MB

english, 2018

30

In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

Stoltenburg, Regina, Schubert, Thomas, Strehlitz, Beate, Barash, Danny

Journal:

Year:

2015

Language:

english

File:

PDF, 3.62 MB

english, 2015

31

Energy Parameters and Novel Algorithms for an Extended Nearest Neighbor Energy Model of RNA

Dotu, Ivan, Mechery, Vinodh, Clote, Peter, Barash, Danny

Journal:

Year:

2014

Language:

english

File:

PDF, 1019 KB

english, 2014

32

RNAthermsw: Direct Temperature Simulations for Predicting the Location of RNA Thermometers

Churkin, Alexander, Avihoo, Assaf, Shapira, Michal, Barash, Danny, Uversky, Vladimir N.

Journal:

Year:

2014

Language:

english

File:

PDF, 575 KB

english, 2014

33

Designing Anti-Influenza Aptamers: Novel Quantitative Structure Activity Relationship Approach Gives Insights into Aptamer – Virus Interaction

Musafia, Boaz, Oren-Banaroya, Rony, Noiman, Silvia, Barash, Danny

Journal:

Year:

2014

Language:

english

File:

PDF, 1.12 MB

english, 2014

34

A Parallel Implementation of the Wuchty Algorithm with Additional Experimental Filters to More Thoroughly Explore RNA Conformational Space

Stone, Jonathan W., Bleckley, Samuel, Lavelle, Sean, Schroeder, Susan J., Barash, Danny

Journal:

Year:

2015

Language:

english

File:

PDF, 2.74 MB

english, 2015

35

Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures

Fu, Yinghan, Xu, Zhenjiang Zech, Lu, Zhi J., Zhao, Shan, Mathews, David H., Barash, Danny

Journal:

Year:

2015

Language:

english

File:

PDF, 3.44 MB

english, 2015

36

An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding

Drory Retwitzer, Matan, Kifer, Ilona, Sengupta, Supratim, Yakhini, Zohar, Barash, Danny, Tuller, Tamir

Journal:

Year:

2015

Language:

english

File:

PDF, 3.24 MB

english, 2015

37

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

Theis, Corinna, Zirbel, Craig L., zu Siederdissen, Christian Höner, Anthon, Christian, Hofacker, Ivo L., Nielsen, Henrik, Gorodkin, Jan, Barash, Danny

Journal:

Year:

2015

Language:

english

File:

PDF, 391 KB

english, 2015

38

Network Properties of the Ensemble of RNA Structures

Clote, Peter, Bayegan, Amir, Barash, Danny

Journal:

Year:

2015

Language:

english

File:

PDF, 3.66 MB

english, 2015

39

Non-Specific Blocking of miR-17-5p Guide Strand in Triple Negative Breast Cancer Cells by Amplifying Passenger Strand Activity

Jin, Yuan-Yuan, Andrade, Jade, Wickstrom, Eric, Barash, Danny

Journal:

Year:

2015

Language:

english

File:

PDF, 2.94 MB

english, 2015

40

Accurate Classification of RNA Structures Using Topological Fingerprints

Huang, Jiajie, Li, Kejie, Gribskov, Michael, Barash, Danny

Journal:

Year:

2016

Language:

english

File:

PDF, 2.91 MB

english, 2016

41

A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics

Zarai, Yoram, Margaliot, Michael, Tuller, Tamir, Barash, Danny

Journal:

Year:

2017

Language:

english

File:

PDF, 6.36 MB

english, 2017

42

A Robust and Efficient Numerical Method for RNA-Mediated Viral Dynamics

Reinharz, Vladimir, Churkin, Alexander, Dahari, Harel, Barash, Danny

Journal:

Frontiers in Applied Mathematics and Statistics

Year:

2017

Language:

english

File:

PDF, 2.93 MB

english, 2017

43

AIP Conference Proceedings [Author(s) INTERNATIONAL CONFERENCE OF NUMERICAL ANALYSIS AND APPLIED MATHEMATICS (ICNAAM 2017) - Thessaloniki, Greece (25–30 September 2017)] - HCVMultiscaleDyn: A simulator for the multiscale model of hepatitis C virus dynamics

Churkin, Alexander, Reinharz, Vladimir, Dahari, Harel, Barash, Danny

Year:

2018

Language:

english

File:

PDF, 272 KB

english, 2018

44

Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates

Pan, Xiaoyong, Wenzel, Anne, Jensen, Lars Juhl, Gorodkin, Jan, Barash, Danny

Journal:

Year:

2018

Language:

english

File:

PDF, 2.33 MB

english, 2018

45

Extracting information from RNA SHAPE data: Kalman filtering approach

Vaziri, Sana, Koehl, Patrice, Aviran, Sharon, Barash, Danny

Journal:

Year:

2018

Language:

english

File:

PDF, 1.62 MB

english, 2018

46

Resistance to paclitaxel is associated with a variant of the gene BCL2 in multiple tumor types

Ben-Hamo, Rotem, Zilberberg, Alona, Cohen, Helit, Bahar-Shany, Keren, Wachtel, Chaim, Korach, Jacob, Aviel-Ronen, Sarit, Barshack, Iris, Barash, Danny, Levanon, Keren, Efroni, Sol

Journal:

npj Precision Oncology

Year:

2019

Language:

english

File:

PDF, 1.79 MB

english, 2019

47

Resistance to paclitaxel is associated with a variant of the gene BCL2 in multiple tumor types

Ben-Hamo, Rotem, Zilberberg, Alona, Cohen, Helit, Bahar-Shany, Keren, Wachtel, Chaim, Korach, Jacob, Aviel-Ronen, Sarit, Barshack, Iris, Barash, Danny, Levanon, Keren, Efroni, Sol

Journal:

npj Precision Oncology

Year:

2019

File:

PDF, 1.79 MB

2019

48

A Parameter Estimation Method for Multiscale Models of Hepatitis C Virus Dynamics

Reinharz, Vladimir, Churkin, Alexander, Lewkiewicz, Stephanie, Dahari, Harel, Barash, Danny

Journal:

Bulletin of Mathematical Biology

Year:

2019

Language:

english

File:

PDF, 2.36 MB

english, 2019

49

A Parameter Estimation Method for Multiscale Models of Hepatitis C Virus Dynamics

Reinharz, Vladimir, Churkin, Alexander, Lewkiewicz, Stephanie, Dahari, Harel, Barash, Danny

Journal:

Bulletin of Mathematical Biology

Year:

2019

File:

PDF, 2.36 MB

2019

50

incaRNAfbinv 2.0 - A webserver and software with motif control for fragment-based design of RNAs

Retwitzer, Matan Drory, Reinharz, Vladimir, Churkin, Alexander, Ponty, Yann, Waldispühl, Jérôme, Barash, Danny, Valencia, Alfonso

Journal:

Year:

2020

Language:

english

File:

PDF, 277 KB

english, 2020