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1

Bacterial Riboswitches Cooperatively Bind Ni2+ or Co2+ Ions and Control Expression of Heavy Metal Transporters

Furukawa, Kazuhiro, Ramesh, Arati, Zhou, Zhiyuan, Weinberg, Zasha, Vallery, Tenaya, Winkler, Wade C., Breaker, Ronald R.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.17 MB

english, 2015

2

Discovery and characterization of a fourth class of guanidine riboswitches

Lenkeit, Felina, Eckert, Iris, Hartig, JÃ¶rg S, Weinberg, Zasha

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 3.64 MB

2020

3

A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate

Tyler D. Ames, Dmitry A. Rodionov, Zasha Weinberg, Ronald R. Breaker

Journal:

Chemistry & Biology

Year:

2010

Language:

english

File:

PDF, 363 KB

english, 2010

4

R2R - software to speed the depiction of aesthetic consensus RNA secondary structures

Zasha Weinberg, Ronald R Breaker

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 557 KB

english, 2011

5

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

Elizabeth E. Regulski, Ryan H. Moy, Zasha Weinberg, Jeffrey E. Barrick, Zizhen Yao, Walter L. Ruzzo, Ronald R. Breaker

Journal:

Molecular Microbiology

Year:

2008

Language:

english

File:

PDF, 589 KB

english, 2008

6

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis

Weinberg, Zasha, Perreault, Jonathan, Meyer, Michelle M., Breaker, Ronald R.

Journal:

Year:

2009

Language:

english

File:

PDF, 407 KB

english, 2009

7

Identification of candidate structured RNAs in the marine organism 'CandidatusPelagibacter ubique'

Michelle M Meyer, Tyler D Ames, Daniel P Smith, Zasha Weinberg, Michael S Schwalbach, Stephen J Giovannoni, Ronald R Breaker

Journal:

Year:

2009

Language:

english

File:

PDF, 521 KB

english, 2009

8

Small, Highly Active DNAs That Hydrolyze DNA

Gu, Hongzhou, Furukawa, Kazuhiro, Weinberg, Zasha, Berenson, Daniel F., Breaker, Ronald R.

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 3.72 MB

english, 2013

9

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino…

Journal:

Year:

2010

Language:

english

File:

PDF, 1.19 MB

english, 2010

10

Riboswitches in eubacteria sense the second messenger c-di-AMP

Nelson, James W, Sudarsan, Narasimhan, Furukawa, Kazuhiro, Weinberg, Zasha, Wang, Joy X, Breaker, Ronald R

Journal:

Nature Chemical Biology

Year:

2013

Language:

english

File:

PDF, 902 KB

english, 2013

11

A widespread self-cleaving ribozyme class is revealed by bioinformatics

Roth, Adam, Weinberg, Zasha, Chen, Andy G Y, Kim, Peter B, Ames, Tyler D, Breaker, Ronald R

Journal:

Nature Chemical Biology

Year:

2013

Language:

english

File:

PDF, 935 KB

english, 2013

12

Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes

McCown, Phillip J., Liang, Jonathan J., Weinberg, Zasha, Breaker, Ronald R.

Journal:

Chemistry & Biology

Year:

2014

Language:

english

File:

PDF, 1.93 MB

english, 2014

13

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

Yao, Zizhen, Barrick, Jeffrey, Weinberg, Zasha, Neph, Shane, Breaker, Ronald, Tompa, Martin, Ruzzo, Walter L.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 1.25 MB

english, 2007

14

Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations

Perreault, Jonathan, Weinberg, Zasha, Roth, Adam, Popescu, Olivia, Chartrand, Pascal, Ferbeyre, Gerardo, Breaker, Ronald R., Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.29 MB

english, 2011

15

New classes of self-cleaving ribozymes revealed by comparative genomics analysis

Weinberg, Zasha, Kim, Peter B, Chen, Tony H, Li, Sanshu, Harris, Kimberly A, Lünse, Christina E, Breaker, Ronald R

Journal:

Nature Chemical Biology

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

16

[ACM Press the eighth annual international conference - San Diego, California, USA (2004.03.27-2004.03.31)] Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04 - Faster genome annotation of non-coding RNA families without loss of accuracy

Weinberg, Zasha, Ruzzo, Walter L.

Year:

2004

Language:

english

File:

PDF, 187 KB

english, 2004

17

[ACM Press the 2000 ACM SIGMOD international conference - Dallas, Texas, United States (2000.05.15-2000.05.18)] Proceedings of the 2000 ACM SIGMOD international conference on Management of data - SIGMOD '00 - An approximate search engine for structural databases

Wang, Jason T. L., Wang, Xiong, Shasha, Dennis, Shapiro, Bruce A., Zhang, Kaizhong, Ma, Qicheng, Weinberg, Zasha

Year:

2000

Language:

english

File:

PDF, 83 KB

english, 2000

18

Meeting report of the RNA Ontology Consortium January 8–9, 2011

Birmingham, Amanda, Clemente, Jose C., Desai, Narayan, Gilbert, Jack, Gonzalez, Antonio, Kyrpides, Nikos, Meyer, Folker, Nawrocki, Eric, Sterk, Peter, Stombaugh, Jesse, Weinberg, Zasha, Wendel, Doug,

Journal:

Standards in Genomic Sciences

Year:

2011

Language:

english

File:

PDF, 153 KB

english, 2011

19

FINDING NON-CODING RNAs THROUGH GENOME-SCALE CLUSTERING

TSENG, HUEI-HUN, WEINBERG, ZASHA, GORE, JEREMY, BREAKER, RONALD R., RUZZO, WALTER L.

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2009

Language:

english

File:

PDF, 411 KB

english, 2009

20

Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers

Lünse, Christina E., Weinberg, Zasha, Breaker, Ronald R.

Journal:

Year:

2016

Language:

english

File:

PDF, 573 KB

english, 2016

21

Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

Weinberg, Zasha, Nelson, James W., Lünse, Christina E., Sherlock, Madeline E., Breaker, Ronald R.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.01 MB

english, 2017

22

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

Weinberg, Zasha, Lünse, Christina E., Corbino, Keith A., Ames, Tyler D., Nelson, James W., Roth, Adam, Perkins, Kevin R., Sherlock, Madeline E., Breaker, Ronald R.

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 1.16 MB

english, 2017

23

SAM-VI RNAs Selectively Bind S -adenosylmethionine and Exhibit Similarities to SAM-III Riboswitches

Arachchilage, Gayan Mirihana, Sherlock, Madeline E, Weinberg, Zasha, Breaker, Ronald R

Journal:

Year:

2017

Language:

english

File:

PDF, 1.73 MB

english, 2017

24

Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function

Weinberg, Christina E, Weinberg, Zasha, Hammann, Christian

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 2.51 MB

english, 2019

25

Discovery of 20 novel ribosomal leader candidates in bacteria and archaea

Eckert, Iris, Weinberg, Zasha

Journal:

BMC Microbiology

Year:

2020

File:

PDF, 1016 KB

2020

26

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

Kalvari, Ioanna, Nawrocki, Eric P, Ontiveros-Palacios, Nancy, Argasinska, Joanna, Lamkiewicz, Kevin, Marz, Manja, Griffiths-Jones, Sam, Toffano-Nioche, Claire, Gautheret, Daniel, Weinberg, Zasha, Riva

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 2.54 MB

2020