Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.

Literature DB >> 27797762

CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.

Ankeeta Shah¹, Yingzhi Qian¹, Sebastien M Weyn-Vanhentenryck¹, Chaolin Zhang¹.

Abstract

Summary: UV cross-linking and immunoprecipitation (CLIP), followed by high-throughput sequencing, is a powerful biochemical assay that maps in vivo protein-RNA interactions on a genome-wide scale. The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive CLIP data analysis. This software package extends the scope of our original CIMS package. Availability and Implementation: The software is implemented in Perl. The source code and detailed documentation are available at http://zhanglab.c2b2.columbia.edu/index.php/CTK . Contact: cz2294@columbia.edu.

Entities: Chemical

Mesh：

Substances：
RNA-Binding Proteins
RNA

Year: 2017 PMID： 27797762 PMCID： PMC6041811 DOI： 10.1093/bioinformatics/btw653

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

12 in total

1. Site identification in high-throughput RNA-protein interaction data.

Authors: Philip J Uren; Emad Bahrami-Samani; Suzanne C Burns; Mei Qiao; Fedor V Karginov; Emily Hodges; Gregory J Hannon; Jeremy R Sanford; Luiz O F Penalva; Andrew D Smith
Journal: Bioinformatics Date: 2012-09-28 Impact factor: 6.937

2. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.

Authors: Michael T Lovci; Dana Ghanem; Henry Marr; Justin Arnold; Sherry Gee; Marilyn Parra; Tiffany Y Liang; Thomas J Stark; Lauren T Gehman; Shawn Hoon; Katlin B Massirer; Gabriel A Pratt; Douglas L Black; Joe W Gray; John G Conboy; Gene W Yeo
Journal: Nat Struct Mol Biol Date: 2013-11-10 Impact factor: 15.369

3. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.

Authors: Chaolin Zhang; Robert B Darnell
Journal: Nat Biotechnol Date: 2011-06-01 Impact factor: 54.908

Review 4. HITS-CLIP: panoramic views of protein-RNA regulation in living cells.

Authors: Robert B Darnell
Journal: Wiley Interdiscip Rev RNA Date: 2010-08-02 Impact factor: 9.957

5. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.

Authors: Sebastien M Weyn-Vanhentenryck; Aldo Mele; Qinghong Yan; Shuying Sun; Natalie Farny; Zuo Zhang; Chenghai Xue; Margaret Herre; Pamela A Silver; Michael Q Zhang; Adrian R Krainer; Robert B Darnell; Chaolin Zhang
Journal: Cell Rep Date: 2014-03-06 Impact factor: 9.423

6. PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis.

Authors: Beibei Chen; Jonghyun Yun; Min Soo Kim; Joshua T Mendell; Yang Xie
Journal: Genome Biol Date: 2014-01-22 Impact factor: 13.583

7. CLIPdb: a CLIP-seq database for protein-RNA interactions.

Authors: Yu-Cheng T Yang; Chao Di; Boqin Hu; Meifeng Zhou; Yifang Liu; Nanxi Song; Yang Li; Jumpei Umetsu; Zhi John Lu
Journal: BMC Genomics Date: 2015-02-05 Impact factor: 3.969

8. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

Authors: Eric L Van Nostrand; Gabriel A Pratt; Alexander A Shishkin; Chelsea Gelboin-Burkhart; Mark Y Fang; Balaji Sundararaman; Steven M Blue; Thai B Nguyen; Christine Surka; Keri Elkins; Rebecca Stanton; Frank Rigo; Mitchell Guttman; Gene W Yeo
Journal: Nat Methods Date: 2016-03-28 Impact factor: 28.547

9. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.

Authors: Michael J Moore; Chaolin Zhang; Emily Conn Gantman; Aldo Mele; Jennifer C Darnell; Robert B Darnell
Journal: Nat Protoc Date: 2014-01-09 Impact factor: 13.491

10. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.

Authors: Julian König; Kathi Zarnack; Gregor Rot; Tomaz Curk; Melis Kayikci; Blaz Zupan; Daniel J Turner; Nicholas M Luscombe; Jernej Ule
Journal: Nat Struct Mol Biol Date: 2010-07-04 Impact factor: 15.369

48 in total

1. Mettl3-mediated m⁶A regulates spermatogonial differentiation and meiosis initiation.

Authors: Kai Xu; Ying Yang; Gui-Hai Feng; Bao-Fa Sun; Jun-Qing Chen; Yu-Fei Li; Yu-Sheng Chen; Xin-Xin Zhang; Chen-Xin Wang; Li-Yuan Jiang; Chao Liu; Ze-Yu Zhang; Xiu-Jie Wang; Qi Zhou; Yun-Gui Yang; Wei Li
Journal: Cell Res Date: 2017-08-15 Impact factor: 25.617

2. Determination of isoform-specific RNA structure with nanopore long reads.

Authors: Jong Ghut Ashley Aw; Shaun W Lim; Jia Xu Wang; Finnlay R P Lambert; Wen Ting Tan; Yang Shen; Yu Zhang; Pornchai Kaewsapsak; Chenhao Li; Sarah B Ng; Leah A Vardy; Meng How Tan; Niranjan Nagarajan; Yue Wan
Journal: Nat Biotechnol Date: 2020-10-26 Impact factor: 54.908

3. Aberrant Expression of a Non-muscle RBFOX2 Isoform Triggers Cardiac Conduction Defects in Myotonic Dystrophy.

Authors: Chaitali Misra; Sushant Bangru; Feikai Lin; Kin Lam; Sara N Koenig; Ellen R Lubbers; Jamila Hedhli; Nathaniel P Murphy; Darren J Parker; Lawrence W Dobrucki; Thomas A Cooper; Emad Tajkhorshid; Peter J Mohler; Auinash Kalsotra
Journal: Dev Cell Date: 2020-02-27 Impact factor: 12.270

4. LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs.

Authors: Dmytro Ustianenko; Hua-Sheng Chiu; Thomas Treiber; Sebastien M Weyn-Vanhentenryck; Nora Treiber; Gunter Meister; Pavel Sumazin; Chaolin Zhang
Journal: Mol Cell Date: 2018-07-19 Impact factor: 17.970

Review 5. Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions.

Authors: Xiaoli Chen; Sarah A Castro; Qiuying Liu; Wenqian Hu; Shaojie Zhang
Journal: Methods Date: 2018-12-06 Impact factor: 3.608