Searching journal content for articles similar to Li et al. 24 (7): 1086.

Displaying results 1-10 of 32

For checked items

view abstracts
download to citation manager

Select this article
Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...C. elegans and the fruit fly Drosophila melanogaster were selected for the modENCODE Project in 2007 because of their experimental strengths and prominence as model organisms as well as for their compact, sequenced s, which simplifies the identification of TF binding sites and candidate target genes...
Select this article
Resource: The developmental proteome of Drosophila melanogaster
- Nuria Casas-Vila,
- Alina Bluhm,
- Sergi Sayols,
- Nadja Dinges,
- Mario Dejung,
- Tina Altenhein,
- Dennis Kappei,
- Benjamin Altenhein,
- Jean-Yves Roignant,
- and Falk Butter
Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
..., National University of Singapore, Singapore 117599; 7Institute of Zoology, University of Cologne, 50674 Cologne, Germany Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive...
Select this article
Resource: Comparative validation of the D. melanogaster modENCODE transcriptome annotation
- Zhen-Xia Chen,
- David Sturgill,
- Jiaxin Qu,
- Huaiyang Jiang,
- Soo Park,
- Nathan Boley,
- Ana Maria Suzuki,
- Anthony R. Fletcher,
- David C. Plachetzki,
- Peter C. FitzGerald,
- Carlo G. Artieri,
- Joel Atallah,
- Olga Barmina,
- James B. Brown,
- Kerstin P. Blankenburg,
- Emily Clough,
- Abhijit Dasgupta,
- Sai Gubbala,
- Yi Han,
- Joy C. Jayaseelan,
- Divya Kalra,
- Yoo-Ah Kim,
- Christie L. Kovar,
- Sandra L. Lee,
- Mingmei Li,
- James D. Malley,
- John H. Malone,
- Tittu Mathew,
- Nicolas R. Mattiuzzo,
- Mala Munidasa,
- Donna M. Muzny,
- Fiona Ongeri,
- Lora Perales,
- Teresa M. Przytycka,
- Ling-Ling Pu,
- Garrett Robinson,
- Rebecca L. Thornton,
- Nehad Saada,
- Steven E. Scherer,
- Harold E. Smith,
- Charles Vinson,
- Crystal B. Warner,
- Kim C. Worley,
- Yuan-Qing Wu,
- Xiaoyan Zou,
- Peter Cherbas,
- Manolis Kellis,
- Michael B. Eisen,
- Fabio Piano,
- Karin Kionte,
- David H. Fitch,
- Paul W. Sternberg,
- Asher D. Cutter,
- Michael O. Duff,
- Roger A. Hoskins,
- Brenton R. Graveley,
- Richard A. Gibbs,
- Peter J. Bickel,
- Artyom Kopp,
- Piero Carninci,
- Susan E. Celniker,
- Brian Oliver,
- and Stephen Richards
Genome Res. July 2014 24: 1209-1223; Published in Advance July 1, 2014, doi:10.1101/gr.159384.113
...junction spanning reads in those RNA-seq profiles revealed a much richer set of processed transcripts. Additional RNA-seq data sets, along with cap analysis of gene expression (CAGE-seq) and full-insert cDNA sequencing, have been used to generate the modENCODE D. melanogaster transcriptome annotation...
OPEN ACCESS ARTICLE
Select this article
Method: Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq
- Peng Liu,
- Rajendran Sanalkumar,
- Emery H. Bresnick,
- Sündüz Keleş,
- and Colin N. Dewey
Genome Res. August 2016 26: 1124-1133; Published in Advance July 12, 2016, doi:10.1101/gr.199174.115
...Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq Peng Liu 1 , Rajendran Sanalkumar 2 , Emery H. Bresnick 2 , Sündüz Keleş 1 , 3 and Colin N. Dewey 1 , 4 1Department...
OPEN ACCESS ARTICLE
Select this article
Research: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
- Tess E. Jeffers and
- Jason D. Lieb
Genome Res. January 2017 27: 75-86; Published in Advance November 14, 2016, doi:10.1101/gr.208173.116
...in green and orange, respectively) were considered “fragile” or “resistant.” Jeffers and Lieb 76 Genome Research www..org TFBSs. We collected a set of 35,062 TFBSs bound at any stage of C. elegans development, as identified by TF ChIP-seq from the modENCODE Consortium (Araya et al. 2014). The DNA...
Select this article
Research: Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
- Eric L. Van Nostrand and
- Stuart K. Kim
Genome Res. June 2013 23: 941-953; Published in Advance March 26, 2013, doi:10.1101/gr.152876.112
...Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions Eric L. Van Nostrand 1 and Stuart K. Kim 2 Department of Genetics and Department of Developmental Biology, Stanford University Medical Center, Stanford...
Select this article
Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...RNA-seq compendium of reproducibly expressed splice junctions in C. elegans, assembled from 1682 publicly available RNA-seq experiments (Tourasse et al. 2017). Each splice junction has an associated percent spliced in (PSI) value, which is a measure of the frequency of each splice junction relative...
OPEN ACCESS ARTICLE
Select this article
Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- Stephen G. Landt,
- Georgi K. Marinov,
- Anshul Kundaje,
- Pouya Kheradpour,
- Florencia Pauli,
- Serafim Batzoglou,
- Bradley E. Bernstein,
- Peter Bickel,
- James B. Brown,
- Philip Cayting,
- Yiwen Chen,
- Gilberto DeSalvo,
- Charles Epstein,
- Katherine I. Fisher-Aylor,
- Ghia Euskirchen,
- Mark Gerstein,
- Jason Gertz,
- Alexander J. Hartemink,
- Michael M. Hoffman,
- Vishwanath R. Iyer,
- Youngsook L. Jung,
- Subhradip Karmakar,
- Manolis Kellis,
- Peter V. Kharchenko,
- Qunhua Li,
- Tao Liu,
- X. Shirley Liu,
- Lijia Ma,
- Aleksandar Milosavljevic,
- Richard M. Myers,
- Peter J. Park,
- Michael J. Pazin,
- Marc D. Perry,
- Debasish Raha,
- Timothy E. Reddy,
- Joel Rozowsky,
- Noam Shoresh,
- Arend Sidow,
- Matthew Slattery,
- John A. Stamatoyannopoulos,
- Michael Y. Tolstorukov,
- Kevin P. White,
- Simon Xi,
- Peggy J. Farnham,
- Jason D. Lieb,
- Barbara J. Wold,
- and Michael Snyder
Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
...at physiological levels (DeKoter and Singh 2000; Fernandez et al. 2003). In ENCODE/modENCODE, tagged factors have been used most extensively thus far for C. elegans studies, where factors have been tagged with GFP and shown to complement mutants; six of six tested to date have been found to complement (Zhong...
OPEN ACCESS ARTICLE
Select this article
Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...error rates and the relative lack of bioinformatics tools and analysis pipelines designed for long, error-rich reads.In this study, we have generated an atlas of postembryonic transcript structure using dRNA-seq to sequence RNA extracted from the major stages of the C. elegans developmental life cycle...
OPEN ACCESS ARTICLE
Select this article
Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
...allows us to characterize highly reproducible changes in chromatin accessibility between developmental stages and to identify functional temporal- and tissue-specific novel enhancers in vivo. Our study provides a unique resource for defining C. elegans regulatory regions as well as a guide...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Li et al. 24 (7): 1086.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: