Searching journal content for articles similar to Chen et al. 24 (7): 1209.

Displaying results 1-10 of 58

For checked items

view abstracts
download to citation manager

Select this article
Research: Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data
- Jingyi Jessica Li,
- Haiyan Huang,
- Peter J. Bickel,
- and Steven E. Brenner
Genome Res. July 2014 24: 1086-1101; Published in Advance July 1, 2014, doi:10.1101/gr.170100.113
..., USA Abstract We report a statistical study to discover transcriptome similarity of developmental stages from D. melanogaster and C. elegans using modENCODE RNA-seq data. We focus on “stage-associated genes” that capture specific transcriptional activities in each stage and use them...
OPEN ACCESS ARTICLE
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
...and proteome to study translational delay We compared our embryogenesis proteome with the transcriptome generated as part of the modENCODE Project (Graveley et al. 2011). In agreement with the transcriptome analysis, we found that the general protein complexity is increased during embryogenesis (Fig. 7A...
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
...ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia Stephen G. Landt 1 , 26 , Georgi K. Marinov 2 , 26 , Anshul Kundaje 3 , 26 , Pouya Kheradpour 4 , Florencia Pauli 5 , Serafim Batzoglou 3 , Bradley E...
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
..., Baltimore, Maryland 21218, USA; 3Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding authors: wtimp@jhu.edu, james@taylorlab.org, jnkim@jhu.eduAbstractCurrent transcriptome annotations have largely relied on short read lengths intrinsic to the most widely...
OPEN ACCESS ARTICLE
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
...with the region through protein–protein interactions (Moorman et al. 2006; Gerstein et al. 2010; The modENCODE Consortium 2010; Yip et al. 2012). HOT regions are also associated with histone modification profiles and chromatin signatures characteristic of open chromatin in human and D. melanogaster, with strong...
Select this article
Resource: The Release 6 reference sequence of the Drosophila melanogaster genome
- Roger A. Hoskins,
- Joseph W. Carlson,
- Kenneth H. Wan,
- Soo Park,
- Ivonne Mendez,
- Samuel E. Galle,
- Benjamin W. Booth,
- Barret D. Pfeiffer,
- Reed A. George,
- Robert Svirskas,
- Martin Krzywinski,
- Jacqueline Schein,
- Maria Carmela Accardo,
- Elisabetta Damia,
- Giovanni Messina,
- María Méndez-Lago,
- Beatriz de Pablos,
- Olga V. Demakova,
- Evgeniya N. Andreyeva,
- Lidiya V. Boldyreva,
- Marco Marra,
- A. Bernardo Carvalho,
- Patrizio Dimitri,
- Alfredo Villasante,
- Igor F. Zhimulev,
- Gerald M. Rubin,
- Gary H. Karpen,
- and Susan E. Celniker
Genome Res. March 2015 25: 445-458; Published in Advance January 14, 2015, doi:10.1101/gr.185579.114
....5 Mb with four clone gaps in unsized introns. To validate the Myo81F gene structure and the assembly of the super scaffold, we mapped RNA-seq reads from the modENCODE developmental time course (Graveley et al. 2011) to the cDNA sequence. Myo81F is expressed in the larval and pupal stages, most...
OPEN ACCESS ARTICLE
Select this article
Resource: The Drosophila melanogaster transcriptome by paired-end RNA sequencing
- Bryce Daines,
- Hui Wang,
- Liguo Wang,
- Yumei Li,
- Yi Han,
- David Emmert,
- William Gelbart,
- Xia Wang,
- Wei Li,
- Richard Gibbs,
- and Rui Chen
Genome Res. February 2011 21: 315-324; Published in Advance December 22, 2010, doi:10.1101/gr.107854.110
..., although they are observed in mixed larva and pupa samples (Fig. 2D, ‘‘Male’’). Other clusters express most abundantly in a specific stage (Fig. 2D, ‘‘Larva’’). Figure 1. Deep RNA-seq covers 93% of the annotated D. melanogaster transcriptome. (A) 93.4% and 91.9% of the FlyBase and modENCODE annotated...
Select this article
Method: Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
- T.S. Keshava Prasad,
- Ajeet Kumar Mohanty,
- Manish Kumar,
- Sreelakshmi K. Sreenivasamurthy,
- Gourav Dey,
- Raja Sekhar Nirujogi,
- Sneha M. Pinto,
- Anil K. Madugundu,
- Arun H. Patil,
- Jayshree Advani,
- Srikanth S. Manda,
- Manoj Kumar Gupta,
- Sutopa B. Dwivedi,
- Dhanashree S. Kelkar,
- Brantley Hall,
- Xiaofang Jiang,
- Ashley Peery,
- Pavithra Rajagopalan,
- Soujanya D. Yelamanchi,
- Hitendra S. Solanki,
- Remya Raja,
- Gajanan J. Sathe,
- Sandip Chavan,
- Renu Verma,
- Krishna M. Patel,
- Ankit P. Jain,
- Nazia Syed,
- Keshava K. Datta,
- Aafaque Ahmed Khan,
- Manjunath Dammalli,
- Savita Jayaram,
- Aneesha Radhakrishnan,
- Christopher J. Mitchell,
- Chan-Hyun Na,
- Nirbhay Kumar,
- Photini Sinnis,
- Igor V. Sharakhov,
- Charles Wang,
- Harsha Gowda,
- Zhijian Tu,
- Ashwani Kumar,
- and Akhilesh Pandey
Genome Res. January 2017 27: 133-144; Published in Advance November 15, 2016, doi:10.1101/gr.201368.115
...the is sequenced. Annotation of protein-coding genes is currently based on gene prediction algorithms (Renuse et al. 2011; Megy et al. 2012; Jiang et al. 2014). The annotated genes remain as hypothetical sequences until validated through experiments. The experimental data might include transcriptomic data, which...
Select this article
Research: Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
- Zoe June Assaf,
- Susanne Tilk,
- Jane Park,
- Mark L. Siegal,
- and Dmitri A. Petrov
Genome Res. December 2017 27: 1988-2000; Published in Advance October 27, 2017, doi:10.1101/gr.219956.116
...downloaded the publicly available expression data generated from the D. melanogaster germline by the modENCODE project (Graveley et al. 2011) and measured the density of polymorphisms within genes that are binned by expression level (bin levels 1–8 for low-to-high expression) (see Methods). We find...
Select this article
Research: Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
- Eugene Berezikov,
- Nicolas Robine,
- Anastasia Samsonova,
- Jakub O. Westholm,
- Ammar Naqvi,
- Jui-Hung Hung,
- Katsutomo Okamura,
- Qi Dai,
- Diane Bortolamiol-Becet,
- Raquel Martin,
- Yongjun Zhao,
- Phillip D. Zamore,
- Gregory J. Hannon,
- Marco A. Marra,
- Zhiping Weng,
- Norbert Perrimon,
- and Eric C. Lai
Genome Res. February 2011 21: 203-215; Published in Advance December 22, 2010, doi:10.1101/gr.116657.110
...by the Ambros, Tuschl, and Bartel groups in 2001, more than a hundred studies have sought to identify additional miRNAs in various species. We report here a meta-analysis of short RNA data from Drosophila melanogaster , aggregating published libraries with 76 data sets that we generated for the modENCODE...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Chen et al. 24 (7): 1209.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: