Searching journal content for articles similar to Sousa-Nunes et al. 13 (12): 2609.

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Method: Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
- Lukas Chavez,
- Justyna Jozefczuk,
- Christina Grimm,
- Jörn Dietrich,
- Bernd Timmermann,
- Hans Lehrach,
- Ralf Herwig,
- and James Adjaye
Genome Res. October 2010 20: 1441-1450; Published in Advance August 27, 2010, doi:10.1101/gr.110114.110
...) and investigated lineage-specific gene expression patterns by real-time RT-PCR (Fig. 2D). After 5 d of Activin A treatment, the majority of cells was devoid of the pluripotent marker POU5F1 but, however, showed expression of the TFs SOX17 and FOXA2, which are markers of DE. Importantly, there was a low level...
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LETTER: A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells
- Guglielmo Roma,
- Gilda Cobellis,
- Pamela Claudiani,
- Francesco Maione,
- Pedro Cruz,
- Gaetano Tripoli,
- Marco Sardiello,
- Ivana Peluso,
- and Elia Stupka
Genome Res. July 2007 17: 1051-1060; Published in Advance May 31, 2007, doi:10.1101/gr.5720807
...the best genomic locus for each sequence based on the identity, the length coverage, and the number of exons. Since many genes have multiple copies and, therefore, sequences may have multiple, almost equally good alignments in different genomic locations, we optimized our algorithm in order to distinguish...
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Resource: A large-scale zebrafish gene knockout resource for the genome-wide study of gene function
- Gaurav K. Varshney,
- Jing Lu,
- Derek E. Gildea,
- Haigen Huang,
- Wuhong Pei,
- Zhongan Yang,
- Sunny C. Huang,
- David Schoenfeld,
- Nam H. Pho,
- David Casero,
- Takashi Hirase,
- Deborah Mosbrook-Davis,
- Suiyuan Zhang,
- Li-En Jao,
- Bo Zhang,
- Ian G. Woods,
- Steven Zimmerman,
- Alexander F. Schier,
- Tyra G. Wolfsberg,
- Matteo Pellegrini,
- Shawn M. Burgess,
- and Shuo Lin
Genome Res. April 2013 23: 727-735; Published in Advance February 4, 2013, doi:10.1101/gr.151464.112
...in a laboratory setting. Figure 5 shows several phenotypes identified in the tested alleles. We show four examples of genes that showed early embryonic phenotypes: wee1 mutants showed a very early cell death phenotype (Fig. 5A), eif3i (previously known as eif3s2) mutants showed defects in arterial patterning...
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Research: Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
- Axel M. Hillmer,
- Fei Yao,
- Koichiro Inaki,
- Wah Heng Lee,
- Pramila N. Ariyaratne,
- Audrey S.M. Teo,
- Xing Yi Woo,
- Zhenshui Zhang,
- Hao Zhao,
- Leena Ukil,
- Jieqi P. Chen,
- Feng Zhu,
- Jimmy B.Y. So,
- Manuel Salto-Tellez,
- Wan Ting Poh,
- Kelson F.B. Zawack,
- Niranjan Nagarajan,
- Song Gao,
- Guoliang Li,
- Vikrant Kumar,
- Hui Ping J. Lim,
- Yee Yen Sia,
- Chee Seng Chan,
- See Ting Leong,
- Say Chuan Neo,
- Poh Sum D. Choi,
- Hervé Thoreau,
- Patrick B.O. Tan,
- Atif Shahab,
- Xiaoan Ruan,
- Jonas Bergh,
- Per Hall,
- Valère Cacheux-Rataboul,
- Chia-Lin Wei,
- Khay Guan Yeoh,
- Wing-Kin Sung,
- Guillaume Bourque,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. May 2011 21: 665-675; Published in Advance April 5, 2011, doi:10.1101/gr.113555.110
...Spring Harbor Laboratory Press; ISSN 1088-9051/11; www..org Genome Research 665 www..org tumors frequently exhibit different patterns of somatic mutations, gene copy-number variations (CNV), differential gene expression profiles, and epigenetic modifications (Weir et al. 2007; The Cancer Genome Atlas...
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Resource: A spatial and temporal map of C. elegans gene expression
- W. Clay Spencer,
- Georg Zeller,
- Joseph D. Watson,
- Stefan R. Henz,
- Kathie L. Watkins,
- Rebecca D. McWhirter,
- Sarah Petersen,
- Vipin T. Sreedharan,
- Christian Widmer,
- Jeanyoung Jo,
- Valerie Reinke,
- Lisa Petrella,
- Susan Strome,
- Stephen E. Von Stetina,
- Menachem Katz,
- Shai Shaham,
- Gunnar Rätsch,
- and David M. Miller III
Genome Res. February 2011 21: 325-341; Published in Advance December 22, 2010, doi:10.1101/gr.114595.110
...in the corresponding cell type (see also Supplemental Results SR2). Examples of this application are provided for the embryonic germ cell precursors (see below) and for the larval excretory cell (Supplemental Result SR3). Specific genes are selectively enriched in certain cell types or tissues Among the genes...
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Method: Predicting cell-type–specific gene expression from regions of open chromatin
- Anirudh Natarajan,
- Galip Gürkan Yardımcı,
- Nathan C. Sheffield,
- Gregory E. Crawford,
- and Uwe Ohler
Genome Res. September 2012 22: 1711-1722; doi:10.1101/gr.135129.111
...Carolina 27708, USA; 4 Department of Biostatistics &amp; Bioinformatics, Duke University, Durham, North Carolina 27708, USA Abstract Complex patterns of cell-type–specific gene expression are thought to be achieved by combinatorial binding of transcription factors (TFs) to sequence...
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ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
- Stephen Richards,
- Yue Liu,
- Brian R. Bettencourt,
- Pavel Hradecky,
- Stan Letovsky,
- Rasmus Nielsen,
- Kevin Thornton,
- Melissa J. Hubisz,
- Rui Chen,
- Richard P. Meisel,
- Olivier Couronne,
- Sujun Hua,
- Mark A. Smith,
- Peili Zhang,
- Jing Liu,
- Harmen J. Bussemaker,
- Marinus F. van Batenburg,
- Sally L. Howells,
- Steven E. Scherer,
- Erica Sodergren,
- Beverly B. Matthews,
- Madeline A. Crosby,
- Andrew J. Schroeder,
- Daniel Ortiz-Barrientos,
- Catharine M. Rives,
- Michael L. Metzker,
- Donna M. Muzny,
- Graham Scott,
- David Steffen,
- David A. Wheeler,
- Kim C. Worley,
- Paul Havlak,
- K. James Durbin,
- Amy Egan,
- Rachel Gill,
- Jennifer Hume,
- Margaret B. Morgan,
- George Miner,
- Cerissa Hamilton,
- Yanmei Huang,
- Lenée Waldron,
- Daniel Verduzco,
- Kerstin P. Clerc-Blankenburg,
- Inna Dubchak,
- Mohamed A.F. Noor,
- Wyatt Anderson,
- Kevin P. White,
- Andrew G. Clark,
- Stephen W. Schaeffer,
- William Gelbart,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
...is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis -regulatory sequences emerges as important themes of genome divergence between these species of Drosophila . Footnotes [Supplemental material is available online at www...
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LETTER: A 7.5 Mb Sequence-Ready PAC Contig and Gene Expression Map of Human Chromosome 11p13–p14.1
- Beate Gawin,
- Alexandra Niederführ,
- Nina Schumacher,
- Holger Hummerich,
- Peter F.R. Little,
- and Manfred Gessler
Genome Res. November 1, 1999 9: 1074-1086; doi:10.1101/gr.9.11.1074
...path through the contig is currently under way and will facilitate these expression studies by in silico gene identification approaches. One step towards the functional understanding of the human is large-scale sequencing followed by sequence-based gene identification. Sequencing is performed...
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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...scheme captures the intron-based definition described by Tilgner et al. (2013), but SQANTI goes a step further by describing and subclassifying the type of novelties introduced by transcripts not matching the splice pattern of annotated references. Transcripts in novel genes are classified as “Intergenic...
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Research: Nucleotide composition-linked divergence of vertebrate core promoter architecture
- Simon J. van Heeringen,
- Waseem Akhtar,
- Ulrike G. Jacobi,
- Robert C. Akkers,
- Yutaka Suzuki,
- and Gert Jan C. Veenstra
Genome Res. March 2011 21: 410-421; Published in Advance January 10, 2011, doi:10.1101/gr.111724.110
...validation data sets for Xenopus and human to ensure that the analysis is not biased toward TSS-seq or CAGE. For this purpose, we predicted TSSs based on a strict selection of spliced ESTs that overlap with the 59 exons of known genes and share the same orientation relative to genomic sequence (Ohler et al...

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