Results 41 to 50 of about 928,042 (281)

Bayesian transcriptome assembly [PDF]

Genome Biology, 2014
AbstractRNA sequencing allows for simultaneous transcript discovery and quantification, but reconstructing complete transcripts from such data remains difficult. Here, we introduce Bayesembler, a novel probabilistic method for transcriptome assembly built on a Bayesian model of the RNA sequencing process.
Sørensen, Lasse Maretty, Sibbesen, Jonas Andreas, Krogh, Anders   +2 more
openaire   +5 more sources

Palindrome-mediated Translocations in Humans: A New Mechanistic Model for Gross Chromosomal Rearrangements

Frontiers in Genetics, 2016
Palindromic DNA sequences, which can form secondary structures, are widely distributed in the human genome. Although the nature of the secondary structure—single-stranded hairpin or double-stranded cruciform—has been extensively investigated in vitro ...
Hidehito Inagaki, Hidehito Inagaki, Takema Kato, Makiko Tsutsumi, Yuya Ouchi, Yuya Ouchi, Tamae Ohye, Hiroki Kurahashi, Hiroki Kurahashi   +8 more
doaj   +1 more source

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts. [PDF]

, 2011
Over 50% of genes in Plasmodium falciparum, the deadliest human malaria parasite, contain predicted introns, yet experimental characterization of splicing in this organism remains incomplete.
DeRisi, Joseph L, Dimon, Michelle T, Sorber, Katherine   +2 more
core   +3 more sources

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

Nature, 2019
Imaging the transcriptome in situ with high accuracy has been a major challenge in single-cell biology, which is particularly hindered by the limits of optical resolution and the density of transcripts in single cells1–5. Here we demonstrate an evolution
C. L. Eng, Michael J. Lawson, Qian Zhu, Ruben Dries, N. Koulena, Yodai Takei, Jina Yun, Christopher J. Cronin, Christoph Karp, Guocheng Yuan, L. Cai   +10 more
semanticscholar   +1 more source

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Nature Neuroscience, 2020
We used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral prefrontal cortex.
K. E. Maynard, L. Collado-Torres, L. Weber, C. Uytingco, B. Barry, S. Williams, J. L. Catallini, M. N. Tran, Z. Besich, M. Tippani, J. Chew, Y. Yin, J. Kleinman, T. Hyde, N. Rao, S. Hicks, K. Martinowich, A. Jaffe   +17 more
semanticscholar   +1 more source

The Human Mitochondrial Transcriptome [PDF]

Cell, 2011
The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs, and rRNAs. Here, we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues.
Mercer, Tim R., Neph, Shane, Dinger, Marcel E., Crawford, Joanna, Smith, Martin A., Shearwood, Anne-Marie J., Haugen, Eric, Bracken, Cameron P., Rackham, Oliver, Stamatoyannopoulos, John A., Filipovska, Aleksandra, Mattick, John S.   +11 more
openaire   +5 more sources

The Escherichia coli transcriptome mostly consists of independently regulated modules [PDF]

, 2019
Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators.
A Anand, A Biton, A Delorme, A Frigyesi, A Hyvärinen, A Santos-Zavaleta, A-M Martoglio, AE Teschendorff, B Dalrymple, B Langmead, B-K Cho, B-K Cho, BM Bolstad, C Vijayendran, CL Turnbough Jr, D Kim, D Marbach, D Risso, D-S Huang, DS Latchman, E Nudler, EJ O’Brien, ENCODE Project Consortium., ER Gansner, F Pedregosa, GI Guzmán, GI Guzmán, H Zou, HS Rhee, I Kristoficova, IM Keseler, J Pouyssegur, J Utrilla, JE Galagan, JJ Faith, JM Buescher, JM Engreitz, JM Monk, JT Leek, K Valgepea, K-K Yan, KF Jensen, KJ Karczewski, L Wang, M Ester, M Kim, M Lawrence, M Moretto, M Scott, M Scott, MB Gerstein, MI Love, NE Lewis, O Alter, P Chiappetta, P Comon, PR Subbarayan, PV Phaneuf, R De Smet, R Kolter, RA LaCroix, RB D’agostino, S Gama-Castro, S Lin, SJ Larsen, SW Seo, T Baba, T Barrett, TM Henkin, W Kong, W Liebermeister, W Saelens, X Zhang, Xin Fang, XW Zhang, Y Gao, Y Yamanaka, Z Wang   +77 more
core   +3 more sources

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

Journal of Neuroscience, 2008
Understanding the cell–cell interactions that control CNS development and function has long been limited by the lack of methods to cleanly separate neural cell types.
John D. Cahoy, B. Emery, Amit Kaushal, L. Foo, Jennifer L Zamanian, K. S. Christopherson, Yi Xing, J. Lubischer, P. Krieg, S. Krupenko, W. Thompson, B. Barres   +11 more
semanticscholar   +1 more source

Transcriptomics in toxicology [PDF]

Food and Chemical Toxicology, 2017
Xenobiotics, of which many are toxic, may enter the human body through multiple routes. Excessive human exposure to xenobiotics may exceed the body's capacity to defend against the xenobiotic-induced toxicity and result in potentially fatal adverse health effects.
openaire   +3 more sources

Analysis of wheat SAGE tags reveals evidence for widespread antisense transcription [PDF]

, 2008
BACKGROUND: Serial Analysis of Gene Expression (SAGE) is a powerful tool for genome-wide transcription studies. Unlike microarrays, it has the ability to detect novel forms of RNA such as alternatively spliced and antisense transcripts, without the need ...
Barker, Gary L A, Berry, Simon, Biggi, Gaia F, Coghill, Jane, Dunwell, Jim, Edwards, Keith J, Gibbings, George, Poole, Rebecca L, Werner, Kay   +8 more
core   +2 more sources