Results 31 to 40 of about 397,925 (266)

Whole genome transcriptome analysis [PDF]

RNA Biology, 2009
Recent studies indicate that the majority of the genome is transcribed, however only a fraction of this transcription is annotated as what we traditionally know as genes. Much of this is low level pervasive, and often overlapping transcription, for which the transcript structure and function, has not as yet been determined.
Forrest, Alistair, Carninci, Piero
openaire   +3 more sources

Cell geometry and membrane protein crowding constrain Escherichia coli growth rate, overflow metabolism, respiration, and maintenance energy

FEBS Letters, EarlyView.
The physical dimensions and shape of bacterial cells define the surface area available to acquire nutrients and the volume available for synthesizing proteins and DNA. Here, we use computational systems biology to decode the importance of cell geometry as a major determinant of prokaryotic phenotype, including growth rate and metabolic efficiency. This
Ross P. Carlson, Tomáš Gedeon, Mauricio Garcia Benitez, Campbell Putnam, William R. Harcombe, Radhakrishnan Mahadevan, Ashley E. Beck   +6 more
wiley   +1 more source

Integrative analysis of the melanoma transcriptome [PDF]

Genome Research, 2010
Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic mutations. We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of ...
Berger, Michael F., Levin, Joshua Z., Vijayendran, Krishna, Sivachenko, Andrey, Adiconis, Xian, Maguire, Jared, Johnson, Laura A., Robinson, James, Verhaak, Roel G., Sougnez, Carrie, Onofrio, Robert, Ziaugra, Liuda, Cibulskis, Kristian, Laine, Elisabeth, Barretina, Jordi, Winckler, Wendy, Fisher, David E., Getz, Gad, Meyerson, Matthew L., Jaffe, David B., Gabriel, Stacey B., Dummer, Reinhard, Gnirke, Andreas, Nusbaum, Chad, Garraway, Levi A., Lander, Eric Steven   +25 more
openaire   +4 more sources

Three phosphatase families form a community: The phosphohydrolases that act upon inositol pyrophosphates

FEBS Letters, EarlyView.
Inositol pyrophosphates are energy‐rich signaling molecules that perform critical functions in cells. Three different families of phosphatases hydrolyze the β phosphate of the inositol pyrophosphate molecules: two have narrow specificities and one is promiscuous.
Ronda J. Rolfes
wiley   +1 more source

Denervated mouse CA1 pyramidal neurons express homeostatic synaptic plasticity following entorhinal cortex lesion

Frontiers in Molecular Neuroscience, 2023
Structural, functional, and molecular reorganization of denervated neural networks is often observed in neurological conditions. The loss of input is accompanied by homeostatic synaptic adaptations, which can affect the reorganization process.
Maximilian Lenz, Amelie Eichler, Pia Kruse, Phyllis Stöhr, Dimitrios Kleidonas, Christos Galanis, Han Lu, Han Lu, Andreas Vlachos, Andreas Vlachos, Andreas Vlachos   +10 more
doaj   +1 more source

Modelling stem cell differentiation related processes—A practical overview for biologists

FEBS Letters, EarlyView.
Stem cell differentiation is complex and difficult to control experimentally. This review introduces suitable computational modelling approaches that can support stem cell research, from mechanistic ODE and abstract models to multiscale and deep learning methods.
Ricco Zeegelaar, Xinqi Yan, Lucas Jansen Klomp, Stefano Schivo, Janine N. Post   +4 more
wiley   +1 more source

Fasting and Refeeding Affect the Goose Liver Transcriptome Mainly Through the PPAR Signaling Pathway

The Journal of Poultry Science, 2021
Nutrition and energy are essential for poultry growth and production performance. Fasting and refeeding have been widely used to study the effects of nutrition, energy, and related mechanisms in chicken.
Zhenzhen Chen, Ya Xing, Xue Fan, Tongjun Liu, Minmeng Zhao, Long Liu, Xuming Hu, Hengmi Cui, Tuoyu Geng, Daoqing Gong   +9 more
doaj   +1 more source

Methods for the analysis of transcriptome dynamics [PDF]

Toxicology Research, 2019
Abstract The transcriptome is the complete set of transcripts in a cell or tissue and includes ribosomal RNA (rRNA), messenger RNA (mRNA), transfer RNA (tRNA), and regulatory noncoding RNA. At steady-state, the transcriptome results from a compensatory variation of the transcription and decay rate to maintain the RNA concentration ...
Daniela F. Rodrigues, Vera M. Costa, Ricardo Silvestre, Maria L. Bastos, Félix Carvalho   +4 more
openaire   +3 more sources

Network divergence analysis identifies adaptive gene modules and two orthogonal vulnerability axes in pancreatic cancer

Molecular Oncology, EarlyView.
Tumors contain diverse cellular states whose behavior is shaped by context‐dependent gene coordination. By comparing gene–gene relationships across biological contexts, we identify adaptive transcriptional modules that reorganize into distinct vulnerability axes.
Brian Nelson, Lyanne Delgado‐Coka, Natalia Marchenko, Luisa F. Escobar‐Hoyos, Kenneth R. Shroyer, Alisa Yurovsky, Trey Ideker, Gábor Balázsi, Thomas MacCarthy, Scott Powers   +9 more
wiley   +1 more source

Transcriptome Analysis Reveals the Resistance Mechanism of Pseudomonas aeruginosa to Tachyplesin I

Infection and Drug Resistance, 2020
Jun Hong, 1, 2 Honghao Jiang, 1 Jianye Hu, 1 Lianzhe Wang, 1 Ruifang Liu 1 1College of Life Science and Engineering, Henan University of Urban Construction, Ping Dingshan 467036, People’s Republic of China; 2Henan Province Key Laboratory of Water
Hong J, Jiang H, Hu J, Wang L, Liu R
doaj