Results 71 to 80 of about 141,521 (289)

DEDB: a database of Drosophila melanogaster exons in splicing graph form

BMC Bioinformatics, 2004
Background A wealth of quality genomic and mRNA/EST sequences in recent years has provided the data required for large-scale genome-wide analysis of alternative splicing.
Tan Tin, Lee Bernett TK, Ranganathan Shoba   +2 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 F. Jansen Klomp, Stefano Schivo, Janine N. Post   +4 more
wiley   +1 more source

Design and analysis strategies for robust microbiome ageing research

FEBS Letters, EarlyView.
The gut microbiome changes with age and associates with age‐related morbidity and mortality, establishing it as a potential biomarker and intervention target for ageing. Realising this potential requires methodological rigour, yet distinguishing biological signals from methodological artefacts remains challenging across cohorts. This review provides an
Mark Olenik, İsmail Güderer, Yi Wang, Tayyaba Alvi, Prasoon Pandey, Handan Melike Dönertaş   +5 more
wiley   +1 more source

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey [PDF]

, 2009
Background The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome,
Kerstens Hindrik HD, Veenendaal, A., Johan T den Dunnen, Martien AM Groenen, Bert W Dibbits, Thomas FC Chin-A-Woeng, Dunnen, J.T., den, Groenen, M.A.M., Dibbits, B.W., Kerstens, H.H.D., Chin-A-Woeng, T.F.C., Dibbits Bert W, Hindrik HD Kerstens, Richard PMA Crooijmans, Veenendaal Albertine, den Dunnen Johan T, Chin-A-Woeng Thomas FC, Crooijmans, R.P.M.A., Albertine Veenendaal, Groenen Martien AM, Crooijmans Richard PMA, den Dunnen, J.T.   +21 more
core   +1 more source

A Flow Procedure for Linearization of Genome Sequence Graphs [PDF]

Journal of Computational Biology, 2018
Efforts to incorporate human genetic variation into the reference human genome have converged on the idea of a graph representation of genetic variation within a species, a genome sequence graph. A sequence graph represents a set of individual haploid reference genomes as paths in a single graph.
David Haussler, Maciej Smuga-Otto, Jordan M. Eizenga, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov   +7 more
openaire   +4 more sources

Graph Neural Networks for Microbial Genome Recovery

CoRR, 2022
Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long ...
Andre Lamurias, Alessandro Tibo, Katja Hose, Mads Albertsen, Thomas Dyhre Nielsen   +4 more
openaire   +2 more sources

The role of miR‐335‐5p in the redifferentiation of BRAF p.V600E thyroid cancers

Molecular Oncology, EarlyView.
The BRAF p.V600E mutation promotes thyroid cancer dedifferentiation and radioiodine resistance. Using a network approach, we identified miR‐335‐5p as a key regulator of BRAF‐mutated thyroid tumors. Restoring miR‐335‐5p increased thyroid‐specific gene expression and iodine uptake in cells and organoids.
Valeria Pecce, Simone Bini, Marialuisa Sponziello, Giorgio Grani, Giulia Fiscon, Paola Paci, Lorenzo Farina, Rosa Falcone, Valentina Maggisano, Sebastiano Filetti, Cosimo Durante, Antonella Verrienti   +11 more
wiley   +1 more source

Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical Production [PDF]

Klebsiella oxytoca is an important microorganism for nitrogen fixation and chemical production. Here, we report an annotated draft genome of K. oxytoca strain M5al that contains 5,256 protein-coding genes and 95 structural RNAs, which provides a genetic ...
Cao, Z., Chen, Z., Bao, G., Li, Y., Ma, Y., Du, Chenyu, Zhang, Y.   +6 more
core   +1 more source

Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. [PDF]

, 2014
Plasmodium falciparum causes most human malaria deaths, having prehistorically evolved from parasites of African Great Apes. Here we explore the genomic basis of P.
Conway, David J, Conway, David J., Ollomo, Benjamin, Ollomo, B., Böhme, Ulrike, Berriman, Matthew, Thomas, A. W., Bohme, U., Rayner, Julian C., Otto, Thomas D, Rayner, Julian C, Otto, Thomas D., Spottiswoode, N., Newbold, C., Otto, T. D., Pain, A., Pain, Arnab, Thomas, Alan W., Rayner, J. C., Berriman, M., Sanders, M., Conway, D. J., Renaud, F., Sanders, Mandy, Quail, Michael, Renaud, François, Quail, M., Thomas, Alan W, Spottiswoode, Natasha, Newbold, Chris, Prugnolle, Franck   +30 more
core   +1 more source

Circular RNA expression landscapes in myelodysplastic neoplasms: Associations with mutational signatures and disease progression

Molecular Oncology, EarlyView.
In this explorative study, the abundance of circular RNA molecules in bone marrow stem cells was found to be elevated in patients with high‐risk myelodysplastic neoplasms, and to be associated with an increased risk of progression to acute myeloid leukemia.
Eileen Wedge, Morten Tulstrup, Gabriele Todisco, Pedro Moura, Christophe Côme, Jakob Werner Hansen, Jakob Schmidt Jespersen, Balthasar Schlotmann, Maria Creignou, Mette Dahl, Claudia Schöllkopf, Klas Raaschou‐Jensen, Krister Wennerberg, Bo Porse, Joachim Weischenfeldt, Eva Hellström‐Lindberg, Lasse Sommer Kristensen, Kirsten Grønbæk   +17 more
wiley   +1 more source