Results 81 to 90 of about 483,132 (293)

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

Objective Functions

, 2013
Multiple sequence alignment involves alignment of more than two sequences and is an NP-complete problem. Therefore, heuristic algorithms that use different criteria to find an approximation to the optimal solution are employed.
Haluk Doğan, Hasan H. Otu, Dogan, Haluk, Otu, Hasan H.   +3 more
core   +1 more source

Reconstructing enzyme evolution by protein engineering

FEBS Letters, EarlyView.
Natural enzyme evolution can be retraced by protein engineering methods such as directed evolution, rational design, and ancestral sequence reconstruction. These approaches reveal how enzymes emerged from ligand‐binding scaffolds, developed varying substrate preferences, formed oligomeric complexes, adapted to environmental changes, and evolved novel ...
Lukas Drexler, Markus R. Busch, Reinhard Sterner   +2 more
wiley   +1 more source

SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation

BMC Bioinformatics, 2011
Background Multiple sequence alignment (MSA) plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields.
Strope Cory L, Anderson Catherine L, Moriyama Etsuko N   +2 more
doaj   +1 more source

Inferring phylogenies of evolving sequences without multiple sequence alignment

, 2014
Alignment-free methods, in which shared properties of sub-sequences (e. g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference.
Bernard, Guillaume, Ragan, Mark A., Poirion, Olivier, Chan, Cheong Xin, Hogan, James M.   +4 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

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

Rose: Generating Sequence Families

, 1997
Stoye J, Evers D, Meyer F. Rose: Generating Sequence Families. Forschungsberichte.
Stoye, Jens ; https://orcid.org/, Evers, Dirk, Meyer, Folker   +2 more
core   +1 more source

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

Data set of phylogenetic analysis inferred based on the complete genomes of the family Nodaviridae

Data in Brief, 2016
In this article, nine complete genomes of viruses from the genus Alphanodavirus and Betanodavirus (Family Nodaviridae) were comparatively analyzed and the data of their evolutionary origins and relatedness are reported.
Chen-Fei Low, Hamidun Bunawan
doaj   +1 more source