Results 121 to 130 of about 66,141 (268)

Estimation of species divergence times in presence of cross-species gene flow

, 2023
Cross-species introgression can have significant impacts on phylogenomic reconstruction of species divergence events. Here, we used simulations to show how the presence of even a small amount of introgression can bias divergence time estimates when gene ...
Jiao, Xiyun, Poelstra, Jelmer W., Bo Xu, Tiley, George P, Flouri, Tomáš, Tomáš Flouri, Xu, Bo, Anne D Yoder, Yoder, Anne D, Yang, Ziheng, Tianqi Zhu, Bruce Rannala, Jelmer W Poelstra, George P Tiley, Poelstra, Jelmer W, Ziheng Yang, Xiyun Jiao, Zhu, Tianqi, Rannala, Bruce   +18 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

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

Estimation of divergence time (thousand years ago, kya) of HPV variants from the most recent common ancestor (MRCA).

, 2018
Estimation of divergence time (thousand years ago, kya) of HPV variants from the most recent common ancestor (MRCA).
Robert D. Burk (35757), Rob DeSalle (175611), Paul K. S. Chan (271343), Mark Schiffman (106112), Zigui Chen (153298), Gary M. Clifford (5921447), Charles E. Wood (513584), Rolando Herrero (106155), Julio C. Ruiz (489263)   +8 more
core   +1 more source

Tumour–host interactions in Drosophila: mechanisms in the tumour micro‐ and macroenvironment

Molecular Oncology, EarlyView.
This review examines how tumour–host crosstalk takes place at multiple levels of biological organisation, from local cell competition and immune crosstalk to organism‐wide metabolic and physiological collapse. Here, we integrate findings from Drosophila melanogaster studies that reveal conserved mechanisms through which tumours hijack host systems to ...
José Teles‐Reis, Tor Erik Rusten
wiley   +1 more source

Sinkhorn Divergence of Topological Signature Estimates for Time Series Classification [PDF]

2018 17th IEEE International Conference on Machine Learning and Applications (ICMLA), 2018
Distinguishing between classes of time series sampled from dynamic systems is a common challenge in systems and control engineering, for example in the context of health monitoring, fault detection, and quality control. The challenge is increased when no underlying model of a system is known, measurement noise is present, and long signals need to be ...
openaire   +2 more sources

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

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

Pre‐analytical optimization of cell‐free DNA and extracellular vesicle‐derived DNA for mutation detection in liquid biopsies

Molecular Oncology, EarlyView.
Pre‐analytical handling critically determines liquid biopsy performance. This study defines practical best‐practice conditions for cell‐free DNA (cfDNA) and extracellular vesicle–derived DNA (evDNA), showing how processing time, storage conditions, tube type, and plasma input volume affect DNA integrity and mutation detection.
Jonas Dohmen, Lucrezia De Santis, Bret M. Stephens, Vincent Bernard, Jörg C. Kalff, Lara Braun, Phillipp Leyendecker, Johannes Röttgen, Daniel Weissinger, Anirban Maitra, Paola A. Guerrero, Alexander Semaan   +11 more
wiley   +1 more source

Variance of Ks distribution corrects the bias in the divergence caused by the ancestral population size

Frontiers in Genetics
Ks distribution, the distribution of the synonymous substitutions, has been widely used to estimate the species divergence using orthologous genes. However, conventional approaches often ignore the underlying bias that species divergence is delayed to ...
Mi-Jia Li, Xiao-Xue Li, Lin-Lin Xu, Bo-Wen Zhang   +3 more
doaj   +1 more source