Results 111 to 120 of about 8,935,685 (345)

Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes

bioRxiv, 2016
Two-component signaling (TCS) is the primary means by which bacteria sense and respond to the environment. TCS involves two partner proteins working in tandem, which interact to perform cellular functions while limiting interactions with non-partners (i ...
R. R. Cheng, Olle Nordesjö, R. L. Hayes, H. Levine, S. Flores, J. Onuchic, F. Morcos   +6 more
semanticscholar   +1 more source

CCDC80 suppresses high‐grade serous ovarian cancer migration via negative regulation of B7‐H3

Molecular Oncology, EarlyView.
PAX8 is a lineage‐specific master regulator of transcription in high‐grade serous ovarian cancer (HGSC) progression. We show for the first time that PAX8 facilitates proliferation and metastasis by repressing the cell autonomous tumor suppressor CCDC80 and inducing B7‐H3 expression.
Aya Saleh, Nitzan Medina‐Itzhaki, Milena Chekov, Eden Gal‐Swisa, Roba Gabesh‐Wahabi, Inbar Savyon, Inna Naroditsky, Hilary A. Kenny, Basem Fares, Lina Korsensky, Einav Girsh, Liron Berger, Ruth Perets   +12 more
wiley   +1 more source

Cell‐cycle‐specific lesion evolution rather than inhibition of double‐strand‐break repair underpins cisplatin radiosensitization

Molecular Oncology, EarlyView.
We analyze cisplatin–DNA adducts (CDAs) and double‐strand breaks (DSBs) in a cell‐cycle‐dependent manner. We find that CDAs form similarly across all cell cycle phases. DSBs arise only in S‐phase. CDAs might not directly impair DSB repair, but S‐phase DSB lesions evolve in the presence of CDAs and disrupt repair in G2, also causing radiosensitization ...
Ye Qiu, Xixi Lin, Emil Mladenov, Veronika Mladenova, Jürgen Thomale, Ali Sak, Yao Wang, Yunxuan Deng, Eleni Gkika, Martin Stuschke, George Iliakis   +10 more
wiley   +1 more source

Joint Generation of Protein Sequence and Structure with RoseTTAFold Sequence Space Diffusion

bioRxiv, 2023
S. Lisanza, J. Gershon, S. Tipps, L. Arnoldt, Samuel Hendel, J. Sims, Xinting Li, D. Baker   +7 more
semanticscholar   +1 more source

Hijacking emergency granulopoiesis: Neutrophil ontogeny and reprogramming in cancer

Molecular Oncology, EarlyView.
Neutrophils are highly plastic innate immune cells; their functions in cancer extend beyond the tumour microenvironment. This Review summarises current understanding of neutrophil maturation and heterogeneity and highlights tumour‐induced granulopoiesis as a systemic programme that expands immature, immunosuppressive neutrophils via tumour‐derived ...
Gabriela Marinescu, Yi Feng
wiley   +1 more source

Improved Bayesian methods for detecting recombination and rate heterogeneity in DNA sequence alignments

, 2011
DNA sequence alignments are usually not homogeneous. Mosaic structures may result as a consequence of recombination or rate heterogeneity. Interspecific recombination, in which DNA subsequences are transferred between different (typically viral or ...
Mantzaris, Alexander Vassilios, Husmeier, Dirk, Husmeir, Dirk   +2 more
core  

yaopeihu/Sequence-working-memory:

, 2021
Refer to Science article: Xie, Hu et al. Geometry of Sequence Working Memory in Macaque Prefrontal Cortex. 2021 Data used in the code is available at Zenodo Feel free to open a issue if you have any question.
yaopeihu
core   +1 more source

Generalized Difference Lacunary Weak Convergence of Sequences [PDF]

Sahand Communications in Mathematical Analysis
In this paper, we introduce the concept of generalized difference lacunary weak convergence of sequences. Using the concept of difference operator, we have introduced some new classes of sequences. We investigated several of its algebraic and topological
Bibhajyoti Tamuli, Binod Tripathy
doaj   +1 more source

Interpreting the effects of DNA polymerase variants at the structural level

Molecular Oncology, EarlyView.
Using MAVISp and molecular dynamics simulations, we analyzed over 60 000 missense variants in POLE and POLD1 from ClinVar, COSMIC, cBioPortal, and saturation mutagenesis. Identified mechanistic indicators, including stability, binding, and long‐range, enable structural interpretation, providing ACMG‐like evidence for possible reclassification of VUS ...
Matteo Arnaudi, Karolina Krzesińska, Ludovica Beltrame, Pablo Sánchez‐Izquierdo Besora, Matteo Tiberti, Mef Nilbert, Anna Rohlin, Elena Papaleo   +7 more
wiley   +1 more source

Epistasis facilitates functional evolution in an ancient transcription factor

eLife
A protein’s genetic architecture – the set of causal rules by which its sequence produces its functions – also determines its possible evolutionary trajectories.
Brian PH Metzger, Yeonwoo Park, Tyler N Starr, Joseph W Thornton   +3 more
doaj   +1 more source