이번 주 논문들

6월 4주차 ; 6월 5주차 ; 7월 1주차

Cho et al. 2022. 6. 26.

MicroRNA profile in the squamous cell carcinoma: prognostic and diagnostic roles - ScienceDirect

 

MicroRNA profile in the squamous cell carcinoma: prognostic and diagnostic roles

Head and neck squamous cell carcinomas (HNSCCs) are human malignancies associated with both genetic and environmental factors. MicroRNAs (miRNAs) as a…

www.sciencedirect.com

 

MicroRNAs and head and neck cancer: Reviewing the first decade of research - ScienceDirect

 

MicroRNAs and head and neck cancer: Reviewing the first decade of research

MicroRNAs are a class of non-coding RNA which regulate gene expression. Their discovery in humans in 2000 has led to an explosion in research in this …

www.sciencedirect.com

 

https://www.pacb.com/blog/ploidy-haplotypes-and-phasing/

 

Sequencing 101: ploidy, haplotypes, and phasing — how to get more from your sequencing data - PacBio

Phasing involves separating maternally and paternally inherited copies of each chromosome into haplotypes to get a complete picture of genetic variation.

www.pacb.com

Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA | Nature Biotechnology

Mitochondrial RNA modifications shape metabolic plasticity in metastasis | Nature

 

Mitochondrial RNA modifications shape metabolic plasticity in metastasis - Nature

a, Metastasis-initiating CD44+CD36+ cells. b,c, Flow cytometry (b) and CMXROS quantification (c) of CD36 and CD44 high (H) and low (L) VDH01 cells (n = 3 sorts). d, NSUN3 RNA in FaDu subpopulations (n = 9; 3 quantitative PCR with reverse transcript

www.nature.com

De novo design of discrete, stable 310-helix peptide assemblies | Nature

The metastatic spread of breast cancer accelerates during sleep | Nature

Tumor necrosis factor induces pathogenic mitochondrial ROS in tuberculosis through reverse electron transport (science.org)

Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function (science.org)

Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation (science.org)

Mutations linked to neurological disease enhance self-association of low-complexity protein sequences (science.org)

The microbiome and gut homeostasis (science.org)

APOE told me put my fat in the bag and nobody gets hurt: Cell

Antibiotic discovery with machine learning | Nature Biotechnology

Interpreting the B-cell receptor repertoire with single-cell gene expression using Benisse | Nature Machine Intelligence

Antibodies to combat viral infections: development strategies and progress | Nature Reviews Drug Discovery

Adaptive immune resistance at the tumour site: mechanisms and therapeutic opportunities | Nature Reviews Drug Discovery

Advancing code sharing in the computational biology community | PLOS Computational Biology

 

Advancing code sharing in the computational biology community

Citation: Cadwallader L, Mac Gabhann F, Papin J, Pitzer VE (2022) Advancing code sharing in the computational biology community. PLoS Comput Biol 18(6): e1010193. https://doi.org/10.1371/journal.pcbi.1010193 Published: June 2, 2022 Copyright: © 2022 Cadwa

journals.plos.org

Spatial modelling for population replacement of mosquito vectors at continental scale | PLOS Computational Biology

 

Spatial modelling for population replacement of mosquito vectors at continental scale

Author summary Conventional control methods have dramatically reduced malaria, but it still kills over 300,000 children in Africa each year, and this number could increase as their effectiveness wanes. Novel control methods using gene drives rapidly reduce

journals.plos.org

Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies | PLOS Computational Biology

 

Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies

Author summary Affinity maturation of B cell receptors is an important mechanism by which our body designs neutralizing antibodies to defend us against pathogens, including broadly neutralizing antibodies, which target a wide range of variants of the same

journals.plos.org

Characterizing collaborative transcription regulation with a graph-based deep learning approach | PLOS Computational Biology

 

Characterizing collaborative transcription regulation with a graph-based deep learning approach

Author summary Human transcription activities are regulated by chromatin features including transcription factor binding, histone modification, and DNase I hypersensitive site. Recently many computational models are proposed to predict chromatin features f

journals.plos.org

Identification of upstream transcription factor binding sites in orthologous genes using mixed Student’s t-test statistics | PLOS Computational Biology

Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue | PLOS Computational Biology

 

Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue

Author summary High-resolution imaging techniques have revealed that abnormal cells developing in epithelial tissues are mechanically eliminated via contraction at the interface between the abnormal cells and normal surrounding cells. This phenomenon is se

journals.plos.org

Explainable detection of adverse drug reaction with imbalanced data distribution | PLOS Computational Biology

 

Explainable detection of adverse drug reaction with imbalanced data distribution

Author summary Post-marketing drug safety surveillance offers the chance to detect serious ADRs resulting in hospitalization and ADRs occurring in patients, e.g., patients with high comorbidity and receiving drugs that are administered only in hospitals. T

journals.plos.org

Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach | PLOS Computational Biology

 

Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algori

Author summary Non synonymous single nucleotide polymorphism (nsSNP) is a process in which amino acid sequence of a protein is altered as a result of single nucleotide alteration in the coding region (mRNA) of any living organism. Therefore, the entire pro

journals.plos.org

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues | PLOS Computational Biology

 

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Author summary We have reanalysed 23 baseline mass spectrometry-based public proteomics datasets stored in the PRIDE database. Overall, the aggregated dataset contained 211 samples, coming from 34 different tissues across 14 organs, comprising 9 mouse and

journals.plos.org

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation | PLOS Computational Biology

The transformational role of GPU computing and deep learning in drug discovery | Nature Machine Intelligence

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