Results 71 to 80 of about 67,014 (277)

Rust-Bio - a fast and safe bioinformatics library

, 2015
We present Rust-Bio, the first general purpose bioinformatics library for the innovative Rust programming language. Rust-Bio leverages the unique combination of speed, memory safety and high-level syntax offered by Rust to provide a fast and safe set of ...
Köster, Johannes
core   +2 more sources

FM-Indexing Grammars Induced by Suffix Sorting for Long Patterns

2022 Data Compression Conference (DCC), 2022
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological sequences. Compared to grammar indexes, the size of the RLBWT is often much bigger, but queries like counting the ...
Deng, Jin Jie, Hon, Wing-Kai, Köppl, Dominik, Sadakane, Kunihiko   +3 more
openaire   +2 more sources

Dihydroorotate dehydrogenase (DHODH) regulates trophoblast syncytialization through organelle stress–induced cellular senescence

FEBS Open Bio, EarlyView.
The inhibition of mitochondrial dihydroorotate dehydrogenase (DHODH) impairs syncytialization and induces cellular senescence via mitochondrial and endoplasmic reticulum stress in human trophoblast stem cells, elevating sFlt1/PlGF levels, a hallmark of placental dysfunction in hypertensive disorders of pregnancy.
Kanoko Yoshida, Kazuya Kusama, Ayaka Horiuchi, Yu Kawaguchi, Atsuya Tsuru, Mikihiro Yoshie, Kazuhiro Tamura   +6 more
wiley   +1 more source

Anchorage‐independent and faster growth in clonal population from UV‐irradiated NER‐deficient cells

FEBS Open Bio, EarlyView.
UV‐irradiated cells expressing a DDB2 mutant protein unable to interact with PCNA (DDB2PCNA‐) form clones able to grow without anchorage. Different experimental approaches reveal heterogeneity in cell cycle regulation and drug response within these clones, emphasizing the crucial role of the DDB2‐PCNA interaction in preventing cellular transformation ...
Paola Perucca, Anna Tricarico, Martina Furfaro, Priyam Ghosh, Ennio Prosperi, Lucia Anna Stivala, Ornella Cazzalini   +6 more
wiley   +1 more source

n-step FM-Index for Faster Pattern Matching

Procedia Computer Science, 2013
AbstractFast pattern matching is a requirement for many problems, specially for bioinformatics sequence analysis like short read mapping applications. This work presents a variation of the FM-index method, denoted n-step FM-index, that is applied in exact match genome search.We propose an alternative two-dimensional FM-index structure that allows ...
Chacón, Alejandro, Moure, Juan Carlos, Espinosa, Antonio, Hernández, Porfidio   +3 more
openaire   +1 more source

A novel fast multiple nucleotide sequence alignment method based on FM-index

Briefings in Bioinformatics, 2021
AbstractMultiple sequence alignment (MSA) is fundamental to many biological applications. But most classical MSA algorithms are difficult to handle large-scale multiple sequences, especially long sequences. Therefore, some recent aligners adopt an efficient divide-and-conquer strategy to divide long sequences into several short sub-sequences. Selecting
Huan, Liu, Quan, Zou, Yun, Xu
openaire   +2 more sources

Erythropoietin modulates hepatic inflammation, glucose homeostasis, and soluble epoxide hydrolase and epoxides in high‐fat diet‐induced obese mice

FEBS Open Bio, EarlyView.
Erythropoietin administration suppresses hepatic soluble epoxide hydrolase (sEH) expression, leading to increased CYP‐derived epoxides. This is associated with a shift in hepatic macrophage polarization characterized by reduced M1 markers and increased M2 markers, along with reduced hepatic inflammation, suppressed hepatic lipogenesis, and attenuated ...
Takeshi Goda, Satoru Sugimoto, Chiharu Cho, Madoka Konishi, Nozomi Inoue, Satoshi Miyagaki, Yasuhiro Kawabe, Takuro Okamura, Masahide Hamaguchi, Hisakazu Nakajima, Michiaki Fukui, Masakazu Shinohara, Tomoko Iehara   +12 more
wiley   +1 more source

Mitigation of hepatic and gastric impairments induced by flunixin meglumine through co-administration with alpha lipoic acid in male rats

BMC Veterinary Research
Long term use of Flunixin meglumine produces many gastric and hepatic hazards. The current study aimed to investigate using Alpha lipoic acid (ALA) for treating flunixin meglumine (FM)-induced liver and gastrointestinal problems in male rats.
Zeynab Kh. El-Maddawy, Abdel-wahed A. Mashalla, Sulaiman Mohammed Alnasser, Abd El-Salam F. El-Sawy, Walied Abdo, Maher A. Kamel, Meshal Alotaibi, Mohsen A. Khormi, Ali M. Aborasain, Hanan H. Abd-El-Hafeez, Amal A. Awad   +10 more
doaj   +1 more source

Optimal-Time Text Indexing in BWT-runs Bounded Space

, 2017
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts is $r$, the
Gagie, Travis, Navarro, Gonzalo, Prezza, Nicola   +2 more
core   +1 more source

Proteasomal degradation of intracellularly expressed Amblyomin‐X limits suicide gene therapy potential in melanoma cells

FEBS Open Bio, EarlyView.
This study explores the feasibility of expressing the antitumoral protein Amblyomin‐X through a suicide gene therapy approach and investigates its intracellular fate after gene delivery. Although the gene is efficiently expressed, melanoma cells rapidly degrade the Amblyomin‐X protein via proteasome activity.
Victor Dal Posolo Cinel, Carlos DeOcesano Pereira, Aline Ramos Maia Lobba, Melissa Regina Fessel, Ana Marisa Chudzinski‐Tavassi   +4 more
wiley   +1 more source