Results 71 to 80 of about 300,948 (293)

Whole-Genome Annotation with BRAKER [PDF]

, 2019
BRAKER is a pipeline for highly accurate and fully automated gene prediction in novel eukaryotic genomes. It combines two major tools: GeneMark-ES/ET and AUGUSTUS. GeneMark-ES/ET learns its parameters from a novel genomic sequence in a fully automated fashion; if available, it uses extrinsic evidence for model refinement.
Katharina J. Hoff, Mario Stanke, Alexandre Lomsadze, Mark Borodovsky, Mark Borodovsky   +4 more
openaire   +2 more sources

MET and NF2 alterations confer primary and early resistance to first‐line alectinib treatment in ALK‐positive non‐small‐cell lung cancer

Molecular Oncology, EarlyView.
Alectinib resistance in ALK+ NSCLC depends on treatment sequence and EML4‐ALK variants. Variant 1 exhibited off‐target resistance after first‐line treatment, while variant 3 and later lines favored on‐target mutations. Early resistance involved off‐target alterations, like MET and NF2, while on‐target mutations emerged with prolonged therapy.
Jie Hu, Ning Ding, Xiaobo Xu, Yedan Chen, Yong Zhang, Jingwen Liu, Jiebai Zhou, Hairong Bao, Donghui Zhang, Yijun Song, Yang Shao, Yuanlin Song   +11 more
wiley   +1 more source

VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

BMC Bioinformatics, 2019
Background With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance.
Ryan C. Shean, Negar Makhsous, Graham D. Stoddard, Michelle J. Lin, Alexander L. Greninger   +4 more
doaj   +1 more source

Chemoresistome mapping in individual breast cancer patients unravels diversity in dynamic transcriptional adaptation

Molecular Oncology, EarlyView.
This study used longitudinal transcriptomics and gene‐pattern classification to uncover patient‐specific mechanisms of chemotherapy resistance in breast cancer. Findings reveal preexisting drug‐tolerant states in primary tumors and diverse gene rewiring patterns across patients, converging on a few dysregulated functional modules. Despite receiving the
Maya Dadiani, Gilgi Friedlander, Gili Perry, Nora Balint‐Lahat, Shlomit Gilad, Dana Morzaev‐Sulzbach, Anjana Shenoy, Noa Bossel Ben‐Moshe, Anya Pavlovsky, Rinat Bernstein‐Molho, Eytan Domany, Iris Barshack, Tamar Geiger, Bella Kaufman, Einav Nili Gal‐Yam   +14 more
wiley   +1 more source

Annotation of 2,507 Saccharomyces cerevisiae genomes

Microbiology Spectrum
Saccharomyces cerevisiae (baker’s yeast, budding yeast) is one of the most important model organisms for biological research and is a crucial microorganism in industry.
Meng Wang, Xuan Li, Xian Liu, Xiaoping Hou, Yang He, Jun-Hong Yu, Shumin Hu, Hua Yin, Bin-Bin Xie   +8 more
doaj   +1 more source

Tonic signaling of the B‐cell antigen‐specific receptor is a common functional hallmark in chronic lymphocytic leukemia cell phosphoproteomes at early disease stages

Molecular Oncology, EarlyView.
B‐cell chronic lymphocytic leukemia (B‐CLL) and monoclonal B‐cell lymphocytosis (MBL) show altered proteomes and phosphoproteomes, analyzed using mass spectrometry, protein microarrays, and western blotting. Identifying 2970 proteins and 316 phosphoproteins, including 55 novel phosphopeptides, we reveal BCR and NF‐kβ/STAT3 signaling in disease ...
Paula Díez, Pablo Juanes‐Velasco, Marina L. García‐Vaquero, Conrad Droste, Alicia Landeira‐Viñuela, Miguel Alcoceba, Helena Fidalgo‐Gómez, Sara Misiego‐Herrero, Almudena Navarro‐Bailón, Mónica Baile, José M. Bastida, Jose Manuel Sanchez‐Santos, Rafael Góngora, Julia Almeida, Marcos Gonzalez‐Diaz, Alberto Orfao, Javier De Las Rivas, Manuel Fuentes   +17 more
wiley   +1 more source

Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation. [version 1; peer review: 2 approved, 1 approved with reservations]

F1000Research, 2023
Background: Advancements in DNA sequencing technology have transformed the field of bacterial genomics, allowing for faster and more cost effective chromosome level assemblies compared to a decade ago.
Tatiana Amabile de Campos, Georgios Joannis Pappas Jr, Felipe Marques de Almeida   +2 more
doaj  

Vgas: A Viral Genome Annotation System

Frontiers in Microbiology, 2019
The in-depth study of viral genomes is of great help in many aspects, especially in the treatment of human diseases caused by viral infections. With the rapid accumulation of viral sequencing data, improved, or alternative gene-finding systems have ...
Kai-Yue Zhang, Yi-Zhou Gao, Meng-Ze Du, Shuo Liu, Chuan Dong, Feng-Biao Guo   +5 more
doaj   +1 more source

Aberrant expression of nuclear prothymosin α contributes to epithelial‐mesenchymal transition in lung cancer

Molecular Oncology, EarlyView.
Nuclear prothymosin α inhibits epithelial‐mesenchymal transition (EMT) in lung cancer by increasing Smad7 acetylation and competing with Smad2 for binding to SNAI1, TWIST1, and ZEB1 promoters. In early‐stage cancer, ProT suppresses TGF‐β‐induced EMT, while its loss in the nucleus in late‐stage cancer leads to enhanced EMT and poor prognosis.
Liyun Chen, Chung‐Teng Wang, Jia‐Ming Chang, Ai‐Li Shiau, Gia‐Shing Shieh, Yau‐Lin Tseng, Yi‐Ting Yen, Tang‐Hsiu Huang, Li‐Hsin Cheng, Yu‐Chih Wu, Chao‐Liang Wu, Bing‐Hua Su, Pensee Wu   +12 more
wiley   +1 more source

Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

BMC Genomics, 2013
Background The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced,
Eckalbar Walter L, Hutchins Elizabeth D, Markov Glenn J, Allen April N, Corneveaux Jason J, Lindblad-Toh Kerstin, Di Palma Federica, Alföldi Jessica, Huentelman Matthew J, Kusumi Kenro   +9 more
doaj   +1 more source