Results 171 to 180 of about 4,504,319 (408)

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Genome Biology, 2013
TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat.
Daehwan Kim, G. Pertea, C. Trapnell, Harold Pimentel, Ryan M. Kelley, S. Salzberg   +5 more
semanticscholar   +1 more source

Thermal proteome profiling and proteome analysis using high‐definition mass spectrometry demonstrate modulation of cholesterol biosynthesis by next‐generation galeterone analog VNPP433‐3β in castration‐resistant prostate cancer

Molecular Oncology, EarlyView.
Elevated level of cholesterol is positively correlated to prostate cancer development and disease severity. Cholesterol‐lowering drugs, such as statins, are demonstrated to inhibit prostate cancer. VNPP433‐3β interrupts multiple signaling and metabolic pathways, including cholesterol biosynthesis, AR‐mediated transcription of several oncogenes, mRNA 5′
Retheesh S. Thankan, Elizabeth Thomas, Mehari M. Weldemariam, Puranik Purushottamachar, Weiliang Huang, Maureen A. Kane, Yuji Zhang, Nicholas Ambulos, Bi‐Dar Wang, David Weber, Vincent C. O. Njar   +10 more
wiley   +1 more source

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

BMC Bioinformatics, 2006
Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model.
Dowell Robin D, Eddy Sean R
doaj   +1 more source

Exploration of heterogeneity and recurrence signatures in hepatocellular carcinoma

Molecular Oncology, EarlyView.
This study leveraged public datasets and integrative bioinformatic analysis to dissect malignant cell heterogeneity between relapsed and primary HCC, focusing on intercellular communication, differentiation status, metabolic activity, and transcriptomic profiles.
Wen‐Jing Wu, Jianchao Wang, Fuqing Chen, Xuefeng Wang, Bin Lan, Ruyi Fu, Hong Wen, Fangfang Chen, Wei Hong, Tian‐Yu Tang, Ying He, Gang Chen, Jianyin Zhou, Hai‐Long Piao, Di Chen, Shu‐Yong Lin   +15 more
wiley   +1 more source

The atypical KRASQ22K mutation directs TGF‐β response towards partial epithelial‐to‐mesenchymal transition in patient‐derived colorectal cancer tumoroids

Molecular Oncology, EarlyView.
TGF‐β has a complex role in cancer, exhibiting both tumor‐suppressive and tumor‐promoting properties. Using a series of differentiated tumoroids, derived from different stages and mutational background of colorectal cancer patients, we replicate this duality of TGF‐β in vitro. Notably, the atypical but highly aggressive KRASQ22K mutation rendered early‐
Theresia Mair, Philip König, Milena Mijović, Jessica Kalla, Anil Baskan, Loan Tran, Kristina Draganić, Pedro Morata Saldaña, Carlos Uziel Pérez Malla, Janette Pfneissl, Andreas Tiefenbacher, Julijan Kabiljo, Velina S. Atanasova, Lisa Wozelka‐Oltjan, Leonhard Müllauer, Michael Bergmann, Raheleh Sheibani‐Tezerji, Gerda Egger   +17 more
wiley   +1 more source

Zero Knowledge Proof for Multiple Sequence Alignment [PDF]

arXiv
Multiple sequence alignment (MSA) is a fundamental algorithm in bioinformatics. In a situation when the alignment might need to be protected while revealing the other information such the input sequences and the alignment score, zero knowledge proof can be used.
arxiv  

Amino acid sequence of the Bb fragment from human complement Factor B. Alignment of the cyanogen bromide-cleavage peptides [PDF]

, 1983
Jean Gagnon, David L. Christie
openalex   +1 more source

A large‐scale retrospective study in metastatic breast cancer patients using circulating tumour DNA and machine learning to predict treatment outcome and progression‐free survival

Molecular Oncology, EarlyView.
There is an unmet need in metastatic breast cancer patients to monitor therapy response in real time. In this study, we show how a noninvasive and affordable strategy based on sequencing of plasma samples with longitudinal tracking of tumour fraction paired with a statistical model provides valuable information on treatment response in advance of the ...
Emma J. Beddowes, Mario Ortega Duran, Solon Karapanagiotis, Alistair Martin, Meiling Gao, Riccardo Masina, Ramona Woitek, James Tanner, Fleur Tippin, Justine Kane, Jonathan Lay, Anja Brouwer, Stephen‐John Sammut, Suet‐Feung Chin, Davina Gale, Dana W. Y. Tsui, Sarah‐Jane Dawson, Nitzan Rosenfeld, Maurizio Callari, Oscar M. Rueda, Carlos Caldas   +20 more
wiley   +1 more source

BWTaligner: a genome short-read aligner

Vietnam Journal of Science, Technology and Engineering, 2018
The development of next-generation sequencing technologies has helped sequence large genomes easily, producing a huge number of short-reads - small fragments of DNA. Despite the existence of many developed alignment tools, mapping short-read datasets to
Lam Nguyen, Xuan Thi Trinh, Hien Trinh, Dang Hung Tran, Cuong Nguyen   +4 more
doaj   +1 more source

Comparative analysis of multiple protein-sequence alignment methods. [PDF]

, 1994
Marcella A. McClure, T K Vasi, W M Fitch
openalex   +1 more source