Results 21 to 30 of about 160,024 (241)

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nature Communications, 2020
With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes
Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium   +20 more
doaj   +1 more source

Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome

Frontiers in Genetics, 2019
It is broadly expected that next generation sequencing will ultimately generate a complete genome as is the latest goat reference genome (ARS1), which is considered to be one of the most continuous assemblies in livestock.
Ran Li, Weiwei Fu, Rui Su, Xiaomeng Tian, Duo Du, Yue Zhao, Zhuqing Zheng, Qiuming Chen, Shan Gao, Yudong Cai, Xihong Wang, Jinquan Li, Yu Jiang   +12 more
doaj   +1 more source

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

BMC Bioinformatics, 2009
Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates.
Zhang Wei, Deng Xiangyu, Phillippy Adam M, Salzberg Steven L   +3 more
doaj   +1 more source

Getting insight into the pan-genome structure with PangTree

BMC Genomics, 2020
Background The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes ...
Paulina Dziadkiewicz, Norbert Dojer
doaj   +1 more source

Inhibiting stearoyl‐CoA desaturase suppresses bone metastatic prostate cancer by modulating cellular stress, mTOR signaling, and DNA damage response

FEBS Letters, EarlyView.
Bone metastasis in prostate cancer (PCa) patients is a clinical hurdle due to the poor understanding of the supportive bone microenvironment. Here, we identify stearoyl‐CoA desaturase (SCD) as a tumor‐promoting enzyme and potential therapeutic target in bone metastatic PCa.
Alexis Wilson, Mackenzie K Herroon, Shane Mecca, Laimar C Garmo, Jacob Lindquist, Shrila Rajendran, Steve M. Patrick, Izabela Podgorski   +7 more
wiley   +1 more source

Bridging the gap: Multi‐stakeholder perspectives of molecular diagnostics in oncology

Molecular Oncology, EarlyView.
Although molecular diagnostics is transforming cancer care, implementing novel technologies remains challenging. This study identifies unmet needs and technology requirements through a two‐step stakeholder involvement. Liquid biopsies for monitoring applications and predictive biomarker testing emerge as key unmet needs. Technology requirements vary by
Jorine Arnouts, Senada Koljenović, Elise Daems, Karolien De Wael, Marc Peeters, Léon C. van Kempen, Greetje Vanhoutte, Karen Zwaenepoel, Timon Vandamme   +8 more
wiley   +1 more source

Investigating the cell of origin and novel molecular targets in Merkel cell carcinoma: a historic misnomer

Molecular Oncology, EarlyView.
This study indicates that Merkel cell carcinoma (MCC) does not originate from Merkel cells, and identifies gene, protein & cellular expression of immune‐linked and neuroendocrine markers in primary and metastatic Merkel cell carcinoma (MCC) tumor samples, linked to Merkel cell polyomavirus (MCPyV) status, with enrichment of B‐cell and other immune cell
Richie Jeremian, Sriraam Sivachandran, Melissa Galati, Brandon Ramchatesingh, Hibo Rijal, Johnny Hanna, Elena Netchiporouk, May Chergui, Margaret Redpath, Samy Abou Setah, Ivan V. Litvinov   +10 more
wiley   +1 more source

PRAP: Pan Resistome analysis pipeline

BMC Bioinformatics, 2020
Background Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species.
Yichen He, Xiujuan Zhou, Ziyan Chen, Xiangyu Deng, Andrew Gehring, Hongyu Ou, Lida Zhang, Xianming Shi   +7 more
doaj   +1 more source

Integrated genomic and proteomic profiling reveals insights into chemoradiation resistance in cervical cancer

Molecular Oncology, EarlyView.
A comprehensive genomic and proteomic analysis of cervical cancer revealed STK11 and STX3 as a potential biomarkers of chemoradiation resistance. Our study demonstrated EGFR as a therapeutic target, paving the way for precision strategies to overcome treatment failure and the DNA repair pathway as a critical mechanism of resistance.
Janani Sambath, Irene A. George, Srikanth S. Manda, Prasanth Ariyannur, Ekta R. Dhawale, Raja Sekhar Kommu, Rajan Datar, Darshana Patil, Vinita Trivedi, Manisha Singh, Kumar Prabhash, Sewanti Limaye, Richa Chauhan, Prashant Kumar   +13 more
wiley   +1 more source

Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar

Frontiers in Microbiology, 2017
Food safety is a global concern, with upward of 2.2 million deaths due to enteric disease every year. Current whole-genome sequencing platforms allow routine sequencing of enteric pathogens for surveillance, and during outbreaks; however, a remaining ...
Chad R. Laing, Matthew D. Whiteside, Victor P. J. Gannon   +2 more
doaj   +1 more source