Results 91 to 100 of about 1,074,205 (395)

ParMap, an Algorithm for the Identification of Complex Genomic Variations in Nextgen Sequencing Data [PDF]

, 2010
Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions.
Adolfo A. Ferrando, Hossein Khiabanian, Pieter Van Vlierberghe, Raul Rabadan, Teresa Palomero   +4 more
core   +1 more source

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies [PDF]

, 2018
In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for ...
Angelidaki, Irini, Campanaro, Stefano, Kougias, Panagiotis G., Treu, Laura, Zhu, Xinyu   +4 more
core   +3 more sources

Diagnostic high-throughput sequencing of 2,396 patients with bleeding, thrombotic and platelet disorders.

Blood, 2019
A targeted high-throughput sequencing (HTS) panel test for clinical diagnostics requires careful consideration of the inclusion of appropriate diagnostic-grade genes, the ability to detect multiple types of genomic variation with high levels of analytic ...
K. Downes, Karyn Megy, Daniel Duarte, Minka J. A. Vries, J. Gebhart, S. Hofer, O. Shamardina, Sri V. V. Deevi, J. Stephens, R. Mapeta, Salih Tuna, Namir Al Hasso, M. Besser, N. Cooper, L. Daugherty, Nicholas S. Gleadall, D. Greene, M. Haimel, H. Martin, S. Papadia, S. Revel-Vilk, S. Sivapalaratnam, E. Symington, W. Thomas, C. Thys, A. Tolios, C. Penkett, W. Ouwehand, S. Abbs, M. Laffan, E. Turro, Ilenia Simeoni, A. Mumford, Y. Henskens, I. Pabinger, K. Gomez, K. Freson   +36 more
semanticscholar   +1 more source

Liquid biopsy epigenetics: establishing a molecular profile based on cell‐free DNA

Molecular Oncology, EarlyView.
Cell‐free DNA (cfDNA) fragments in plasma from cancer patients carry epigenetic signatures reflecting their cells of origin. These epigenetic features include DNA methylation, nucleosome modifications, and variations in fragmentation. This review describes the biological properties of each feature and explores optimal strategies for harnessing cfDNA ...
Christoffer Trier Maansson, Anders Lade Nielsen, Boe Sandahl Sorensen   +2 more
wiley   +1 more source

Coverage statistics for sequence census methods [PDF]

, 2010
Background: We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments.
Evans, Steven N., Hower, Valerie, Pachter, Lior   +2 more
core   +6 more sources

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

BMC Bioinformatics, 2019
Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes.
Tobias Neumann, Veronika A. Herzog, M. Muhar, A. Haeseler, J. Zuber, Stefan L Ameres, Philipp Rescheneder   +6 more
semanticscholar   +1 more source

High‐throughput sequencing of the melanoma genome [PDF]

Experimental Dermatology, 2012
AbstractNext‐generation sequencing technologies are now common for whole‐genome, whole‐exome and whole‐transcriptome sequencing (RNA‐seq) of tumors to identify point mutations, structural or copy number alterations and changes in gene expression. A substantial number of studies have already been performed for melanoma. One study analysed eight melanoma
Manfred, Kunz, Michael, Dannemann, Janet, Kelso   +2 more
openaire   +2 more sources

In vitro models of cancer‐associated fibroblast heterogeneity uncover subtype‐specific effects of CRISPR perturbations

Molecular Oncology, EarlyView.
Development of therapies targeting cancer‐associated fibroblasts (CAFs) necessitates preclinical model systems that faithfully represent CAF–tumor biology. We established an in vitro coculture system of patient‐derived pancreatic CAFs and tumor cell lines and demonstrated its recapitulation of primary CAF–tumor biology with single‐cell transcriptomics ...
Elysia Saputra, Shamsudheen Karuthedath Vellarikkal, Lixia Li, Hong Sun, Khoa Nguyen, Amber Montano, Suchitra Natarajan, Federica Piccioni, Alex Michael Tamburino, Xin Yu, Aleksandra Katarzyna Olow   +10 more
wiley   +1 more source

Methods to study splicing from high-throughput RNA Sequencing data

, 2015
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned
A Ameur, A Bhasi, A Dobin, A Mortazavi, A Oshlack, A Roberts, A Roberts, AM Mezlini, AN Brooks, B Jackson, B Kakaradov, B Langmead, B Li, B Li, BJ Haas, BJ Haas, C Trapnell, C Trapnell, C Trapnell, D Hiller, D Singh, DL Wood, DW Bryant, E Eyras, E Lee, E Turro, ET Wang, F Birzele, F Bona De, F Denoeud, F Tang, G Robertson, G Xu, GA Sacomoto, GR Grant, GS Slater, H Bao, H Jiang, H Jiang, H Kim, H Richard, J Behr, J Du, J Feng, J Hu, J Lovén, J Martin, J Salzman, J Seok, J Seok, J Wu, J Wu, JE Allen, JJ Li, JP Venables, K Schneeberger, K Wang, KD Hansen, KF Au, KL Howe, KM Borgwardt, L Chen, L Chen, L Wang, L Wang, LY Chen, M Aschoff, M Fiume, M Garber, M Griffith, M Guttman, M Stanke, M Stanke, M Sultan, MC Ryan, MF Rogers, MG Grabherr, MH Schulz, MT Dimon, N Cloonan, N Cloonan, N Deng, N Leng, N Nicolae, N Philippe, N Vijay, NA Fonseca, O Stegle, P Drewe, P Glaus, PL Martelli, PP Labaj, Q Liu, Q Liu, Q Pan, QY Zhao, R Bohnert, R Guigó, R Li, S Anders, S Djebali, S Filichkin, S Heber, S Huang, S Lee, S Mangul, S Marco-Sola, S Shen, S Sonnenburg, S Srivastava, S Tang, S Zheng, SB Montgomery, SH Nagaraj, SK Lou, T Bonfert, TA Clark, TD Wu, TD Wu, W Li, W Li, W Wang, WJ Kent, Y Hu, Y Katz, Y Li, Y Liao, Y Surget-Groba, Y Xing, Y Xing, Y Zhang, Z Xia   +131 more
core   +1 more source

Whole-genome sequencing and the clinician: a tale of two cities [PDF]

, 2014
Clinicians are faced with unprecedented opportunities to identify the genetic aetiologies of hitherto molecularly uncharacterised conditions via the use of high-throughput sequencing.
A. R. Foley, Dickens, Dubowitz, F. Muntoni, Foley, Gualandi, J. He, J. Kim, Jöbsis, Jöbsis, Kim, Lupski, M. G. Hanna, Mercuri, Mercuri, Morrow, N. M. Pearson, Pace, Pan, Phimister, R. D. S. Pitceathly, Straub   +21 more
core   +2 more sources