Results 31 to 40 of about 98,363 (283)

Optical mapping approaches to molecular genomics

Current Opinion in Biotechnology, 1997
A variety of physical mapping methods exist for the analysis of nucleic acids or genomes, including hybridization, sequence tagged site mapping, restriction enzyme fingerprinting, radiation hybrid mapping and optical mapping. Single-molecule approaches offer numerous advantages, including very high resolution, small sample size requirements, and ...
D C, Schwartz, A, Samad
openaire   +2 more sources

Optical Genome Mapping for Cytogenetic Diagnostics in AML

Cancers, 2023
The classification and risk stratification of acute myeloid leukemia (AML) is based on reliable genetic diagnostics. A broad and expanding variety of relevant aberrations are structural variants beyond single-nucleotide variants. Optical Genome Mapping is an unbiased, genome-wide, amplification-free method for the detection of structural variants.
Verena Nilius-Eliliwi, Wanda M. Gerding, Roland Schroers, Huu Phuc Nguyen, Deepak B. Vangala   +4 more
openaire   +2 more sources

Optical mapping discerns genome wide DNA methylation profiles [PDF]

BMC Molecular Biology, 2008
Methylation of CpG dinucleotides is a fundamental mechanism of epigenetic regulation in eukaryotic genomes. Development of methods for rapid genome wide methylation profiling will greatly facilitate both hypothesis and discovery driven research in the field of epigenetics.
Ananiev, Gene E, Goldstein, Steve, Runnheim, Rod, Forrest, Dan K, Zhou, Shiguo, Potamousis, Konstantinos, Churas, Chris P, Bergendahl, Veit, Thomson, James A, Schwartz, David C   +9 more
openaire   +2 more sources

Optical mapping as a routine tool for bacterial genome sequence finishing

BMC Genomics, 2007
Background In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts.
Gaudriault Sophie, Forst Steve, Du Zijin, Darby Creg, Bode Helge B, Barbazuk Brad, Miller Nancy, Henkhaus John, Goldman Barry S, Norton Stacie, Latreille Phil, Goodner Brad, Goodrich-Blair Heidi, Slater Steven   +13 more
doaj   +1 more source

Feasibility of Optical Genome Mapping in Cytogenetic Diagnostics of Hematological Neoplasms: A New Way to Look at DNA

Diagnostics, 2023
Optical genome mapping (OGM) is a new genome-wide technology that can reveal both structural genomic variations (SVs) and copy number variations (CNVs) in a single assay.
Nicoletta Coccaro, Luisa Anelli, Antonella Zagaria, Francesco Tarantini, Cosimo Cumbo, Giuseppina Tota, Crescenzio Francesco Minervini, Angela Minervini, Maria Rosa Conserva, Immacolata Redavid, Elisa Parciante, Maria Giovanna Macchia, Giorgina Specchia, Pellegrino Musto, Francesco Albano   +14 more
doaj   +1 more source

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology [PDF]

, 2016
Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different
Aguiar, Edgar L., Azevedo, Vasco A. C., Barh, Debmalya, Benevides, Leandro, Figueiredo, Henrique C. P., Folador, Edson L., Ghosh, Preetam, Guimarães, Luís C., Mariano, Diego C. B., Oliveira, Letícia C., Pereira, Felipe L., Ramos, Rommel T. J., Silva, Artur, Sousa, Thiago J.   +13 more
core   +3 more sources

Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions

Plants, 2023
High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors.
Luca Marcolungo, Leonardo Vincenzi, Matteo Ballottari, Michela Cecchin, Emanuela Cosentino, Thomas Mignani, Antonina Limongi, Irene Ferraris, Matteo Orlandi, Marzia Rossato, Massimo Delledonne   +10 more
doaj   +1 more source

OMSim : a simulator for optical map data [PDF]

, 2017
Motivation: The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire ...
Audenaert, Pieter, Fostier, Jan, Miclotte, Giles, Plaisance, Stéphane, Rombauts, Stephane, Van de Peer, Yves   +5 more
core   +2 more sources

DeepOM: Single-molecule optical genome mapping via deep learning

Bioinformatics, 2022
AbstractEfficient tapping into genomic information from a single microscopic image of an intact DNA molecule fragment is an outstanding challenge and its solution will open new frontiers in molecular diagnostics. Here, a new computational method for optical genome mapping utilizing Deep Learning is presented, termed DeepOM.
Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman   +6 more
openaire   +2 more sources

A Powerful New Quantitative Genetics Platform, Combining Caenorhabditis elegans High-Throughput Fitness Assays with a Large Collection of Recombinant Strains. [PDF]

, 2015
The genetic variants underlying complex traits are often elusive even in powerful model organisms such as Caenorhabditis elegans with controlled genetic backgrounds and environmental conditions.
Andersen, Erik C, Bloom, Joshua S, Crissman, Jonathan R, Gerke, Justin P, Ghosh, Rajarshi, Kruglyak, Leonid, Seidel, Hannah S, Shimko, Tyler C   +7 more
core   +5 more sources