Results 41 to 50 of about 103,477 (279)

Aligning sequence from molecular inversion probes [PDF]

, 2014
ABSTRACTSummaryMolecular inversion probes (MIP’s) allow efficient enrichment of genomic regions of interest for the purpose of targeted sequencing. To date, there is a paucity of simple-to-use software to align sequences derived from this method. Here, we describe a single program that performs mapping, arm removal, and deduplication before outputting ...
Brent S. Pedersen, Elissa Murphy, Ivana V. Yang, David A. Schwartz   +3 more
openaire   +1 more source

Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes

International Journal of Molecular Sciences, 2022
To ensure efficiency in discovery and development, the application of computational technology is essential. Although virtual screening techniques are widely applied in the early stages of drug discovery research, the computational methods used in lead optimization to improve activity and reduce the toxicity of compounds are still evolving.
Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa   +3 more
openaire   +2 more sources

Profiling of the metabolic transcriptome via single molecule molecular inversion probes [PDF]

Scientific Reports, 2017
AbstractCancer-specific metabolic alterations are of high interest as therapeutic targets. These alterations vary between tumor types, and to employ metabolic targeting to its fullest potential there is a need for robust methods that identify candidate targetable metabolic pathways in individual cancers.
Bitter, T.J.J. de, Water, C. van de, Heuvel, C.N.A.M. van den, Zeelen, C., Eijkelenboom, A., Tops, B.B., Oosterwijk, E., Kolev, D., Mulders, P.F.A., Laan, M. ter, Lith, S.A. van, Leenders, W.P.   +11 more
openaire   +4 more sources

Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells? [PDF]

, 2012
Field cancerization effects as well as isolated tumor cell foci extending well beyond the invasive tumor margin have been described previously to account for local recurrence rates following breast conserving surgery despite adequate surgical margins and
Benz, Christopher C, Benz, Stephen C, Eppenberger-Castori, Serenella, Gray, Joe W, Lal, Aseem, Sadanandam, Anguraj, Scott, Gary, Spellman, Paul, Waldman, Fred   +8 more
core   +2 more sources

microDuMIP: target-enrichment technique for microarray-based duplex molecular inversion probes [PDF]

Nucleic Acids Research, 2014
Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of ...
Yoon, Jung-Ki, Ahn, Jinwoo, Kim, Han Sang, Han, Soo Min, Jang, Hoon, Lee, Min Goo, Lee, Ji Hyun, Bang, Duhee   +7 more
openaire   +4 more sources

MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing [PDF]

Bioinformatics, 2014
Abstract Summary Molecular inversion probes (MIPs) enable cost-effective multiplex targeted gene resequencing in large cohorts. However, the design of individual MIPs is a critical parameter governing the performance of this technology with respect to capture uniformity and specificity.
Evan A, Boyle, Brian J, O'Roak, Beth K, Martin, Akash, Kumar, Jay, Shendure   +4 more
openaire   +2 more sources

Characterizing the Pharmacogenome using Molecular Inversion Probes for Targeted Next-Generation Sequencing [PDF]

Pharmacogenomics, 2019
Aim: This study assesses the technical performance and cost of a targeted next-generation sequencing (NGS) multigene pharmacogenetic (PGx) test. Materials & methods: A genetic test was developed for 21 PGx genes using molecular inversion probes to generate library fragments for NGS.
Oscar, Suzuki, Olivia M, Dong, Rachel M, Howard, Tim, Wiltshire   +3 more
openaire   +2 more sources

Molecular Inversion Probes for targeted resequencing in non-model organisms

Scientific Reports, 2016
AbstractApplications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available.
Niedzicka, Marta, Fijarczyk, Anna, Dudek, Katarzyna, Stuglik, Michał, Babik, Wiesław   +4 more
openaire   +3 more sources

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs) [PDF]

, 2016
Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers.
Stuart, Cantsilieris, Holly A, Stessman, Jay, Shendure, Evan E, Eichler   +3 more
openaire   +2 more sources

12mm line survey of the dense molecular gas towards the W28 field TeV gamma-ray sources [PDF]

, 2010
We present 12mm Mopra observations of dense molecular gas towards the W28 supernova remnant (SNR) field. The focus is on the dense molecular gas towards the TeV gamma-ray sources detected by the H.E.S.S.
A. Kawamura, A. Walsh, Acciari, Acord, Aharonian, Aharonian, Aharonian, Aharonian, Albert, Araudo, Arikawa, B. Nicholas, Barrett, Bergin, Breen, Brogan, Bronfman, Chapmann, Churchwell, Claussen, Codella, Dame, Dame, Draine, Dubner, E. Keto, Faúndez, Feinstein, Frail, Fujita, Fukui, G. Rowell, Gabici, Giuliani, Goldsmith, Goudis, Gómez, Harvey, Hewitt, Ho, Hollenbach, Hollenbach, Hunter, Johnston, Kaspi, Keto, Keto, Keto, Kim, Kim, Klaassen, Kuchar, Lefloch, Liszt, Lockman, Longmore, Lozinskaya, M. G. Burton, MacLaren, Marquez-Lugo, Mizuno, Neufeld, Ott, Ott, Pillai, Protheroe, Reach, Reach, Rho, S. Longmore, Sevenster, Sollins, Stahler, Suzuki, Tafalla, Thompson, Torres, Ungerechts, Velázquez, Walmsley, Walmsley, Walsh, Wood, Y. Fukui, Yusef-Zadeh   +84 more
core   +1 more source