Results 31 to 40 of about 458,823 (303)

Mapping ribonucleotides embedded in genomic DNA to single-nucleotide resolution using Ribose-Map [PDF]

Nature Protocols, 2020
ABSTRACTRibose-Map is a user-friendly, standardized bioinformatics toolkit for the comprehensive analysis of ribonucleotide sequencing experiments. It allows researchers to map the locations of ribonucleotides in DNA to single-nucleotide resolution and identify biological signatures of ribonucleotide incorporation.
Alli L. Gombolay, Francesca Storici
openaire   +2 more sources

RNA elements directing in vivo assembly of the 7SK/MePCE/Larp7 transcriptional regulatory snRNP [PDF]

, 2013
Through controlling the nuclear level of active positive transcription elongation factor b (P-TEFb), the 7SK small nuclear RNA (snRNA) functions as a key regulator of RNA polymerase II transcription.
Bayfield, Bhattacharya, Biewenga, Blazek, Chambers, Cheng, de Almeida, Diribarne, Egloff, Goodall, Gupta, Gupta, Jeronimo, Jobert, Kiss, Kiss, Kiss, L. Muniz, Markert, Michels, Muniz, Nguyen, O'Keeffe, Peterlin, Price, S. Egloff, Shimba, Shimba, Shumyatsky, Shumyatsky, Singh, Singh, Singh, T. Kiss, Takahasi, Van Herreweghe, Wada, Wassarman, Yamaguchi, Yang, Yik, Yik, Zhou, Zhou   +43 more
core   +3 more sources

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

BMC Bioinformatics, 2019
Background 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, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres, Philipp Rescheneder   +6 more
doaj   +1 more source

Use of Denaturing HPLC to Map Human and Murine Genes and to Validate Single-Nucleotide Polymorphisms

BioTechniques, 2000
Linkage mapping has been extensively applied in the murine and human genomes. It remains a powerful approach to mapping genes and identifying genetic variants.
Lynn M. Schriml, Raymond J. Peterson, Bernard Gerrard, Michael Dean   +3 more
doaj   +1 more source

NMR Studies of Retroviral Genome Packaging

Viruses, 2020
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs.
Patricia S. Boyd, Janae B. Brown, Joshua D. Brown, Jonathan Catazaro, Issac Chaudry, Pengfei Ding, Xinmei Dong, Jan Marchant, Colin T. O’Hern, Karndeep Singh, Canessa Swanson, Michael F. Summers, Saif Yasin   +12 more
doaj   +1 more source

A mutate-and-map protocol for inferring base pairs in structured RNA

, 2013
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling.
CS Chow, D Moazed, DH Mathews, EE Regulski, JB Lucks, JG Underwood, JP Staley, KA Wilkinson, M Kertesz, M Mandal, N Kulshina, NB Leontis, P Cordero, P Cordero, P Rocca-Serra, P Tijerina, PJ Lukavsky, R Rydzanicz, RC Spitale, RF Gesteland, S Mitra, S Washietl, S Yoon, SA Mortimer, SE Wells, SM Vasa, SW Brostoff, VD Sood, W Kladwang, W Kladwang, W Kladwang, W Kladwang, Y Rhee   +32 more
core   +1 more source

Integration of genetics into a systems model of electrocardiographic traits using humanCVD BeadChip [PDF]

, 2012
<p>Background—Electrocardiographic traits are important, substantially heritable determinants of risk of arrhythmias and sudden cardiac death.</p> <p>Methods and Results—In this study, 3 population-based cohorts (n=10 526) genotyped ...
Adeniran, I., Amuzu, A., Braund, P.S., Burton, P.R., Casas, J.-P., Day, I.N.M., Drenos, F., Eriksson, P., Folkersen, L., Gaunt, T.R., Hancox, J.C., Hingorani, A.D., Humphries, S.E., Kivimaki, M., Kumari, M., Lawlor, D.A., Macfarlane, P.W., Nelson, C.P., Samani, N.J., Shah, S., Talmud, P.J., Tobin, M.D., Tomaszewski, M., Whittaker, J., Zhang, H.   +24 more
core   +1 more source

A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome [PDF]

, 2019
DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability.
Allison, Rachal M, Cooper, Tim J, Gittens, William H, Johnson, Dominic J, Neale, Matthew J, Thomas, Holly   +5 more
core   +1 more source

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

BMC Genomics, 2017
Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference.
Peng Zhou, Kevin A. T. Silverstein, Thiruvarangan Ramaraj, Joseph Guhlin, Roxanne Denny, Junqi Liu, Andrew D. Farmer, Kelly P. Steele, Robert M. Stupar, Jason R. Miller, Peter Tiffin, Joann Mudge, Nevin D. Young   +12 more
doaj   +1 more source

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution [PDF]

, 2018
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, P.
Arnathau, Céline, Boundenga, Larson, Durand, Patrick, Franzon, Blaise, Gilabert, Aude, Makanga, Boris, Moukodoum, Nancy D., Ngoubangoye, Barthélémy, Okouga, Alain-Prince, Ollomo, Benjamin, Otto, Thomas D., Paupy, Christophe, Prugnolle, Franck, Renaud, François, Rougeron, Virginie, Rutledge, Gavin G.   +15 more
core   +5 more sources