Works matching DE "EUKARYOTIC genomes"

Results: 1115

Structure of a Yeast 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex.

Published in:

Nature Structural & Molecular Biology, 2015, v. 22, n. 3, p. 269, doi. 10.1038/nsmb.2963

By:

Aylett, Christopher H S;
Boehringer, Daniel;
Erzberger, Jan P;
Schaefer, Tanja;
Ban, Nenad

Publication type:

Article

Delivering nonidentical twins.

Published in:

Nature Structural & Molecular Biology, 2014, v. 21, n. 8, p. 649, doi. 10.1038/nsmb.2852

By:

Kunkel, Thomas A;
Burgers, Peter M

Publication type:

Article

The human cap-binding complex is functionally connected to the nuclear RNA exosome.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 12, p. 1367, doi. 10.1038/nsmb.2703

By:

Andersen, Peter Refsing;
Domanski, Michal;
Kristiansen, Maiken S;
Storvall, Helena;
Ntini, Evgenia;
Verheggen, Celine;
Schein, Aleks;
Bunkenborg, Jakob;
Poser, Ina;
Hallais, Marie;
Sandberg, Rickard;
Hyman, Anthony;
LaCava, John;
Rout, Michael P;
Andersen, Jens S;
Bertrand, Edouard;
Jensen, Torben Heick

Publication type:

Article

Nucleosome sliding mechanisms: new twists in a looped history.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 9, p. 1026, doi. 10.1038/nsmb.2648

By:

Mueller-Planitz, Felix;
Klinker, Henrike;
Becker, Peter B

Publication type:

Article

Noncoding RNAs prevent spreading of a repressive histone mark.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 8, p. 994, doi. 10.1038/nsmb.2619

By:

Keller, Claudia;
Kulasegaran-Shylini, Raghavendran;
Shimada, Yukiko;
Hotz, Hans-Rudolf;
Bühler, Marc

Publication type:

Article

Structure of the MutLα C-terminal domain reveals how Mlh1 contributes to Pms1 endonuclease site.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 4, p. 461, doi. 10.1038/nsmb.2511

By:

Gueneau, Emeric;
Dherin, Claudine;
Legrand, Pierre;
Tellier-Lebegue, Carine;
Gilquin, Bernard;
Bonnesoeur, Pierre;
Londino, Floriana;
Quemener, Cathy;
Le Du, Marie-Hélene;
Márquez, Josan A;
Moutiez, Mireille;
Gondry, Muriel;
Boiteux, Serge;
Charbonnier, Jean-Baptiste

Publication type:

Article

The ATPase domain of ISWI is an autonomous nucleosome remodeling machine.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 1, p. 82, doi. 10.1038/nsmb.2457

By:

Mueller-Planitz, Felix;
Klinker, Henrike;
Ludwigsen, Johanna;
Becker, Peter B

Publication type:

Article

Targeted Histone Peptides: Insights into the Spatial Regulation of the Methyltransferase PRC2 by using a Surrogate of Heterotypic Chromatin.

Published in:

Angewandte Chemie, 2015, v. 127, n. 22, p. 6557, doi. 10.1002/ange.201500085

By:

Brown, Zachary Z.;
Müller, Manuel M.;
Kong, Ha Eun;
Lewis, Peter W.;
Muir, Tom W.

Publication type:

Article

The landscape of transposable element distribution in the genome of Neotropical fish Apareiodon sp. (Characiformes: Parodontidae).

Published in:

Chromosome Research, 2025, v. 33, n. 1, p. 1, doi. 10.1007/s10577-025-09765-3

By:

de Oliveira, Fernanda Souza;
Brann, Toby;
Wolf, Ivan Rodrigo;
Nogaroto, Viviane;
Martins, Cesar;
Protasio, Anna Victoria;
Vicari, Marcelo Ricardo

Publication type:

Article

Seq'ing identity and function in a repeat-derived noncoding RNA world.

Published in:

Chromosome Research, 2020, v. 28, n. 1, p. 111, doi. 10.1007/s10577-020-09628-z

By:

O'Neill, Rachel J.

Publication type:

Article

Mammalian transposable elements and their impacts on genome evolution.

Published in:

Chromosome Research, 2018, v. 26, n. 1/2, p. 25, doi. 10.1007/s10577-017-9570-z

By:

Platt, Roy N.;
Vandewege, Michael W.;
Ray, David A.

Publication type:

Article

Proliferating cell nuclear antigen (PCNA) contributes to the high-order structure and stability of heterochromatin in Saccharomyces cerevisiae.

Published in:

Chromosome Research, 2017, v. 25, n. 2, p. 89, doi. 10.1007/s10577-016-9540-x

By:

Bi, Xin;
Ren, Yue;
Kath, Morgan

Publication type:

Article

Repetitive DNA in eukaryotic genomes.

Published in:

Chromosome Research, 2015, v. 23, n. 3, p. 415, doi. 10.1007/s10577-015-9499-z

By:

Biscotti, Maria;
Olmo, Ettore;
Heslop-Harrison, J.

Publication type:

Article

Intragenomic distribution of RTE retroelements suggests intrachromosomal movement.

Published in:

Chromosome Research, 2015, v. 23, n. 2, p. 211, doi. 10.1007/s10577-014-9461-5

By:

Montiel, Eugenia;
Ruiz-Ruano, Francisco;
Cabrero, Josefa;
Marchal, Juan;
Sánchez, Antonio;
Perfectti, Francisco;
López-León, María;
Camacho, Juan

Publication type:

Article

An analysis and prediction of nucleosome positioning based on information content.

Published in:

Chromosome Research, 2013, v. 21, n. 1, p. 63, doi. 10.1007/s10577-013-9338-z

By:

Xing, Yong-qiang;
Liu, Guo-qing;
Zhao, Xiu-juan;
Cai, Lu

Publication type:

Article

Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities.

Published in:

Microbial Ecology, 2018, v. 75, n. 4, p. 875, doi. 10.1007/s00248-017-1085-9

By:

Röhl, Oliver;
Graupner, Nadine;
Peršoh, Derek;
Kemler, Martin;
Mittelbach, Moritz;
Boenigk, Jens;
Begerow, Dominik

Publication type:

Article

Eukaryotic Community Shift in Response to Organic Loading Rate of an Aerobic Trickling Filter (Down-Flow Hanging Sponge Reactor) Treating Domestic Sewage.

Published in:

Microbial Ecology, 2017, v. 73, n. 4, p. 801, doi. 10.1007/s00248-016-0871-0

By:

Miyaoka, Yuma;
Hatamoto, Masashi;
Yamaguchi, Takashi;
Syutsubo, Kazuaki

Publication type:

Article

Mapping of <italic>Hieracium</italic> (Asteraceae) chromosomes with genus-specific satDNA elements derived from next-generation sequencing data.

Published in:

Plant Systematics & Evolution, 2018, v. 304, n. 3, p. 387, doi. 10.1007/s00606-017-1483-y

By:

Belyayev, Alexander;
Paštová, Ladislava;
Fehrer, Judith;
Josefiová, Jiřina;
Chrtek, Jindřich;
Mráz, Patrik

Publication type:

Article

RUBI: rapid proteomic-scale prediction of lysine ubiquitination and factors influencing predictor performance.

Published in:

Amino Acids, 2014, v. 46, n. 4, p. 853, doi. 10.1007/s00726-013-1645-3

By:

Walsh, Ian;
Domenico, Tomás;
Tosatto, Silvio

Publication type:

Article

Lysosomal sulfatases: a growing family.

Published in:

Biochemical Journal, 2020, v. 477, n. 20, p. 3963, doi. 10.1042/BCJ20200586

By:

Lübke, Torben;
Damme, Markus

Publication type:

Article

HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.

Published in:

Bioinformatics, 2018, v. 34, n. 4, p. 675, doi. 10.1093/bioinformatics/btx625

By:

Anil, Anandashankar;
Spalinskas, Rapolas;
Åkerborg, Örjan;
Sahlén, Pelin

Publication type:

Article

DeepLoc: prediction of protein subcellular localization using deep learning.

Published in:

Bioinformatics, 2017, v. 33, n. 21, p. 3387, doi. 10.1093/bioinformatics/btx431

By:

Almagro Armenteros, José Juan;
Sønderby, Casper Kaae;
Sønderby, Søren Kaae;
Nielsen, Henrik;
Winther, Ole

Publication type:

Article

EUPAN enables pan-genome studies of a large number of eukaryotic genomes.

Published in:

Bioinformatics, 2017, v. 33, n. 15, p. 2408, doi. 10.1093/bioinformatics/btx170

By:

Zhiqiang Hu;
Chen Sun;
Kuang-Chen Lu;
Xixia Chu;
Yue Zhao;
Jinyuan Lu;
Jianxin Shi;
Chaochun Wei

Publication type:

Article

Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets.

Published in:

Bioinformatics, 2017, v. 33, n. 14, p. 2194, doi. 10.1093/bioinformatics/btx141

By:

Monfort, Matthias;
Furlong, Eileen E. M.;
Girardot, Charles

Publication type:

Article

Kollector: transcript-informed, targeted de novo assembly of gene loci.

Published in:

Bioinformatics, 2017, v. 33, n. 12, p. 1782, doi. 10.1093/bioinformatics/btx078

By:

Kucuk, Erdi;
Chu, Justin;
Vandervalk, Benjamin P.;
Hammond, S. Austin;
Warren, René L.;
Birol, Inanc

Publication type:

Article

MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins.

Published in:

Bioinformatics, 2017, v. 33, n. 9, p. 1402, doi. 10.1093/bioinformatics/btx015

By:

Necci, Marco;
Piovesan, Damiano;
Dosztányi, Zsuzsanna;
Tosatto, Silvio C. E.

Publication type:

Article

RECKONER: read error corrector based on KMC.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 1086, doi. 10.1093/bioinformatics/btw746

By:

Długosz, Maciej;
Deorowicz, Sebastian

Publication type:

Article

Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

Published in:

Bioinformatics, 2017, v. 33, n. 7, p. 971, doi. 10.1093/bioinformatics/btw776

By:

Leimeister, Chris-André;
Sohrabi-Jahromi, Salma;
Morgenstern, Burkhard

Publication type:

Article

AltORFev facilitates the prediction of alternative open reading frames in eukaryotic mRNAs.

Published in:

Bioinformatics, 2017, v. 33, n. 6, p. 923, doi. 10.1093/bioinformatics/btw736

By:

Kochetov, Alex V.;
Allmer, Jens;
Klimenko, Alexandra I.;
Zuraev, Bulat S.;
Matushkin, Yury G.;
Lashin, Sergey A.

Publication type:

Article

Simulation-based estimation of branching models for LTR retrotransposons.

Published in:

Bioinformatics, 2017, v. 33, n. 3, p. 320, doi. 10.1093/bioinformatics/btw622

By:

Moulin, Serge;
Seux, Nicolas;
Chrétien, Stéphane;
Guyeux, Christophe;
Lerat, Emmanuelle

Publication type:

Article

TADtool: visual parameter identification for TAD-calling algorithms.

Published in:

2016

By:

Kruse, Kai;
Hug, Clemens B.;
Hernández-Rodríguez, Benjamín;
Vaquerizas, Juan M.

Publication type:

Product Review

MGEScan: a Galaxy-based system for identifying retrotransposons in genomes.

Published in:

Bioinformatics, 2016, v. 32, n. 16, p. 2502, doi. 10.1093/bioinformatics/btw157

By:

Hyungro Lee;
Minsu Lee;
Ismail, Wazim Mohammed;
Mina Rho;
Fox, Geoffrey C.;
Sangyoon Oh;
Haixu Tang

Publication type:

Article

phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats.

Published in:

Bioinformatics, 2016, v. 32, n. 12, p. i209, doi. 10.1093/bioinformatics/btw258

By:

Schaeffer, Carly E.;
Figueroa, Nathaniel D.;
Xiaolin Liu;
Karro, John E.

Publication type:

Article

Maligner: a fast ordered restriction map aligner.

Published in:

Bioinformatics, 2016, v. 32, n. 7, p. 1016, doi. 10.1093/bioinformatics/btv711

By:

Mendelowitz, Lee M.;
Schwartz, David C.;
Pop, Mihai

Publication type:

Article

The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes.

Published in:

Bioinformatics, 2016, v. 32, n. 6, p. 835, doi. 10.1093/bioinformatics/btv679

By:

Utro, Filippo;
Di Benedetto, Valeria;
Corona, Davide F. V.;
Giancarlo, Raffaele

Publication type:

Article

TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.

Published in:

Bioinformatics, 2015, v. 31, n. 22, p. 3593, doi. 10.1093/bioinformatics/btv422

By:

Ying Jin;
Tam, Oliver H.;
Paniagua, Eric;
Hammell, Molly

Publication type:

Article

hiHMM: Bayesian non-parametric joint inference of chromatin state maps.

Published in:

Bioinformatics, 2015, v. 31, n. 13, p. 2066, doi. 10.1093/bioinformatics/btv117

By:

Kyung-Ah Sohn;
Ho, Joshua W. K.;
Djordjevic, Djordje;
Hyun-hwan Jeong;
Park, Peter J.;
Ju Han Kim

Publication type:

Article

Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition.

Published in:

Bioinformatics, 2014, v. 30, n. 11, p. 1569, doi. 10.1093/bioinformatics/btu021

By:

Hunt, Kristopher A.;
Folsom, James P.;
Taffs, Reed L.;
Carlson, Ross P.

Publication type:

Article

SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes.

Published in:

Bioinformatics, 2014, v. 30, n. 8, p. 1081, doi. 10.1093/bioinformatics/btt727

By:

Jaron, Kamil S.;
Moravec, Jiří C.;
Martínková, Natália

Publication type:

Article

PARSEC: PAtteRn SEarch and Contextualization.

Published in:

Bioinformatics, 2013, v. 29, n. 20, p. 2643, doi. 10.1093/bioinformatics/btt455

By:

Allot, Alexis;
Anno, Yannick-Noël;
Poidevin, Laetitia;
Ripp, Raymond;
Poch, Olivier;
Lecompte, Odile

Publication type:

Article

Haplotype assembly in polyploid genomes and identical by descent shared tracts.

Published in:

Bioinformatics, 2013, v. 29, n. 13, p. i352, doi. 10.1093/bioinformatics/btt213

By:

Aguiar, Derek;
Istrail, Sorin

Publication type:

Article

The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.

Published in:

Bioinformatics, 2013, v. 29, n. 8, p. 981, doi. 10.1093/bioinformatics/btt089

By:

Indio, Valentina;
Martelli, Pier Luigi;
Savojardo, Castrense;
Fariselli, Piero;
Casadio, Rita

Publication type:

Article

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.

Published in:

Bioinformatics, 2012, v. 28, n. 19, p. 2458

By:

Li, Wenyuan;
Zhang, Shihua;
Liu, Chun-Chi;
Zhou, Xianghong Jasmine

Publication type:

Article

Genomes on a Tree (GoaT): A centralized resource for eukaryotic genome sequencing initiatives.

Published in:

Biodiversity Information Science & Standards, 2021, p. 1, doi. 10.3897/biss.5.74138

By:

Sotero-Caio, Cibele Gomes;
Challis, Richard;
Kumar, Sujai;
Blaxter, Mark

Publication type:

Article

CTCF: an architectural protein bridging genome topology and function.

Published in:

Nature Reviews Genetics, 2014, v. 15, n. 4, p. 234, doi. 10.1038/nrg3663

By:

Ong, Chin-Tong;
Corces, Victor G.

Publication type:

Article

A Pipeline NanoTRF as a New Tool for De Novo Satellite DNA Identification in the Raw Nanopore Sequencing Reads of Plant Genomes.

Published in:

Plants (2223-7747), 2022, v. 11, n. 16, p. 2103, doi. 10.3390/plants11162103

By:

Kirov, Ilya;
Kolganova, Elizaveta;
Dudnikov, Maxim;
Yurkevich, Olga Yu.;
Amosova, Alexandra V.;
Muravenko, Olga V.

Publication type:

Article

Detecting Genetic Mobility Using a Transposon-Based Marker System in Gamma-Ray Irradiated Soybean Mutants.

Published in:

Plants (2223-7747), 2021, v. 10, n. 2, p. 373, doi. 10.3390/plants10020373

By:

Hung, Nguyen Ngoc;
Kim, Dong-Gun;
Lyu, Jae Il;
Park, Kyong-Cheul;
Kim, Jung Min;
Kim, Jin-Baek;
Ha, Bo-Keun;
Kwon, Soon-Jae;
Anai, Toyoaki

Publication type:

Article

Celebrating Mendel, McClintock, and Darlington: On end-to-end chromosome fusions and nested chromosome fusions.

Published in:

Plant Cell, 2022, v. 34, n. 7, p. 2475, doi. 10.1093/plcell/koac116

By:

Lysak, Martin A.

Publication type:

Article

xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.

Published in:

Plant Cell, 2016, v. 28, n. 4, p. 840, doi. 10.1105/tpc.15.00933

By:

Duvick, Jon;
Standage, Daniel S.;
Merchant, Nirav;
Brendel, Volker P.

Publication type:

Article

Rice MULEs Transpose in Yeast.

Published in:

Plant Cell, 2015, v. 27, n. 1, p. 5, doi. 10.1105/tpc.114.136143

By:

Mach, Jennifer

Publication type:

Article