NAR genomics and bioinformatics

Keyphrases

Publications

volume 5, number 2, 2023

Gaëlle Munsch, Carole Proust, Sylvie Labrouche-Colomer, Dylan Aïssi, Anne Boland, Pierre-Emmanuel Morange, Anne Roche, Luc de Chaisemartin, Annie Harroche, Robert Olaso, Jean François Deleuze, Chloé James, Joseph Emmerich, David M Smadja, Hélène Jacqmin-Gadda, David-Alexandre Trégouët
Genome-wide association study of a semicontinuous trait: illustration of the impact of the modeling strategy through the study of Neutrophil Extracellular Traps levels. NAR genomics and bioinformatics 5 (2) (2023)
Lucile Jeusset, Nika Abdollahi, Thibaud Verny, Marine Armand, Anne Langlois De Septenville, Frédéric Davi, Juliana Silva Bernardes
ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors. NAR genomics and bioinformatics 5 (2) (2023)
Rafael R C Cuadrat, Adelheid Kratzer, Hector Giral Arnal, Anja C Rathgeber, Katarzyna Wreczycka, Alexander Blume, Irem B Gündüz, Veronika Ebenal, Tiina Mauno, Brendan Osberg, Minoo Moobed, Johannes Hartung, Kai Jakobs, Claudio Seppelt, Denitsa Meteva, Arash Haghikia, David M Leistner, Ulf Landmesser, Altuna Akalin
Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation. NAR genomics and bioinformatics 5 (2) (2023)
Michael Prummer, Anne Bertolini, Lars Bosshard, Florian Barkmann, Josephine Yates, Valentina Boeva, null null, Daniel Johannes Stekhoven, Franziska Singer
scROSHI: robust supervised hierarchical identification of single cells. NAR genomics and bioinformatics 5 (2) (2023)
Lucile Jeusset, Nika Abdollahi, Thibaud Verny, Marine Armand, Anne Langlois De Septenville, Frédéric Davi, Juliana Silva Bernardes
ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors. NAR genomics and bioinformatics 5 (2) (2023)
Sijie Yao, Biwei Cao, Tingyi Li, Denise Kalos, Yading Yuan, Xuefeng Wang
Prediction-oriented prognostic biomarker discovery with survival machine learning methods. NAR genomics and bioinformatics 5 (2) (2023)
Simon H Stitzinger, Salma Sohrabi-Jahromi, Johannes Söding
Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains. NAR genomics and bioinformatics 5 (2) (2023)
Callum Henfrey, Shona Murphy, Michael Tellier
Regulation of mature mRNA levels by RNA processing efficiency. NAR genomics and bioinformatics 5 (2) (2023)
Yair D J Prawer, Josie Gleeson, Ricardo De Paoli-Iseppi, Michael B Clark
Pervasive effects of RNA degradation on Nanopore direct RNA sequencing. NAR genomics and bioinformatics 5 (2) (2023)
Pia Keukeleire, Stavros Makrodimitris, Marcel J T Reinders
Cell type deconvolution of methylated cell-free DNA at the resolution of individual reads. NAR genomics and bioinformatics 5 (2) (2023)

volume 5, number 3, 2023

Anna Korsakova, Anh-Tuan Phan
Prediction of G4 formation in live cells with epigenetic data: a deep learning approach. NAR genomics and bioinformatics 5 (3) (2023)
Zheng Zuo
Quantifying the arms race between LINE-1 and KRAB-zinc finger genes through TECookbook. NAR genomics and bioinformatics 5 (3) (2023)
Pengyu Ni, Siwen Wu, Zhengchang Su
Underlying causes for prevalent false positives and false negatives in STARR-seq data. NAR genomics and bioinformatics 5 (3) (2023)
Xuewei Cao, Ling Zhang, Md Khairul Islam, Mingxia Zhao, Cheng He, Kui Zhang, Sanzhen Liu, Qiuying Sha, Hairong Wei
TGPred: efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning and optimization. NAR genomics and bioinformatics 5 (3) (2023)
Kristoffer Vitting-Seerup
Most protein domains exist as variants with distinct functions across cells, tissues and diseases. NAR genomics and bioinformatics 5 (3) (2023)
Youngbin Moon, Dominik Burri, Mihaela Zavolan
Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS. NAR genomics and bioinformatics 5 (3) (2023)
Zachary K Barth, Drew T Dunham, Kimberley D Seed
Nuclease genes occupy boundaries of genetic exchange between bacteriophages. NAR genomics and bioinformatics 5 (3) (2023)
Alexander Wichmann, Etienne Buschong, André Müller, Daniel Jünger, Andreas Hildebrandt, Thomas Hankeln, Bertil Schmidt
MetaTransformer: deep metagenomic sequencing read classification using self-attention models. NAR genomics and bioinformatics 5 (3) (2023)
Alisa Prusokiene, Augustinas Prusokas, Renata Retkute
Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes. NAR genomics and bioinformatics 5 (3) (2023)
Hugo Caro, Sulyvan Dollin, Anne Biton, Bryan Brancotte, Dimitri Desvillechabrol, Yoann Dufresne, Blaise Li, Etienne Kornobis, Frederic Lemoine, Nicolas Maillet, Amandine Perrin, Nicolas Traut, Bertrand Néron, Thomas Cokelaer
BioConvert: a comprehensive format converter for life sciences. NAR genomics and bioinformatics 5 (3) (2023)
Lena Maria Hackl, Amit Fenn, Zakaria Louadi, Jan Baumbach, Tim Kacprowski, Markus List, Olga Tsoy
Alternative splicing impacts microRNA regulation within coding regions. NAR genomics and bioinformatics 5 (3) (2023)
Carlos D Ordóñez, Carmen Mayoral-Campos, Conceição Egas, Modesto Redrejo-Rodríguez
A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences. NAR genomics and bioinformatics 5 (3) (2023)
Jessica Severin, Saumya Agrawal, Jordan A Ramilowski, Ruslan Deviatiiarov, Jay W Shin, Piero Carninci, Michiel J L de Hoon
ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data. NAR genomics and bioinformatics 5 (3) (2023)
Jianqiang Sun, Moeko Okada, Toshiaki Tameshige, Rie Shimizu-Inatsugi, Reiko Akiyama, Atsushi J Nagano, Jun Sese, Kentaro K Shimizu
A low-coverage 3' RNA-seq to detect homeolog expression in polyploid wheat. NAR genomics and bioinformatics 5 (3) (2023)
Lieke Michielsen, Mohammad Lotfollahi, Daniel Strobl, Lisa Sikkema, Marcel J T Reinders, Fabian Joachim Theis, Ahmed Mahfouz
Single-cell reference mapping to construct and extend cell-type hierarchies. NAR genomics and bioinformatics 5 (3) (2023)
Aziz Fouché, Loïc Chadoutaud, Olivier Delattre, Andrei Zinovyev
Transmorph : a unifying computational framework for modular single-cell RNA-seq data integration. NAR genomics and bioinformatics 5 (3) (2023)
Sergio Arredondo-Alonso, Rebecca A Gladstone, Anna K Pöntinen, João A Gama, Anita C Schürch, Val F Lanza, Pål Jarle Johnsen, Ørjan Samuelsen, Gerry Q Tonkin-Hill, Jukka Corander
Mge-cluster: a reference-free approach for typing bacterial plasmids. NAR genomics and bioinformatics 5 (3) (2023)
Manish Yadav, Martijn Zuiddam, Helmut Schiessel
The role of transcript regions and amino acid choice in nucleosome positioning. NAR genomics and bioinformatics 5 (3) (2023)
Christopher Klapproth, Siegfried Zötzsche, Felix Kühnl, Jörg Fallmann, Peter F Stadler, Sven Findeiß
Tailored machine learning models for functional RNA detection in genome-wide screens. NAR genomics and bioinformatics 5 (3) (2023)
Lotte Vanheer, Federica Fantuzzi, San Kit To, Andrea Schiavo, Matthias Van Haele, Tessa Ostyn, Tine Haesen, Xiaoyan Yi, Adrian Janiszewski, Joel Chappell, Adrien Rihoux, Toshiaki Sawatani, Tania Roskams, Francois Pattou, Julie Kerr-Conte, Gabriel Santos, Vincent Pasque
Inferring regulators of cell identity in the human adult pancreas. NAR genomics and bioinformatics 5 (3) (2023)
Yazdan Asgari, Pierre-Emmanuel Sugier, Taban Baghfalaki, Elise Lucotte, Mojgan Karimi, Mohammed Sedki, Amélie Ngo, Benoit Liquet, Thérèse Truong
GCPBayes pipeline: a tool for exploring pleiotropy at the gene level. NAR genomics and bioinformatics 5 (3) (2023)

volume 5, number 4, 2023

Arnaud Liehrmann, Etienne Delannoy, Alexandra Launay-Avon, Elodie Gilbault, Olivier Loudet, Benoît Castandet, Guillem J Rigaill
DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection. NAR genomics and bioinformatics 5 (4) (2023)
Alexander P Gultyaev, Celine Koster, Diederik Cames van Batenburg, Tom Sistermans, Niels van Belle, Daan Vijfvinkel, Andreas Roussis
Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements. NAR genomics and bioinformatics 5 (4) (2023)
Benjamin Spiegl, Faruk Kapidzic, Sebastian Röner, Martin Kircher, Michael R Speicher
GCparagon: evaluating and correcting GC biases in cell-free DNA at the fragment level. NAR genomics and bioinformatics 5 (4) (2023)
Thibault Poinsignon, Mélina Gallopin, Pierre Grognet, Fabienne Malagnac, Gaëlle Lelandais, Pierre Poulain
3D models of fungal chromosomes to enhance visual integration of omics data. NAR genomics and bioinformatics 5 (4) (2023)
Florian Haselbeck, Maura John, Yuqi Zhang, Jonathan Pirnay, Juan Pablo Fuenzalida-Werner, Rubén D Costa, Dominik G Grimm
Superior protein thermophilicity prediction with protein language model embeddings. NAR genomics and bioinformatics 5 (4) (2023)
Di Xiao, Michael Lin, Chunlei Liu, Thomas A Geddes, James G Burchfield, Benjamin L Parker, Sean J Humphrey, Pengyi Yang
SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data. NAR genomics and bioinformatics 5 (4) (2023)
Felix G Teufel, Magnús Halldór Gíslason, José Juan Almagro Armenteros, Alexander Rosenberg Johansen, Ole Winther, Henrik Nielsen
GraphPart: homology partitioning for biological sequence analysis. NAR genomics and bioinformatics 5 (4) (2023)
Rona Merdler-Rabinowicz, David Gorelik, Jiwoon Park, Cem Meydan, Jonathan Foox, Miriam Karmon, Hillel S Roth, Roni Cohen-Fultheim, Galit Shohat-Ophir, Eli Eisenberg, Lipika R Pal, Christopher E Mason, Erez Y Levanon
Elevated A-to-I RNA editing in COVID-19 infected individuals. NAR genomics and bioinformatics 5 (4) (2023)
Felix Brechtmann, Thibault Bechtler, Shubhankar Londhe, Christian Mertes, Julien Gagneur
Evaluation of input data modality choices on functional gene embeddings. NAR genomics and bioinformatics 5 (4) (2023)
Georg Back, Dirk Walther
Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility. NAR genomics and bioinformatics 5 (4) (2023)
Cyril Kurylo, Cervin Guyomar, Sylvain Foissac, Sarah Djebali
TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data. NAR genomics and bioinformatics 5 (4) (2023)
Giovanni Scala, Susanna Ambrosio, Margherita Menna, Francesca Gorini, Carmen Caiazza, Marcus S Cooke, Barbara Majello, Stefano Amente
Accumulation of 8-oxodG within the human mitochondrial genome positively associates with transcription. NAR genomics and bioinformatics 5 (4) (2023)
Qingbo S Wang, Ryuya Edahiro, Ho Namkoong, Takanori Hasegawa, Yuya Shirai, Kyuto Sonehara, null null, Atsushi Kumanogoh, Makoto Ishii, Ryuji Koike, Akinori Kimura, Seiya Imoto, Satoru Miyano, Seishi Ogawa, Takanori Kanai, Koichi Fukunaga, Yukinori Okada
Estimating gene-level false discovery probability improves eQTL statistical fine-mapping precision. NAR genomics and bioinformatics 5 (4) (2023)
Angbaji Suo, Jun Yang, Chunyi Mao, Wanran Li, Xingwang Wu, Wenping Xie, Zhengan Yang, Shiyong Guo, Binglian Zheng, Yun Zheng
Phased secondary small interfering RNAs in Camellia sinensis var. assamica . NAR genomics and bioinformatics 5 (4) (2023)
George Howitt, Yuzhou Feng, Lucas Tobar, Dane Vassiliadis, Peter Hickey, Mark A Dawson, Sarath Ranganathan, Shivanthan Shanthikumar, Melanie Neeland, Jovana Maksimovic, Alicia Oshlack
Benchmarking single-cell hashtag oligo demultiplexing methods. NAR genomics and bioinformatics 5 (4) (2023)
Sneider Alexander Gutierrez Guarnizo, Morgana K Kellogg, Sarah C Miller, Elena B Tikhonova, Zemfira N Karamysheva, Andrey L Karamyshev
Pathogenic signal peptide variants in the human genome. NAR genomics and bioinformatics 5 (4) (2023)
Gabija Kavaliauskaite, Jesper Grud Skat Madsen
Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops. NAR genomics and bioinformatics 5 (4) (2023)
Shanika L Amarasinghe, Phil Yang, Oliver Voogd, Haoyu Yang, Mei R M Du, Shian Su, Daniel V Brown, Jafar S Jabbari, Rory Bowden, Matthew E Ritchie
scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor. NAR genomics and bioinformatics 5 (4) (2023)
Jasper Braun, Rafik Neme, Yi Feng, Laura F Landweber, Nataša Jonoska
SDRAP for annotating scrambled or rearranged genomes. NAR genomics and bioinformatics 5 (4) (2023)