NAR genomics and bioinformatics

Keyphrases

Publications

volume 6, number 3, 2024

Adam M B Allen, Anthony Maxwell
Phylogenetic distribution of DNA topoisomerase VI and its distinction from SPO11. NAR genomics and bioinformatics 6 (3) (2024)
Elsa Claude, Mickaël Leclercq, Patricia Thébault, Arnaud Droit, Raluca Uricaru
Optimizing hybrid ensemble feature selection strategies for transcriptomic biomarker discovery in complex diseases. NAR genomics and bioinformatics 6 (3) (2024)
Montserrat Corominas, Tomàs Marquès-Bonet, Miquel A Arnedo, Mònica Bayés, Jordina Belmonte, Hector Escrivà, Rosa Fernández, Toni Gabaldon, Teresa Garnatje, Josep Germain, Manel Niell, Ferran Palero, Joan Pons, Pere Puigdomènech, The Catalan Initiative For The Earth BioGenome Project, null null, Vanesa Arroyo, Cristian Cuevas-Caballé, Joan Ferrer Obiol, Ivo Gut, Marta Gut, Oriane Hidalgo, Guillem Izquierdo-Arànega, Laia Pérez-Sorribes, Emilio Righi, Marta Riutort, Joan Vallès, Julio Rozas, Tyler Alioto, Roderic Guigó
The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics. NAR genomics and bioinformatics 6 (3) (2024)
Benjamin A Story, Lars Velten, Gregor Mönke, Ahrmad Annan, Lars M Steinmetz
Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants. NAR genomics and bioinformatics 6 (3) (2024)
Xenia Lainscsek, Leila Taher
ENT3C: an entropy-based similarity measure for Hi-C and micro-C derived contact matrices. NAR genomics and bioinformatics 6 (3) (2024)
George Marchment, Bryan Brancotte, Marie Schmit, Frederic Lemoine, Sarah Cohen-Boulakia
BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization. NAR genomics and bioinformatics 6 (3) (2024)
Vladimir V Raditsa, Anton V Tsukanov, Anton G Bogomolov, Victor G Levitsky
Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data. NAR genomics and bioinformatics 6 (3) (2024)
Diego Forni, Uberto Pozzoli, Alessandra Mozzi, Rachele Cagliani, Manuela Sironi
Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures. NAR genomics and bioinformatics 6 (3) (2024)
Jose Gavalda-Garcia, David Bickel, Joel Roca-Martinez, Daniele Raimondi, Gabriele Orlando, Wim F Vranken
Data-driven probabilistic definition of the low energy conformational states of protein residues. NAR genomics and bioinformatics 6 (3) (2024)
Nathan J LeRoy, Jason P Smith, Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Donald E Brown, Aidong Zhang, Nathan C Sheffield
Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings. NAR genomics and bioinformatics 6 (3) (2024)
Bo Wang, Kapeel Chougule, Yinping Jiao, Andrew Olson, Vivek Kumar, Nicholas Gladman, Jian Huang, Victor Llaca, Kevin Fengler, Xuehong Wei, Liya Wang, Xiaofei Wang, Michael Regulski, Jorg Drenkow, Thomas Gingeras, Chad Hayes, J Scott Armstrong, Yinghua Huang, Zhanguo Xin, Doreen H Ware
High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436. NAR genomics and bioinformatics 6 (3) (2024)
Israel Barrios-Núñez, Gemma I Martínez-Redondo, Patricia Medina-Burgos, Ildefonso Cases, Rosa Fernández, Ana M Rojas
Decoding functional proteome information in model organisms using protein language models. NAR genomics and bioinformatics 6 (3) (2024)
Alexander J Ritter, Andrew Wallace, Neda Ronaghi, Jeremy R Sanford
junctionCounts: comprehensive alternative splicing analysis and prediction of isoform-level impacts to the coding sequence. NAR genomics and bioinformatics 6 (3) (2024)
Tamim Abdelaal, Laurens M Grossouw, Ronald Jeroen Pasterkamp, Boudewijn P F Lelieveldt, Marcel J T Reinders, Ahmed Mahfouz
SIRV: spatial inference of RNA velocity at the single-cell resolution. NAR genomics and bioinformatics 6 (3) (2024)
Bixuan Wang, Stephen M Mount
Latent Dirichlet allocation mixture models for nucleotide sequence analysis. NAR genomics and bioinformatics 6 (3) (2024)
Giulia Calia, Alessandro Cestaro, Hannes Schuler, Katrin Janik, Claudio Donati, Mirko Moser, Silvia Bottini
Definition of the effector landscape across 13 phytoplasma proteomes with LEAPH and EffectorComb. NAR genomics and bioinformatics 6 (3) (2024)
Giulia Calia, Alessandro Cestaro, Hannes Schuler, Katrin Janik, Claudio Donati, Mirko Moser, Silvia Bottini
Definition of the effector landscape across 13 phytoplasma proteomes with LEAPH and EffectorComb. NAR genomics and bioinformatics 6 (3) (2024)
Maximilian Seege, Erich Schöls, Lars Barquist
s CIRCLE-An interactive visual exploration tool for single cell RNA-Seq data. NAR genomics and bioinformatics 6 (3) (2024)
Chenguang Zhao, Tong Liu, Zheng Wang
PANDA-3D: protein function prediction based on AlphaFold models. NAR genomics and bioinformatics 6 (3) (2024)
Konstantina Kitsou, Aris Katzourakis, Gkikas Magiorkinis
Limitations of current high-throughput sequencing technologies lead to biased expression estimates of endogenous retroviral elements. NAR genomics and bioinformatics 6 (3) (2024)
Konstantina Kitsou, Aris Katzourakis, Gkikas Magiorkinis
Limitations of current high-throughput sequencing technologies lead to biased expression estimates of endogenous retroviral elements. NAR genomics and bioinformatics 6 (3) (2024)
Nathan J LeRoy, Jason P Smith, Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Donald E Brown, Aidong Zhang, Nathan C Sheffield
Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings. NAR genomics and bioinformatics 6 (3) (2024)
Venkatesh Kamaraj, Himanshu Sinha
SCI-VCF: a cross-platform GUI solution to summarize, compare, inspect and visualize the variant call format. NAR genomics and bioinformatics 6 (3) (2024)
Emily R Crossley, Larisa Fedorova, Oleh A Mulyar, Ryan Freeman, Sadik Khuder, Alexei Fedorov
Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing. NAR genomics and bioinformatics 6 (3) (2024)
Amanda Araújo Serrão de Andrade, Otávio José Brustolini, Marco Grivet, Carlos G Schrago, Ana Tereza Ribeiro de Vasconcelos
Predicting novel mosquito-associated viruses from metatranscriptomic dark matter. NAR genomics and bioinformatics 6 (3) (2024)
Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Nathan J LeRoy, Aidong Zhang, Nathan C Sheffield
Methods for evaluating unsupervised vector representations of genomic regions. NAR genomics and bioinformatics 6 (3) (2024)
Xenia Lainscsek, Leila Taher
ENT3C: an entropy-based similarity measure for Hi-C and micro-C derived contact matrices. NAR genomics and bioinformatics 6 (3) (2024)
Veerendra P Gadekar, Alexander Welford Munk, Milad Miladi, Alexander Junge, Rolf Backofen, Stefan Ernst Seemann, Jan Gorodkin
Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites. NAR genomics and bioinformatics 6 (3) (2024)
Veerendra P Gadekar, Alexander Welford Munk, Milad Miladi, Alexander Junge, Rolf Backofen, Stefan Ernst Seemann, Jan Gorodkin
Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites. NAR genomics and bioinformatics 6 (3) (2024)
Bixuan Wang, Stephen M Mount
Latent Dirichlet allocation mixture models for nucleotide sequence analysis. NAR genomics and bioinformatics 6 (3) (2024)
Guangtao Zheng, Julia Rymuza, Erfaneh Gharavi, Nathan J LeRoy, Aidong Zhang, Nathan C Sheffield
Methods for evaluating unsupervised vector representations of genomic regions. NAR genomics and bioinformatics 6 (3) (2024)
Juris Viksna, Karlis Cerans, Lelde Lace, Gatis Melkus
Characterizing behavioural differentiation in gene regulatory networks with representation graphs. NAR genomics and bioinformatics 6 (3) (2024)
Chenguang Zhao, Tong Liu, Zheng Wang
PANDA-3D: protein function prediction based on AlphaFold models. NAR genomics and bioinformatics 6 (3) (2024)
Bo Wang, Kapeel Chougule, Yinping Jiao, Andrew Olson, Vivek Kumar, Nicholas Gladman, Jian Huang, Victor Llaca, Kevin Fengler, Xuehong Wei, Liya Wang, Xiaofei Wang, Michael Regulski, Jorg Drenkow, Thomas Gingeras, Chad Hayes, J Scott Armstrong, Yinghua Huang, Zhanguo Xin, Doreen H Ware
High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436. NAR genomics and bioinformatics 6 (3) (2024)
Adam M B Allen, Anthony Maxwell
Phylogenetic distribution of DNA topoisomerase VI and its distinction from SPO11. NAR genomics and bioinformatics 6 (3) (2024)
George Marchment, Bryan Brancotte, Marie Schmit, Frederic Lemoine, Sarah Cohen-Boulakia
BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization. NAR genomics and bioinformatics 6 (3) (2024)
Diego Forni, Uberto Pozzoli, Alessandra Mozzi, Rachele Cagliani, Manuela Sironi
Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures. NAR genomics and bioinformatics 6 (3) (2024)
Tamim Abdelaal, Laurens M Grossouw, Ronald Jeroen Pasterkamp, Boudewijn P F Lelieveldt, Marcel J T Reinders, Ahmed Mahfouz
SIRV: spatial inference of RNA velocity at the single-cell resolution. NAR genomics and bioinformatics 6 (3) (2024)
Montserrat Corominas, Tomàs Marquès-Bonet, Miquel A Arnedo, Mònica Bayés, Jordina Belmonte, Hector Escrivà, Rosa Fernández, Toni Gabaldon, Teresa Garnatje, Josep Germain, Manel Niell, Ferran Palero, Joan Pons, Pere Puigdomènech, The Catalan Initiative For The Earth BioGenome Project, null null, Vanesa Arroyo, Cristian Cuevas-Caballé, Joan Ferrer Obiol, Ivo Gut, Marta Gut, Oriane Hidalgo, Guillem Izquierdo-Arànega, Laia Pérez-Sorribes, Emilio Righi, Marta Riutort, Joan Vallès, Julio Rozas, Tyler Alioto, Roderic Guigó
The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics. NAR genomics and bioinformatics 6 (3) (2024)
Vladimir V Raditsa, Anton V Tsukanov, Anton G Bogomolov, Victor G Levitsky
Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data. NAR genomics and bioinformatics 6 (3) (2024)
Maximilian Seege, Erich Schöls, Lars Barquist
s CIRCLE-An interactive visual exploration tool for single cell RNA-Seq data. NAR genomics and bioinformatics 6 (3) (2024)
Juris Viksna, Karlis Cerans, Lelde Lace, Gatis Melkus
Characterizing behavioural differentiation in gene regulatory networks with representation graphs. NAR genomics and bioinformatics 6 (3) (2024)
Venkatesh Kamaraj, Himanshu Sinha
SCI-VCF: a cross-platform GUI solution to summarize, compare, inspect and visualize the variant call format. NAR genomics and bioinformatics 6 (3) (2024)
Jose Gavalda-Garcia, David Bickel, Joel Roca-Martinez, Daniele Raimondi, Gabriele Orlando, Wim F Vranken
Data-driven probabilistic definition of the low energy conformational states of protein residues. NAR genomics and bioinformatics 6 (3) (2024)
Alexander J Ritter, Andrew Wallace, Neda Ronaghi, Jeremy R Sanford
junctionCounts: comprehensive alternative splicing analysis and prediction of isoform-level impacts to the coding sequence. NAR genomics and bioinformatics 6 (3) (2024)
Benjamin A Story, Lars Velten, Gregor Mönke, Ahrmad Annan, Lars M Steinmetz
Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants. NAR genomics and bioinformatics 6 (3) (2024)
Elsa Claude, Mickaël Leclercq, Patricia Thébault, Arnaud Droit, Raluca Uricaru
Optimizing hybrid ensemble feature selection strategies for transcriptomic biomarker discovery in complex diseases. NAR genomics and bioinformatics 6 (3) (2024)
Israel Barrios-Núñez, Gemma I Martínez-Redondo, Patricia Medina-Burgos, Ildefonso Cases, Rosa Fernández, Ana M Rojas
Decoding functional proteome information in model organisms using protein language models. NAR genomics and bioinformatics 6 (3) (2024)
Emily R Crossley, Larisa Fedorova, Oleh A Mulyar, Ryan Freeman, Sadik Khuder, Alexei Fedorov
Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing. NAR genomics and bioinformatics 6 (3) (2024)
Amanda Araújo Serrão de Andrade, Otávio José Brustolini, Marco Grivet, Carlos G Schrago, Ana Tereza Ribeiro de Vasconcelos
Predicting novel mosquito-associated viruses from metatranscriptomic dark matter. NAR genomics and bioinformatics 6 (3) (2024)