Works matching IS 2047217X AND DT 2023 AND VI 12 AND IP 1

Results: 112

DrugSim2DR: systematic prediction of drug functional similarities in the context of specific disease for drug repurposing.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad104

By:

Wu, Jiashuo;
Li, Ji;
He, Yalan;
Huang, Junling;
Zhao, Xilong;
Pan, Bingyue;
Wang, Yahui;
Cheng, Liang;
Han, Junwei

Publication type:

Article

A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad102

By:

Chen, Stephanie H;
Martino, Alyssa M;
Luo, Zhenyan;
Schwessinger, Benjamin;
Jones, Ashley;
Tolessa, Tamene;
Bragg, Jason G;
Tobias, Peri A;
Edwards, Richard J

Publication type:

Article

AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad101

By:

Silva, Jorge M;
Qi, Weihong;
Pinho, Armando J;
Pratas, Diogo

Publication type:

Article

DriverMP enables improved identification of cancer driver genes.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad106

By:

Liu, Yangyang;
Han, Jiyun;
Kong, Tongxin;
Xiao, Nannan;
Mei, Qinglin;
Liu, Juntao

Publication type:

Article

Imputation method for single-cell RNA-seq data using neural topic model.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad098

By:

Qi, Yueyang;
Han, Shuangkai;
Tang, Lin;
Liu, Lin

Publication type:

Article

MLcps: machine learning cumulative performance score for classification problems.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad108

By:

Akshay, Akshay;
Abedi, Masoud;
Shekarchizadeh, Navid;
Burkhard, Fiona C;
Katoch, Mitali;
Bigger-Allen, Alex;
Adam, Rosalyn M;
Monastyrskaya, Katia;
Gheinani, Ali Hashemi

Publication type:

Article

Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad100

By:

Cosma, Bianca-Maria;
Shirali Hossein Zade, Ramin;
Jordan, Erin Noel;
van Lent, Paul;
Peng, Chengyao;
Pillay, Stephanie;
Abeel, Thomas

Publication type:

Article

Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad105

By:

Wang, Jing;
Xu, Qing;
Chen, Min;
Chen, Yang;
Wang, Chunde;
Chen, Nansheng

Publication type:

Article

Variability analysis of LC-MS experimental factors and their impact on machine learning.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad096

By:

Rehfeldt, Tobias Greisager;
Krawczyk, Konrad;
Echers, Simon Gregersen;
Marcatili, Paolo;
Palczynski, Pawel;
Röttger, Richard;
Schwämmle, Veit

Publication type:

Article

Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad095

By:

Li, Zihao;
Sun, Yunong;
Ding, Lingjun;
Yang, Jing;
Huang, Jinrong;
Cheng, Mengnan;
Wu, Liang;
Zhuang, Zhenkun;
Chen, Cheng;
Huang, Yunqi;
Zhu, Zhiyong;
Jiang, Siyuan;
Huang, Fubaoqian;
Wang, Chunqing;
Liu, Shiping;
Liu, Longqi;
Lei, Ying

Publication type:

Article

Euler characteristic curves and profiles: a stable shape invariant for big data problems.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad094

By:

Dłotko, Paweł;
Gurnari, Davide

Publication type:

Article

Finding haplotypic signatures in proteins.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad093

By:

Vašíček, Jakub;
Skiadopoulou, Dafni;
Kuznetsova, Ksenia G;
Wen, Bo;
Johansson, Stefan;
Njølstad, Pål R;
Bruckner, Stefan;
Käll, Lukas;
Vaudel, Marc

Publication type:

Article

Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad092

By:

Taniguti, Cristiane Hayumi;
Taniguti, Lucas Mitsuo;
Amadeu, Rodrigo Rampazo;
Lau, Jeekin;
Gesteira, Gabriel de Siqueira;
Oliveira, Thiago de Paula;
Ferreira, Getulio Caixeta;
Pereira, Guilherme da Silva;
Byrne, David;
Mollinari, Marcelo;
Riera-Lizarazu, Oscar;
Garcia, Antonio Augusto Franco

Publication type:

Article

Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad091

By:

Umu, Sinan U;
Rapp Vander-Elst, Karoline;
Karlsen, Victoria T;
Chouliara, Manto;
Bækkevold, Espen Sønderaal;
Jahnsen, Frode Lars;
Domanska, Diana

Publication type:

Article

The chromosome-level genome of Chinese praying mantis Tenodera sinensis (Mantodea: Mantidae) reveals its biology as a predator.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad090

By:

Yuan, Ruizhong;
Zheng, Boying;
Li, Zekai;
Ma, Xingzhou;
Shu, Xiaohan;
Qu, Qiuyu;
Ye, Xiqian;
Li, Sheng;
Tang, Pu;
Chen, Xuexin

Publication type:

Article

MetGENE: gene-centric metabolomics information retrieval tool.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad089

By:

Srinivasan, Sumana;
Maurya, Mano R;
Ramachandran, Srinivasan;
Fahy, Eoin;
Subramaniam, Shankar

Publication type:

Article

Ontology-driven analysis of marine metagenomics: what more can we learn from our data?

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad088

By:

Blumberg, Kai;
Miller, Matthew;
Ponsero, Alise;
Hurwitz, Bonnie

Publication type:

Article

epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad087

By:

Nikolaienko, Oleksii;
Lønning, Per Eystein;
Knappskog, Stian

Publication type:

Article

Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad086

By:

Aso, Hirofumi;
Ito, Jumpei;
Ozaki, Haruka;
Kashima, Yukie;
Suzuki, Yutaka;
Koyanagi, Yoshio;
Sato, Kei

Publication type:

Article

Computational prediction of human deep intronic variation.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad085

By:

Barbosa, Pedro;
Savisaar, Rosina;
Carmo-Fonseca, Maria;
Fonseca, Alcides

Publication type:

Article

A community resource to mass explore the wheat grain proteome and its application to the late-maturity alpha-amylase (LMA) problem.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad084

By:

Vincent, Delphine;
Bui, AnhDuyen;
Ezernieks, Vilnis;
Shahinfar, Saleh;
Luke, Timothy;
Ram, Doris;
Rigas, Nicholas;
Panozzo, Joe;
Rochfort, Simone;
Daetwyler, Hans;
Hayden, Matthew

Publication type:

Article

Machine learning–based feature selection to search stable microbial biomarkers: application to inflammatory bowel disease.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad083

By:

Lee, Youngro;
Cappellato, Marco;
Di Camillo, Barbara

Publication type:

Article

SpheroScan: a user-friendly deep learning tool for spheroid image analysis.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad082

By:

Akshay, Akshay;
Katoch, Mitali;
Abedi, Masoud;
Shekarchizadeh, Navid;
Besic, Mustafa;
Burkhard, Fiona C;
Bigger-Allen, Alex;
Adam, Rosalyn M;
Monastyrskaya, Katia;
Gheinani, Ali Hashemi

Publication type:

Article

Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad081

By:

Hazelaar, Daan M;
van Riet, Job;
Hoogstrate, Youri;
van de Werken, Harmen J G

Publication type:

Article

GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad080

By:

Kilar, Agata M;
Fajkus, Petr;
Fajkus, Jiří

Publication type:

Article

Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad079

By:

Cui, Jinteng;
Zhu, Yunke;
Du, Hai;
Liu, Zhenhua;
Shen, Siqian;
Wang, Tongxin;
Cui, Wenwen;
Zhang, Rong;
Jiang, Sanjie;
Wu, Yanmin;
Gu, Xiaofeng;
Yu, Hao;
Liang, Zhe

Publication type:

Article

metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad078

By:

Zafeiropoulos, Haris;
Beracochea, Martin;
Ninidakis, Stelios;
Exter, Katrina;
Potirakis, Antonis;
De Moro, Gianluca;
Richardson, Lorna;
Corre, Erwan;
Machado, João;
Pafilis, Evangelos;
Kotoulas, Georgios;
Santi, Ioulia;
Finn, Robert D;
Cox, Cymon J;
Pavloudi, Christina

Publication type:

Article

Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad077

By:

Qi, Haigang;
Cong, Rihao;
Wang, Yanjun;
Li, Li;
Zhang, Guofan

Publication type:

Article

Correction to: KOREF_S1: Phased, parental trio-binned Korean reference genome using long reads and Hi-C sequencing methods.

Published in:: 2023
Publication type:: Correction Notice

Allele-specific regulatory effects on the pig transcriptome.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad076

By:

Lin, Yu;
Li, Jing;
Chen, Li;
Bai, Jingyi;
Zhang, Jiaman;
Wang, Yujie;
Liu, Pengliang;
Long, Keren;
Ge, Liangpeng;
Jin, Long;
Gu, Yiren;
Li, Mingzhou

Publication type:

Article

simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad074

By:

Kanduri, Chakravarthi;
Scheffer, Lonneke;
Pavlović, Milena;
Rand, Knut Dagestad;
Chernigovskaya, Maria;
Pirvandy, Oz;
Yaari, Gur;
Greiff, Victor;
Sandve, Geir K

Publication type:

Article

Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad073

By:

Fu, Yunfan;
Bedő, Justin;
Papenfuss, Anthony T;
Rubin, Alan F

Publication type:

Article

A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei).

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad072

By:

R. N. Ferreira, João Gabriel;
A. Americo, Juliana;
L. A. S. do Amaral, Danielle;
Sendim, Fábio;
R. da Cunha, Yasmin;
Programme, Tree of Life;
Blaxter, Mark;
Uliano-Silva, Marcela;
de F. Rebelo, Mauro

Publication type:

Article

Confound-leakage: confound removal in machine learning leads to leakage.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad071

By:

Hamdan, Sami;
Love, Bradley C;
von Polier, Georg G;
Weis, Susanne;
Schwender, Holger;
Eickhoff, Simon B;
Patil, Kaustubh R

Publication type:

Article

Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad075

By:

Herráez-Pérez, Ana;
Pardos-Blas, José Ramón;
Afonso, Carlos M L;
Tenorio, Manuel J;
Zardoya, Rafael

Publication type:

Article

Container Profiler: Profiling resource utilization of containerized big data pipelines.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad069

By:

Hoang, Varik;
Hung, Ling-Hong;
Perez, David;
Deng, Huazeng;
Schooley, Raymond;
Arumilli, Niharika;
Yeung, Ka Yee;
Lloyd, Wes

Publication type:

Article

BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad062

By:

Piñeiro, César;
Pichel, Juan C

Publication type:

Article

The founding charter of the Omic Biodiversity Observation Network (Omic BON).

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad068

By:

Meyer, Raïssa;
Davies, Neil;
Pitz, Kathleen J;
Meyer, Chris;
Samuel, Robyn;
Anderson, Jane;
Appeltans, Ward;
Barker, Katharine;
Chavez, Francisco P;
Duffy, J Emmett;
Goodwin, Kelly D;
Hudson, Maui;
Hunter, Margaret E;
Karstensen, Johannes;
Laney, Christine M;
Leinen, Margaret;
Mabee, Paula;
Macklin, James A;
Muller-Karger, Frank;
Pade, Nicolas

Publication type:

Article

Correction to: Scientists without borders: lessons from Ukraine.

Published in:: GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad066
Publication type:: Article

Suggesting disease associations for overlooked metabolites using literature from metabolic neighbors.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad065

By:

Delmas, Maxime;
Filangi, Olivier;
Duperier, Christophe;
Paulhe, Nils;
Vinson, Florence;
Rodriguez-Mier, Pablo;
Giacomoni, Franck;
Jourdan, Fabien;
Frainay, Clément

Publication type:

Article

Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad064

By:

Lötter, Anneri;
Duong, Tuan A;
Candotti, Julia;
Mizrachi, Eshchar;
Wegrzyn, Jill L;
Myburg, Alexander A

Publication type:

Article

Chromosome-level genome and recombination map of the male buffalo.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad063

By:

Wang, Xiaobo;
Li, Zhipeng;
Feng, Tong;
Luo, Xier;
Xue, Lintao;
Mao, Chonghui;
Cui, Kuiqing;
Li, Hui;
Huang, Jieping;
Huang, Kongwei;
Rehman, Saif-ur;
Shi, Deshun;
Wu, Dongdong;
Ruan, Jue;
Liu, Qingyou

Publication type:

Article

ARA: a flexible pipeline for automated exploration of NCBI SRA datasets.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad067

By:

Maurya, Anand;
Szymanski, Maciej;
Karlowski, Wojciech M

Publication type:

Article

Genome resequencing reveals independent domestication and breeding improvement of naked oat.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad061

By:

Nan, Jinsheng;
Ling, Yu;
An, Jianghong;
Wang, Ting;
Chai, Mingna;
Fu, Jun;
Wang, Gaochao;
Yang, Cai;
Yang, Yan;
Han, Bing

Publication type:

Article

Health record hiccups—5,526 real-world time series with change points labelled by crowdsourced visual inspection.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad060

By:

Quan, T Phuong;
Lacey, Ben;
Peto, Tim E A;
Walker, A Sarah

Publication type:

Article

GADMA2: more efficient and flexible demographic inference from genetic data.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad059

By:

Noskova, Ekaterina;
Abramov, Nikita;
Iliutkin, Stanislav;
Sidorin, Anton;
Dobrynin, Pavel;
Ulyantsev, Vladimir I

Publication type:

Article

SODAR: managing multiomics study data and metadata.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad052

By:

Nieminen, Mikko;
Stolpe, Oliver;
Kuhring, Mathias;
Weiner, January;
Pett, Patrick;
Beule, Dieter;
Holtgrewe, Manuel

Publication type:

Article

A new haplotype-resolved turkey genome to enable turkey genetics and genomics research.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad051

By:

Barros, Carolina P;
Derks, Martijn F L;
Mohr, Jeff;
Wood, Benjamin J;
Crooijmans, Richard P M A;
Megens, Hendrik-Jan;
Bink, Marco C A M;
Groenen, Martien A M

Publication type:

Article

Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad058

By:

Mendes de Farias, Tarcisio;
Wollbrett, Julien;
Robinson-Rechavi, Marc;
Bastian, Frederic

Publication type:

Article

Metaphor—A workflow for streamlined assembly and binning of metagenomes.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad055

By:

Salazar, Vinícius W;
Shaban, Babak;
Quiroga, Maria del Mar;
Turnbull, Robert;
Tescari, Edoardo;
Rossetto Marcelino, Vanessa;
Verbruggen, Heroen;
Lê Cao, Kim-Anh

Publication type:

Article