SUBJECTS : Open Data | Big Data | Life Sciences | Biomedicin
GigaScience: 2022, vol: 12, issue:
- 1)- . Correction to: KOREF_S1: Phased, parental trio-binned Korean reference genome using long reads and Hi-C sequencing methods. GigaScience. 2022, 12:
Cited : 0Read More - 2)- Agata M Kilar, Petr Fajkus, Jiří Fajkus. GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context. GigaScience. 2022, 12: Cited : 0Read More
- 3)- Haigang Qi, Rihao Cong, Yanjun Wang, Li Li, Guofan Zhang. Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas. GigaScience. 2022, 12: Cited : 6Read More
- 4)- Sami Hamdan, Bradley C Love, Georg G von Polier, Susanne Weis, Holger Schwender, Simon B Eickhoff, Kaustubh R Patil. Confound-leakage: confound removal in machine learning leads to leakage. GigaScience. 2022, 12: Cited : 7Read More
- 5)- Jinteng Cui, Yunke Zhu, Hai Du, Zhenhua Liu, Siqian Shen, Tongxin Wang, Wenwen Cui, Rong Zhang, Sanjie Jiang, Yanmin Wu, Xiaofeng Gu, Hao Yu, Zhe Liang. Chromosome-level reference genome of tetraploid Isoetes sinensis provides insights into evolution and adaption of lycophytes. GigaScience. 2022, 12: Cited : 0Read More
- 6)- João Gabriel R N Ferreira, Juliana A Americo, Danielle L A S do Amaral, Fábio Sendim, Yasmin R da Cunha, , Mark Blaxter, Marcela Uliano-Silva, Mauro de F Rebelo. A chromosome-level assembly supports genome-wide investigation of the DMRT gene family in the golden mussel (Limnoperna fortunei). GigaScience. 2022, 12: Cited : 0Read More
- 7)- Yu Lin, Jing Li, Li Chen, Jingyi Bai, Jiaman Zhang, Yujie Wang, Pengliang Liu, Keren Long, Liangpeng Ge, Long Jin, Yiren Gu, Mingzhou Li. Allele-specific regulatory effects on the pig transcriptome. GigaScience. 2022, 12: Cited : 2Read More
- 8)- Ana Herráez-Pérez, José Ramón Pardos-Blas, Carlos M L Afonso, Manuel J Tenorio, Rafael Zardoya. Chromosome-level genome of the venomous snail Kalloconus canariensis: a valuable model for venomics and comparative genomics. GigaScience. 2022, 12: Cited : 0Read More
- 9)- Yunfan Fu, Justin Bedő, Anthony T Papenfuss, Alan F Rubin. Integrating deep mutational scanning and low-throughput mutagenesis data to predict the impact of amino acid variants. GigaScience. 2022, 12: Cited : 2Read More
- 10)- Maxime Delmas, Olivier Filangi, Christophe Duperier, Nils Paulhe, Florence Vinson, Pablo Rodriguez-Mier, Franck Giacomoni, Fabien Jourdan, Clément Frainay. Suggesting disease associations for overlooked metabolites using literature from metabolic neighbors. GigaScience. 2022, 12: Cited : 0Read More
- 11)- Anneri Lötter, Tuan A Duong, Julia Candotti, Eshchar Mizrachi, Jill L Wegrzyn, Alexander A Myburg. Haplogenome assembly reveals structural variation in Eucalyptus interspecific hybrids. GigaScience. 2022, 12: Cited : 1Read More
- 12)- Raïssa Meyer, Neil Davies, Kathleen J Pitz, Chris Meyer, Robyn Samuel, Jane Anderson, Ward Appeltans, Katharine Barker, Francisco P Chavez, J Emmett Duffy, Kelly D Goodwin, Maui Hudson, Margaret E Hunter, Johannes Karstensen, Christine M Laney, Margaret Leinen, Paula Mabee, James A Macklin, Frank Muller-Karger, Nicolas Pade, Jay Pearlman, Lori Phillips, Pieter Provoost, Ioulia Santi, Dmitry Schigel, Lynn M Schriml, Alice Soccodato, Saara Suominen, Katherine M Thibault, Visotheary Ung, Jodie van . The founding charter of the Omic Biodiversity Observation Network (Omic BON). GigaScience. 2022, 12: Cited : 6Read More
- 13)- Varik Hoang, Ling-Hong Hung, David Perez, Huazeng Deng, Raymond Schooley, Niharika Arumilli, Ka Yee Yeung, Wes Lloyd. Container Profiler: Profiling resource utilization of containerized big data pipelines. GigaScience. 2022, 12: Cited : 0Read More
- 14)- Daan M Hazelaar, Job van Riet, Youri Hoogstrate, Harmen J G van de Werken. Katdetectr: an R/bioconductor package utilizing unsupervised changepoint analysis for robust kataegis detection. GigaScience. 2022, 12: Cited : 2Read More
- 15)- Ekaterina Noskova, Nikita Abramov, Stanislav Iliutkin, Anton Sidorin, Pavel Dobrynin, Vladimir I Ulyantsev. GADMA2: more efficient and flexible demographic inference from genetic data. GigaScience. 2022, 12: Cited : 2Read More
- 16)- Chunyu Ma, Zhihan Zhou, Han Liu, David Koslicki. KGML-xDTD: a knowledge graph-based machine learning framework for drug treatment prediction and mechanism description. GigaScience. 2022, 12: Cited : 3Read More
- 17)- Tarcisio Mendes de Farias, Julien Wollbrett, Marc Robinson-Rechavi, Frederic Bastian. Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience. GigaScience. 2022, 12: Cited : 2Read More
- 18)- Xiaobo Wang, Zhipeng Li, Tong Feng, Xier Luo, Lintao Xue, Chonghui Mao, Kuiqing Cui, Hui Li, Jieping Huang, Kongwei Huang, Saif-Ur Rehman, Deshun Shi, Dongdong Wu, Jue Ruan, Qingyou Liu. Chromosome-level genome and recombination map of the male buffalo. GigaScience. 2022, 12: Cited : 1Read More
- 19)- Anand Maurya, Maciej Szymanski, Wojciech M Karlowski. ARA: a flexible pipeline for automated exploration of NCBI SRA datasets. GigaScience. 2022, 12: Cited : 0Read More
- 20)- . Correction to: Scientists without borders: lessons from Ukraine. GigaScience. 2022, 12: Cited : 0Read More
- 21)- Jinsheng Nan, Yu Ling, Jianghong An, Ting Wang, Mingna Chai, Jun Fu, Gaochao Wang, Cai Yang, Yan Yang, Bing Han. Genome resequencing reveals independent domestication and breeding improvement of naked oat. GigaScience. 2022, 12: Cited : 3Read More
- 22)- Vinícius W Salazar, Babak Shaban, Maria Del Mar Quiroga, Robert Turnbull, Edoardo Tescari, Vanessa Rossetto Marcelino, Heroen Verbruggen, Kim-Anh Lê Cao. Metaphor-A workflow for streamlined assembly and binning of metagenomes. GigaScience. 2022, 12: Cited : 5Read More
- 23)- César Piñeiro, Juan C Pichel. BigSeqKit: a parallel Big Data toolkit to process FASTA and FASTQ files at scale. GigaScience. 2022, 12: Cited : 1Read More
- 24)- T Phuong Quan, Ben Lacey, Tim E A Peto, A Sarah Walker. Health record hiccups-5,526 real-world time series with change points labelled by crowdsourced visual inspection. GigaScience. 2022, 12: Cited : 2Read More
- 25)- Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, Faisal Alquaddoomi, Dongbo Hu, David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene. Hetnet connectivity search provides rapid insights into how biomedical entities are related. GigaScience. 2022, 12: Cited : 1Read More
- 26)- Delphine Vincent, AnhDuyen Bui, Vilnis Ezernieks, Saleh Shahinfar, Timothy Luke, Doris Ram, Nicholas Rigas, Joe Panozzo, Simone Rochfort, Hans Daetwyler, Matthew Hayden. A community resource to mass explore the wheat grain proteome and its application to the late-maturity alpha-amylase (LMA) problem. GigaScience. 2022, 12: Cited : 2Read More
- 27)- Jiashuo Wu, Ji Li, Yalan He, Junling Huang, Xilong Zhao, Bingyue Pan, Yahui Wang, Liang Cheng, Junwei Han. DrugSim2DR: systematic prediction of drug functional similarities in the context of specific disease for drug repurposing. GigaScience. 2022, 12: Cited : 0Read More
- 28)- Stephanie H Chen, Alyssa M Martino, Zhenyan Luo, Benjamin Schwessinger, Ashley Jones, Tamene Tolessa, Jason G Bragg, Peri A Tobias, Richard J Edwards. A high-quality pseudo-phased genome for Melaleuca quinquenervia shows allelic diversity of NLR-type resistance genes. GigaScience. 2022, 12: Cited : 5Read More
- 29)- Yangyang Liu, Jiyun Han, Tongxin Kong, Nannan Xiao, Qinglin Mei, Juntao Liu. DriverMP enables improved identification of cancer driver genes. GigaScience. 2022, 12: Cited : 0Read More
- 30)- Zihao Li, Yunong Sun, Lingjun Ding, Jing Yang, Jinrong Huang, Mengnan Cheng, Liang Wu, Zhenkun Zhuang, Cheng Chen, Yunqi Huang, Zhiyong Zhu, Siyuan Jiang, Fubaoqian Huang, Chunqing Wang, Shiping Liu, Longqi Liu, Ying Lei. Deciphering the distinct transcriptomic and gene regulatory map in adult macaque basal ganglia cells. GigaScience. 2022, 12: Cited : 0Read More
- 31)- Jorge M Silva, Weihong Qi, Armando J Pinho, Diogo Pratas. AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data. GigaScience. 2022, 12: Cited : 0Read More
- 32)- Akshay Akshay, Masoud Abedi, Navid Shekarchizadeh, Fiona C Burkhard, Mitali Katoch, Alex Bigger-Allen, Rosalyn M Adam, Katia Monastyrskaya, Ali Hashemi Gheinani. MLcps: machine learning cumulative performance score for classification problems. GigaScience. 2022, 12: Cited : 4Read More
- 33)- Bianca-Maria Cosma, Ramin Shirali Hossein Zade, Erin Noel Jordan, Paul van Lent, Chengyao Peng, Stephanie Pillay, Thomas Abeel. Evaluating long-read de novo assembly tools for eukaryotic genomes: insights and considerations. GigaScience. 2022, 12: Cited : 3Read More
- 34)- Yueyang Qi, Shuangkai Han, Lin Tang, Lin Liu. Imputation method for single-cell RNA-seq data using neural topic model. GigaScience. 2022, 12: Cited : 1Read More
- 35)- Sumana Srinivasan, Mano R Maurya, Srinivasan Ramachandran, Eoin Fahy, Shankar Subramaniam. MetGENE: gene-centric metabolomics information retrieval tool. GigaScience. 2022, 12: Cited : 1Read More
- 36)- Tobias Greisager Rehfeldt, Konrad Krawczyk, Simon Gregersen Echers, Paolo Marcatili, Pawel Palczynski, Richard Röttger, Veit Schwämmle. Variability analysis of LC-MS experimental factors and their impact on machine learning. GigaScience. 2022, 12: Cited : 3Read More
- 37)- Paweł Dłotko, Davide Gurnari. Euler characteristic curves and profiles: a stable shape invariant for big data problems. GigaScience. 2022, 12: Cited : 1Read More
- 38)- Kai Blumberg, Matthew Miller, Alise Ponsero, Bonnie Hurwitz. Ontology-driven analysis of marine metagenomics: what more can we learn from our data? GigaScience. 2022, 12: Cited : 0Read More
- 39)- Jing Wang, Qing Xu, Min Chen, Yang Chen, Chunde Wang, Nansheng Chen. Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family. GigaScience. 2022, 12: Cited : 0Read More
- 40)- Oleksii Nikolaienko, Per Eystein Lønning, Stian Knappskog. epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data. GigaScience. 2022, 12: Cited : 1Read More
- 41)- Jakub Vašíček, Dafni Skiadopoulou, Ksenia G Kuznetsova, Bo Wen, Stefan Johansson, Pål R Njølstad, Stefan Bruckner, Lukas Käll, Marc Vaudel. Finding haplotypic signatures in proteins. GigaScience. 2022, 12: Cited : 2Read More
- 42)- Cristiane Hayumi Taniguti, Lucas Mitsuo Taniguti, Rodrigo Rampazo Amadeu, Jeekin Lau, Gabriel de Siqueira Gesteira, Thiago de Paula Oliveira, Getulio Caixeta Ferreira, Guilherme da Silva Pereira, David Byrne, Marcelo Mollinari, Oscar Riera-Lizarazu, Antonio Augusto Franco Garcia. Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps. GigaScience. 2022, 12: Cited : 2Read More
- 43)- Sinan U Umu, Karoline Rapp Vander-Elst, Victoria T Karlsen, Manto Chouliara, Espen Sønderaal Bækkevold, Frode Lars Jahnsen, Diana Domanska. Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis. GigaScience. 2022, 12: Cited : 3Read More
- 44)- Akshay Akshay, Mitali Katoch, Masoud Abedi, Navid Shekarchizadeh, Mustafa Besic, Fiona C Burkhard, Alex Bigger-Allen, Rosalyn M Adam, Katia Monastyrskaya, Ali Hashemi Gheinani. SpheroScan: a user-friendly deep learning tool for spheroid image analysis. GigaScience. 2022, 12: Cited : 2Read More
- 45)- Ruizhong Yuan, Boying Zheng, Zekai Li, Xingzhou Ma, Xiaohan Shu, Qiuyu Qu, Xiqian Ye, Sheng Li, Pu Tang, Xuexin Chen. The chromosome-level genome of Chinese praying mantis Tenodera sinensis (Mantodea: Mantidae) reveals its biology as a predator. GigaScience. 2022, 12: Cited : 0Read More
- 46)- Youngro Lee, Marco Cappellato, Barbara Di Camillo. Machine learning-based feature selection to search stable microbial biomarkers: application to inflammatory bowel disease. GigaScience. 2022, 12: Cited : 3Read More
- 47)- Pedro Barbosa, Rosina Savisaar, Maria Carmo-Fonseca, Alcides Fonseca. Computational prediction of human deep intronic variation. GigaScience. 2022, 12: Cited : 5Read More
- 48)- Haris Zafeiropoulos, Martin Beracochea, Stelios Ninidakis, Katrina Exter, Antonis Potirakis, Gianluca De Moro, Lorna Richardson, Erwan Corre, João Machado, Evangelos Pafilis, Georgios Kotoulas, Ioulia Santi, Robert D Finn, Cymon J Cox, Christina Pavloudi. metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data. GigaScience. 2022, 12: Cited : 2Read More
- 49)- Chakravarthi Kanduri, Lonneke Scheffer, Milena Pavlović, Knut Dagestad Rand, Maria Chernigovskaya, Oz Pirvandy, Gur Yaari, Victor Greiff, Geir K Sandve. simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods. GigaScience. 2022, 12: Cited : 2Read More
- 50)- Hirofumi Aso, Jumpei Ito, Haruka Ozaki, Yukie Kashima, Yutaka Suzuki, Yoshio Koyanagi, Kei Sato. Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections. GigaScience. 2022, 12: Cited : 0Read More
