Search Results - "Genome Biology"

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes by Jin, Jian-Jun, Yu, Wen-Bin, Yang, Jun-Bo, Song, Yu, dePamphilis, Claude W., Yi, Ting-Shuang, Li, De-Zhu

“…GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads…”
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Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies by Rhie, Arang, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M.

“…Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a…”
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Giotto: a toolbox for integrative analysis and visualization of spatial expression data by Dries, Ruben, Zhu, Qian, Dong, Rui, Eng, Chee-Huat Linus, Li, Huipeng, Liu, Kan, Fu, Yuntian, Zhao, Tianxiao, Sarkar, Arpan, Bao, Feng, George, Rani E., Pierson, Nico, Cai, Long, Yuan, Guo-Cheng

“…Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present…”
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Gene content evolution in the arthropods by Thomas, Gregg W. C., Dohmen, Elias, Hughes, Daniel S. T., Murali, Shwetha C., Poelchau, Monica, Glastad, Karl, Anstead, Clare A., Ayoub, Nadia A., Batterham, Phillip, Bellair, Michelle, Binford, Greta J., Chao, Hsu, Chen, Yolanda H., Childers, Christopher, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Duan, Jian J., Dugan, Shannon, Esposito, Lauren A., Friedrich, Markus, Garb, Jessica, Gasser, Robin B., Goodisman, Michael A. D., Gundersen-Rindal, Dawn E., Han, Yi, Handler, Alfred M., Hatakeyama, Masatsugu, Hering, Lars, Hunter, Wayne B., Ioannidis, Panagiotis, Jayaseelan, Joy C., Kalra, Divya, Khila, Abderrahman, Korhonen, Pasi K., Lee, Carol Eunmi, Lee, Sandra L., Li, Yiyuan, Lindsey, Amelia R. I., Mayer, Georg, McGregor, Alistair P., McKenna, Duane D., Misof, Bernhard, Munidasa, Mala, Munoz-Torres, Monica, Muzny, Donna M., Niehuis, Oliver, Osuji-Lacy, Nkechinyere, Palli, Subba R., Panfilio, Kristen A., Pechmann, Matthias, Perry, Trent, Peters, Ralph S., Poynton, Helen C., Prpic, Nikola-Michael, Qu, Jiaxin, Rotenberg, Dorith, Schal, Coby, Schoville, Sean D., Scully, Erin D., Skinner, Evette, Sloan, Daniel B., Stouthamer, Richard, Strand, Michael R., Szucsich, Nikolaus U., Wijeratne, Asela, Young, Neil D., Zattara, Eduardo E., Benoit, Joshua B., Zdobnov, Evgeny M., Pfrender, Michael E., Hackett, Kevin J., Werren, John H., Worley, Kim C., Gibbs, Richard A., Chipman, Ariel D., Waterhouse, Robert M., Bornberg-Bauer, Erich, Hahn, Matthew W., Richards, Stephen

“…Background Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from…”
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LinDA: linear models for differential abundance analysis of microbiome compositional data by Zhou, Huijuan, He, Kejun, Chen, Jun, Zhang, Xianyang

“…Differential abundance analysis is at the core of statistical analysis of microbiome data. The compositional nature of microbiome sequencing data makes false…”
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Mechanisms of enhancer action: the known and the unknown by Panigrahi, Anil, O’Malley, Bert W.

“…Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key…”
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Translation of the circular RNA circβ-catenin promotes liver cancer cell growth through activation of the Wnt pathway by Liang, Wei-Cheng, Wong, Cheuk-Wa, Liang, Pu-Ping, Shi, Mai, Cao, Ye, Rao, Shi-Tao, Tsui, Stephen Kwok-Wing, Waye, Mary Miu-Yee, Zhang, Qi, Fu, Wei-Ming, Zhang, Jin-Fang

“…Background Circular RNAs are a class of regulatory RNA transcripts, which are ubiquitously expressed in eukaryotes. In the current study, we evaluate the…”
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Dynamic DNA methylation reconfiguration during seed development and germination by Kawakatsu, Taiji, Nery, Joseph R., Castanon, Rosa, Ecker, Joseph R.

“…Background Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of…”
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ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis by Pierson, Emma, Yau, Christopher

“…Single-cell RNA-seq data allows insight into normal cellular function and various disease states through molecular characterization of gene expression on the…”
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Alevin efficiently estimates accurate gene abundances from dscRNA-seq data by Srivastava, Avi, Malik, Laraib, Smith, Tom, Sudbery, Ian, Patro, Rob

“…We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping,…”
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Diverse genetic mechanisms underlie worldwide convergent rice feralization by Qiu, Jie, Jia, Lei, Wu, Dongya, Weng, Xifang, Chen, Lijuan, Sun, Jian, Chen, Meihong, Mao, Lingfeng, Jiang, Bowen, Ye, Chuyu, Turra, Guilherme Menegol, Guo, Longbiao, Ye, Guoyou, Zhu, Qian-Hao, Imaizumi, Toshiyuki, Song, Beng-Kah, Scarabel, Laura, Merotto, Aldo, Olsen, Kenneth M., Fan, Longjiang

“…Background Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests…”
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BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies by Li, Zheng, Zhou, Xiang

“…Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a…”
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JBrowse 2: a modular genome browser with views of synteny and structural variation by Diesh, Colin, Stevens, Garrett J, Xie, Peter, De Jesus Martinez, Teresa, Hershberg, Elliot A., Leung, Angel, Guo, Emma, Dider, Shihab, Zhang, Junjun, Bridge, Caroline, Hogue, Gregory, Duncan, Andrew, Morgan, Matthew, Flores, Tia, Bimber, Benjamin N., Haw, Robin, Cain, Scott, Buels, Robert M., Stein, Lincoln D., Holmes, Ian H.

“…We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary…”
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Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing by Alonge, Michael, Lebeigle, Ludivine, Kirsche, Melanie, Jenike, Katie, Ou, Shujun, Aganezov, Sergey, Wang, Xingang, Lippman, Zachary B., Schatz, Michael C., Soyk, Sebastian

“…Advancing crop genomics requires efficient genetic systems enabled by high-quality personalized genome assemblies. Here, we introduce RagTag, a toolset for…”
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OrthoFinder: phylogenetic orthology inference for comparative genomics by Emms, David M., Kelly, Steven

“…Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of…”
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Improved metagenomic analysis with Kraken 2 by Wood, Derrick E., Lu, Jennifer, Langmead, Ben

“…Although Kraken’s k -mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting…”
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Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression by Hafemeister, Christoph, Satija, Rahul

“…Single-cell RNA-seq (scRNA-seq) data exhibits significant cell-to-cell variation due to technical factors, including the number of molecules detected in each…”
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Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment by Kang, Boxi, Camps, Jordi, Fan, Biao, Jiang, Hongpeng, Ibrahim, Mahmoud M., Hu, Xueda, Qin, Shishang, Kirchhoff, Dennis, Chiang, Derek Y., Wang, Shan, Ye, Yingjiang, Shen, Zhanlong, Bu, Zhaode, Zhang, Zemin, Roider, Helge G.

“…Background The tumor microenvironment (TME) has been shown to strongly influence treatment outcome for cancer patients in various indications and to influence…”
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Complete vertebrate mitogenomes reveal widespread repeats and gene duplications by Formenti, Giulio, Rhie, Arang, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Kwak, Woori, Korlach, Jonas, Fungtammasan, Arkarachai, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., Jarvis, Erich D.

“…Background Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist…”
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Transcriptome assembly from long-read RNA-seq alignments with StringTie2 by Kovaka, Sam, Zimin, Aleksey V., Pertea, Geo M., Razaghi, Roham, Salzberg, Steven L., Pertea, Mihaela

“…RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these…”
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