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

“…Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations…”
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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

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

“…Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene…”
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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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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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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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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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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 for…”
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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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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, Jr, Aldo, Olsen, Kenneth M, Fan, Longjiang

“…Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests paddies…”
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Opportunities and challenges in long-read sequencing data analysis by Amarasinghe, Shanika L, Su, Shian, Dong, Xueyi, Zappia, Luke, Ritchie, Matthew E, Gouil, Quentin

“…Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics. Dedicated analysis tools…”
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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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Cytoscape Automation: empowering workflow-based network analysis by Otasek, David, Morris, John H, Bouças, Jorge, Pico, Alexander R, Demchak, Barry

“…Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating…”
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Eleven grand challenges in single-cell data science by Lähnemann, David, Köster, Johannes, Szczurek, Ewa, McCarthy, Davis J, Hicks, Stephanie C, Robinson, Mark D, Vallejos, Catalina A, Campbell, Kieran R, Beerenwinkel, Niko, Mahfouz, Ahmed, Pinello, Luca, Skums, Pavel, Stamatakis, Alexandros, Attolini, Camille Stephan-Otto, Aparicio, Samuel, Baaijens, Jasmijn, Balvert, Marleen, Barbanson, Buys de, Cappuccio, Antonio, Corleone, Giacomo, Dutilh, Bas E, Florescu, Maria, Guryev, Victor, Holmer, Rens, Jahn, Katharina, Lobo, Thamar Jessurun, Keizer, Emma M, Khatri, Indu, Kielbasa, Szymon M, Korbel, Jan O, Kozlov, Alexey M, Kuo, Tzu-Hao, Lelieveldt, Boudewijn P F, Mandoiu, Ion I, Marioni, John C, Marschall, Tobias, Mölder, Felix, Niknejad, Amir, Rączkowska, Alicja, Reinders, Marcel, Ridder, Jeroen de, Saliba, Antoine-Emmanuel, Somarakis, Antonios, Stegle, Oliver, Theis, Fabian J, Yang, Huan, Zelikovsky, Alex, McHardy, Alice C, Raphael, Benjamin J, Shah, Sohrab P, Schönhuth, Alexander

“…The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology…”
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SCANPY: large-scale single-cell gene expression data analysis by Wolf, F Alexander, Angerer, Philipp, Theis, Fabian J

“…SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and…”
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Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance by Wu, Xi, Feng, Hui, Wu, Di, Yan, Shijuan, Zhang, Pei, Wang, Wenbin, Zhang, Jun, Ye, Junli, Dai, Guoxin, Fan, Yuan, Li, Weikun, Song, Baoxing, Geng, Zedong, Yang, Wanli, Chen, Guoxin, Qin, Feng, Terzaghi, William, Stitzer, Michelle, Li, Lin, Xiong, Lizhong, Yan, Jianbing, Buckler, Edward, Yang, Wanneng, Dai, Mingqiu

“…Drought threatens the food supply of the world population. Dissecting the dynamic responses of plants to drought will be beneficial for breeding…”
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