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Genome annotation

Harmonizing and integrating the NCI Genomic Data Commons through accessible, interactive, and cloud-enabled workflows

Ling-Hong Hung, Bryce Fukuda, Robert Schmitz, Varik Hoang, Wes Lloyd, Ka Yee Yeung

published 04 Mar 2025

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Assembly of the salt-secreting mangrove Avicennia rumphiana

Jeremy R. Shearman, Chaiwat Naktang, Chutima Sonthirod, Wasitthee Kongkachana, Sonicha U-thoomporn, Nukoon Jomchai, Chatree Maknual, Suchart Yamprasai, Poonsri Wanthongchai, Wirulda Pootakham, Sithichoke Tangphatsornruang

published 05 Feb 2025

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An insight into the genome-wide analysis of bacterial defense mechanisms in a uropathogenic Morganella morganii isolate from Bangladesh

Syed Muktadir Al Sium, Barna Goswami, Sanjana Fatema Chowdhury, Showti Raheel Naser, Mihir Kanti Sarkar, Md. Jobaid Faruq, Md. Ahashan Habib, Shahina Akter, Tanjina Akhtar Banu, Md. Murshed Hasan Sarkar, Md. Salim Khan

published 23 Jan 2025

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SCRMshaw: Supervised cis-regulatory module prediction for insect genomes

Hasiba Asma, Luna Liu, Marc S. Halfon

published 05 Dec 2024

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Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe

Ngonidzashe Mangoma, Nerve Zhou, Thembekile Ncube

published 02 Dec 2024

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Chromosomal gene order defines several structural classes of Staphylococcus epidermidis genomes

Naya Nagy, Paul Hodor

published 04 Oct 2024

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Differential induction of defense genes in hexaploid wheat roots by the plant-parasitic nematodes Pratylenchus neglectus and P. thornei

Patricia A. Okubara, Richard M. Sharpe, Amy B. Peetz, Xianran Li, Inga A. Zasada

published 29 Aug 2024

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Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca

Andrea Mira-Jover, Eva Graciá, Andrés Giménez, Uwe Fritz, Roberto Carlos Rodríguez-Caro, Yann Bourgeois

published 09 Aug 2024

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Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

Michael R. Winter, Adam P. Taranto, Henok Zemene Yimer, Alison Coomer Blundell, Shahid Siddique, Valerie M. Williamson, David H. Lunt

published 06 Jun 2024

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Functional classes of SNPs related to psychiatric disorders and behavioral traits contrast with those related to neurological disorders

Mark A. Reimers, Kenneth S. Kendler

published 16 May 2024

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Annotation of nuclear lncRNAs based on chromatin interactions

Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Howard Y. Chang, Josée Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J. Makeev, Mickaël Mendez, Yasushi Okazaki, Jordan A. Ramilowski, Andrey I. Sigorskikh, Lisa J. Strug, Ken Yagi, Kayoko Yasuzawa, Chi Wai Yip, Chung Chau Hon, Michael M. Hoffman, Chikashi Terao, Ivan V. Kulakovskiy, Takeya Kasukawa, Jay W. Shin, Piero Carninci, Michiel J. L. de Hoon

published 06 May 2024

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Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome

Iasmim Santos Mangabeira-Silva, Paulo Eduardo Toscano Soares, Yago Tomaz Vieira da Silva, Beatriz Helena Dantas Rodrigues de Albuquerque, Maryana Thalyta Ferreira Câmera de Oliveira, Larissa Alves Honorato Ferreira, Maria Fernanda Bezerra de Souza, Danyllo Vieira de Lucena, Jessica Marina Paiva Pereira, Roseli Pimentel Pinheiro e Silva, Daniel Carlos Ferreira Lanza

published 02 May 2024

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Identification of differentially expressed mRNA/lncRNA modules in acutely regorafenib-treated sorafenib-resistant Huh7 hepatocellular carcinoma cells

Mina Baek, Minjae Kim, Hae In Choi, Bert Binas, Junho Cha, Kyoung Hwa Jung, Sungkyoung Choi, Young Gyu Chai

published 11 Apr 2024

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