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For: Persson E, Sonnhammer ELL. InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm. Bioinformatics 2022;38:2918-2919. [PMID: 35561192 PMCID: PMC9113356 DOI: 10.1093/bioinformatics/btac194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 03/14/2022] [Accepted: 03/29/2022] [Indexed: 02/03/2023] Open

For:	Persson E, Sonnhammer ELL. InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm. Bioinformatics 2022;38:2918-2919. [PMID: 35561192 PMCID: PMC9113356 DOI: 10.1093/bioinformatics/btac194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 03/14/2022] [Accepted: 03/29/2022] [Indexed: 02/03/2023] Open

Number

Cited by Other Article(s)

Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Cherry JM, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, dos Santos G, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Gramates LS, Grove CA, Hale P, Harris T, Hayman GT, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Van Auken K, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources central infrastructure. Genetics 2024;227:iyae049. [PMID: 38552170 PMCID: PMC11075569 DOI: 10.1093/genetics/iyae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/09/2024] Open

Affiliation(s)

The Alliance of Genome Resources Consortium
Suzanne A Aleksander Department of Genetics, Stanford University , Stanford, CA 94305
Anna V Anagnostopoulos The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Giulia Antonazzo Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Valerio Arnaboldi Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Helen Attrill Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Andrés Becerra European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Susan M Bello The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Olin Blodgett The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Yvonne M Bradford Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Carol J Bult The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Scott Cain Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
Brian R Calvi Department of Biology, Indiana University , Bloomington, IN 47408 , USA
Seth Carbon Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
Juancarlos Chan Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Wen J Chen Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
J Michael Cherry Department of Genetics, Stanford University , Stanford, CA 94305
Jaehyoung Cho Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Madeline A Crosby The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Jeffrey L De Pons Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Peter D’Eustachio NYU Grossman School of Medicine, New York , NY 10016
Stavros Diamantakis European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Mary E Dolan The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Gilberto dos Santos The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Sarah Dyer European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Dustin Ebert Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
Stacia R Engel Department of Genetics, Stanford University , Stanford, CA 94305
David Fashena Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Malcolm Fisher Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
Saoirse Foley Department of Biological Sciences, Carnegie Mellon University , 5000 Forbes Ave, Pittsburgh, PA 15203
Adam C Gibson Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Varun R Gollapally Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
L Sian Gramates The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Christian A Grove Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Paul Hale The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Todd Harris Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
G Thomas Hayman Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Yanhui Hu Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
Christina James-Zorn Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
Kamran Karimi Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
Kalpana Karra Department of Genetics, Stanford University , Stanford, CA 94305
Ranjana Kishore Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Anne E Kwitek Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Stanley J F Laulederkind Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Raymond Lee Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Ian Longden The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Manuel Luypaert European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Nicholas Markarian Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Steven J Marygold Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Beverley Matthews The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Monica S McAndrews The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Gillian Millburn Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Stuart Miyasato Department of Genetics, Stanford University , Stanford, CA 94305
Howie Motenko The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Sierra Moxon Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
Hans-Michael Muller Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Christopher J Mungall Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
Anushya Muruganujan Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
Tremayne Mushayahama Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
Robert S Nash Department of Genetics, Stanford University , Stanford, CA 94305
Paulo Nuin Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
Holly Paddock Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Troy Pells Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
Norbert Perrimon Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
Christian Pich Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Mark Quinton-Tulloch European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
Daniela Raciti Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Sridhar Ramachandran Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Joel E Richardson Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Susan Russo Gelbart The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Leyla Ruzicka Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Gary Schindelman Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
David R Shaw The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Gavin Sherlock Department of Genetics, Stanford University , Stanford, CA 94305
Ajay Shrivatsav Department of Genetics, Stanford University , Stanford, CA 94305
Amy Singer Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Constance M Smith The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Cynthia L Smith The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Jennifer R Smith Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Lincoln Stein Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
Paul W Sternberg Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Christopher J Tabone The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Paul D Thomas Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
Ketaki Thorat Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Jyothi Thota Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Monika Tomczuk The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Vitor Trovisco Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Marek A Tutaj Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
Jose-Maria Urbano Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
Kimberly Van Auken Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Ceri E Van Slyke Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Peter D Vize Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
Qinghua Wang Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Shuai Weng Department of Genetics, Stanford University , Stanford, CA 94305
Monte Westerfield Institute of Neuroscience, University of Oregon , Eugene, OR 97403
Laurens G Wilming The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
Edith D Wong Department of Genetics, Stanford University , Stanford, CA 94305
Adam Wright Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
Karen Yook Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
Pinglei Zhou The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
Aaron Zorn Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
Mark Zytkovicz The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA

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Chow CN, Yang CW, Wu NY, Wang HT, Tseng KC, Chiu YH, Lee TY, Chang WC. PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters. Nucleic Acids Res 2024;52:D1569-D1578. [PMID: 37897338 PMCID: PMC10767843 DOI: 10.1093/nar/gkad945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open

Petrova O, Semenova E, Parfirova O, Tsers I, Gogoleva N, Gogolev Y, Nikolaichik Y, Gorshkov V. RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum. Int J Mol Sci 2023;24:17348. [PMID: 38139177 PMCID: PMC10743746 DOI: 10.3390/ijms242417348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open

Affiliation(s)

Olga Petrova Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
Elizaveta Semenova Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
Olga Parfirova Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
Ivan Tsers Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
Natalia Gogoleva Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
Yuri Gogolev Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.) Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
Yevgeny Nikolaichik Department of Molecular Biology, Belarusian State University, 220030 Minsk, Belarus;
Vladimir Gorshkov Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.) Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia

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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Michael Cherry J, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, Santos GD, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Sian Gramates L, Grove CA, Hale P, Harris T, Thomas Hayman G, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Auken KV, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567935. [PMID: 38045425 PMCID: PMC10690154 DOI: 10.1101/2023.11.20.567935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]

Liu Q, Li C, Zhang X, Ding M, Liao X, Yan J, Hu M, Yang L, Wang X, Liao L, Li P, Zhou X. PhcX Is a LqsR-family response regulator that contributes to Ralstonia solanacearum virulence and regulates multiple virulence factors. mBio 2023;14:e0202823. [PMID: 37787568 PMCID: PMC10653808 DOI: 10.1128/mbio.02028-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/15/2023] [Indexed: 10/04/2023] Open

Affiliation(s)

Qingmei Liu Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Chuhao Li Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Xiaohan Zhang Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Mengfan Ding Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Xinyue Liao Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Jinli Yan School of Agricultural Science, Xichang University, Xichang, China
Ming Hu Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Leilei Yang Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Xiaoqing Wang Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Lisheng Liao Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
Peng Li Ministry of Education Key Laboratory for Ecology of Tropical Islands, Hainan Provincial Key Laboratory for Tropical Plant and Animal Ecology, College of Life Sciences, Hainan Normal University, Haikou, China
Xiaofan Zhou Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China

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Yan H, Liu F, Zhang G, Liu S, Ma W, Yang T, Li Y, Yang J, Cui H. PlantCHRs: A comprehensive database of plant chromatin remodeling factors. Comput Struct Biotechnol J 2023;21:4974-4987. [PMID: 37867975 PMCID: PMC10589754 DOI: 10.1016/j.csbj.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open

Naithani S, Deng CH, Sahu SK, Jaiswal P. Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes. Biomolecules 2023;13:1403. [PMID: 37759803 PMCID: PMC10527062 DOI: 10.3390/biom13091403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open

Da L, Li J, Zhao F, Liu H, Shi P, Shi S, Zhang X, Yang J, Zhang H. RoseAP: an analytical platform for gene function of Rosa rugosa. FRONTIERS IN PLANT SCIENCE 2023;14:1197119. [PMID: 37457357 PMCID: PMC10348015 DOI: 10.3389/fpls.2023.1197119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/23/2023] [Indexed: 07/18/2023]

Abstract

Rosa rugosa, a perennial shrub belonging to family Rosaceae, is a well-known ornamental plant. Its petals contain an abundance of essential oils and anthocyanins with enormous economic and health benefits when used as edible or cosmetic ingredients. The whole genome of R. rugosa was sequenced in 2021, which provided opportunities and challenges for gene regulation. However, many gene functions remain unknown. Therefore, an analytical platform named RoseAP (http://www.gzybioinformatics.cn/RoseAP/index.php) for the functional analysis of R. rugosa genes was constructed. It improved the gene annotation rate by integrating and analyzing genomic and transcriptomic datasets. First, 38,815 genes, covering 97.76% of the coding genes, were annotated functionally and structurally using a variety of algorithms and rules. Second, a total of 33 transcriptome samples were integrated, including 23 samples from our lab and 10 samples from the SRA database. A co-expression network containing approximately 29,657 positive or negative gene pairs, covering 74.7% of the coding genes, was constructed based on PCC and MR algorithms. Network analysis revealed that the DFR function was closely related to anthocyanin metabolism. It demonstrated the reliability of the network. Several SAUR genes of R. rugosa shared similar expression patterns. RoseAP was used to determine the sequence, structure, functional annotation, expression profile, regulatory network, and functional modules at the transcriptional and protein levels by inputting gene IDs. In addition, auxiliary analytical tools, including BLAST, gene set enrichment, orthologue conversion, gene sequence extraction, gene expression value extraction, and JBrowse, were utilized. Regular updates to RoseAP are expected to facilitate mining of gene function and promote genetic improvement in R. rugosa.

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Persson E, Sonnhammer ELL. InParanoiDB 9: Ortholog Groups for Protein Domains and Full-Length Proteins. J Mol Biol 2023:168001. [PMID: 36764355 DOI: 10.1016/j.jmb.2023.168001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023]