Genome Res. Table of Contents for June 2024; Vol. 34, No. 6

[Prash]

 

This month Genome Research publishes the Human Gut Microbiome Atlas (HGMA), a resource of over 6,000 human gut metagenome samples across 19 countries and 23 diseases. Researchers performed associations studies to determine healthy vs. disease microbiomes and report depletion or enrichment of species among various disease cohorts, including cancer. This resource has broad applications for studying bacterial diversity and function in human health. Genome Research June 2024; Vol. 34, No. 6 (NOTE: Depending on your browser settings, you might need to refresh your browser or clear your browser's cache if the Table of Contents that you are viewing does not immediately update to reflect this latest issue.) Mini-Review Large-scale genomic analysis of the domestic dog informs biological discovery Reuben M. Buckley and Elaine A. Ostrander Genome Res. 2024; 34: 811-821 Open Access https://genome.cshlp.org/content/34/6/811.abstract Research Single-cell discovery of m6A RNA modifications in the hippocampus Shuangshuang Feng, Maitena Tellaetxe-Abete, Yujie Zhang, Yan Peng, Han Zhou, Mingjie Dong, Erika Larrea, Liang Xue, Li Zhang and Magdalena J. Koziol Genome Res. 2024; 34: 822-836 Open Access https://genome.cshlp.org/content/34/6/822.abstract Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue Aarthi Venkat, Maximillian J. Carlino, Betty R. Lawton, Manju L. Prasad, Matthew Amodio, Courtney E. Gibson, Caroline J. Zeiss, Scott E. Youlten, Smita Krishnaswamy and Diane S. Krause Genome Res. 2024; 34: 837-850 https://genome.cshlp.org/content/34/6/837.abstract Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles Xuejing Wang and Gerald Heckel Genome Res. 2024; 34: 851-862 https://genome.cshlp.org/content/34/6/851.abstract Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior Mohammed Errbii, Jürgen Gadau, Kerstin Becker, Lukas Schrader and Jan Oettler Genome Res. 2024; 34: 863-876 https://genome.cshlp.org/content/34/6/863.abstract Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States Greta Bellinzona, Tiago Nardi, Michele Castelli, Gherard Batisti Biffignandi, Karim Adjou, Martha Betson, Yannick Blanchard, Ioana Bujila, Rachel Chalmers, Rebecca Davidson, Nicoletta D'Avino, Tuulia Enbom, Jacinto Gomes, Gregory Karadjian, Christian Klotz, Emma Östlund, Judith Plutzer, Ruska Rimhanen-Finne, Guy Robinson, Anna Rosa Sannella, Jacek Sroka, Christen Rune Stensvold, Karin Troell, Paolo Vatta, Barbora Zalewska, Claudio Bandi, Davide Sassera and Simone M. Cacciò Genome Res. 2024; 34: 877-887 Open Access https://genome.cshlp.org/content/34/6/877.abstract Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins Nikolaos Vakirlis and Anne Kupczok Genome Res. 2024; 34: 888-903 https://genome.cshlp.org/content/34/6/888.abstract Methods Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine Bo Yan, Duan Wang and Laurence Ettwiller Genome Res. 2024; 34: 904-913 Open Access https://genome.cshlp.org/content/34/6/904.abstract Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters Jens-Uwe Ulrich and Bernhard Y. Renard Genome Res. 2024; 34: 914-924 https://genome.cshlp.org/content/34/6/914.abstract Accurate estimation of pathway activity in single cells for clustering and differential analysis Daniel Davis, Avishai Wizel and Yotam Drier Genome Res. 2024; 34: 925-936 Open Access https://genome.cshlp.org/content/34/6/925.abstract Accurate allocation of multimapped reads enables regulatory element analysis at repeats Alexis Morrissey, Jeffrey Shi, Daniela Q. James and Shaun Mahony Genome Res. 2024; 34: 937-951 https://genome.cshlp.org/content/34/6/937.abstract Resources DEAD box RNA helicases are pervasive protein kinase interactors and activators Alexander Hirth, Edoardo Fatti, Eugen Netz, Sergio P. Acebron, Dimitris Papageorgiou, Andrea Švorinić, Cristina-Maria Cruciat, Emil Karaulanov, Alexandr Gopanenko, Tianheng Zhu, Irmgard Sinning, Jeroen Krijgsveld, Oliver Kohlbacher and Christof Niehrs Genome Res. 2024; 34: 952-966 https://genome.cshlp.org/content/34/6/952.abstract Global compositional and functional states of the human gut microbiome in health and disease Sunjae Lee, Theo Portlock, Emmanuelle Le Chatelier, Fernando Garcia-Guevara, Frederick Clasen, Florian Plaza Oñate, Nicolas Pons, Neelu Begum, Azadeh Harzandi, Ceri Proffitt, Dorines Rosario, Stefania Vaga, Junseok Park, Kalle von Feilitzen, Fredric Johansson, Cheng Zhang, Lindsey A. Edwards, Vincent Lombard, Franck Gauthier, Claire J. Steves, David Gomez-Cabrero, Bernard Henrissat, Doheon Lee, Lars Engstrand, Debbie L. Shawcross, Gordon Proctor, Mathieu Almeida, Jens Nielsen, Adil Mardinoglu, David L. Moyes, Stanislav Dusko Ehrlich, Mathias Uhlen and Saeed Shoaie Genome Res. 2024; 34: 967-978 Open Access https://genome.cshlp.org/content/34/6/967.abstract Corrigendum Corrigendum: Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere Lee H. Wong, Kate H. Brettingham-Moore, Lyn Chan, Julie M. Quach, Melissa A. Anderson, Emma L. Northrop, Ross Hannan, Richard Saffery, Margaret L. Shaw, Evan Williams and K.H. Andy Choo Genome Res. 2024; 34: 979-980 Open Access https://genome.cshlp.org/content/34/6/979.extract

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Prashanth N Suravajhala, Ph.D.
Principal Scientist, Systems Genomics Lab
# 210, Amrita School of Biotechnology

Amrita University, Amritapuri, Kerala 690525, India. 

Group page: http://www.bioinformatics.org/wiki/Prash 

E mail:  prashATamDOTamritaDOTedu 

Twitter: @prashbio

"One rule is important in science- only courageous people win "   ~ Max Planck