Searching journal content for articles similar to Patel et al. 20 (7): 960.

Displaying results 1-10 of 23

For checked items

view abstracts
download to citation manager

Select this article
Method: An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
- Stephen Nayfach,
- Beltran Rodriguez-Mueller,
- Nandita Garud,
- and Katherine S. Pollard
Genome Res. November 2016 26: 1612-1625; Published in Advance October 18, 2016, doi:10.1101/gr.201863.115
...other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic...
OPEN ACCESS ARTICLE
Select this article
Research: A global network of coexisting microbes from environmental and whole-genome sequence data
- Samuel Chaffron,
- Hubert Rehrauer,
- Jakob Pernthaler,
- and Christian von Mering
Genome Res. July 2010 20: 947-959; Published in Advance May 10, 2010, doi:10.1101/gr.104521.109
...A global network of coexisting microbes from environmental and whole-genome sequence data Samuel Chaffron 1 , Hubert Rehrauer 2 , Jakob Pernthaler 3 and Christian von Mering 1 , 4 1 Institute of Molecular Life Sciences and Swiss...
OPEN ACCESS ARTICLE
Select this article
Research: Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
- Catherine Lozupone,
- Karoline Faust,
- Jeroen Raes,
- Jeremiah J. Faith,
- Daniel N. Frank,
- Jesse Zaneveld,
- Jeffrey I. Gordon,
- and Rob Knight
Genome Res. October 2012 22: 1974-1984; Published in Advance June 4, 2012, doi:10.1101/gr.138198.112
...symbionts that can cause disease in permissive genetic or environmental circumstances) are often adapted to early succession. Our approach was to first use a co-occurrence network to reveal how species in Clostridium cluster XIVa codistribute across healthy and diseased individuals, and then test for niche...
OPEN ACCESS ARTICLE
Select this article
Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
....zambonelli@unibo.itAbstractThe genus Tuber (family: Tuberaceae) includes the most economically valuable ectomycorrhizal (ECM), truffle-forming fungi. Previous genomic analyses revealed that massive transposable element (TE) proliferation represents a convergent genomic feature of ECM fungi, including Tuberaceae. Repetitive sequences...
Select this article
Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
...of secretory peptidases (Patra and Yu 2022). In comparison, 58 different secretory peptidase families were identified from the rumen protozoal proteins (Fig. 5D), highlighting their substantial proteolytic potential. Furthermore, the identification of ferredoxin hydrogenase of rumen protozoa (Supplemental...
Select this article
Resource: 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. June 2024 34: 967-978; Published in Advance July 22, 2024, doi:10.1101/gr.278637.123
...database and to hidden Markov models (HMMs) built from each CAZyme family (Terrapon et al. 2017), following a procedure previously described for other metagenomic analyses (Svartström et al. 2017). Proteins in the IGC2 catalog were also annotated to KOs using DIAMOND (version 0.9.22.123) (Buchfink et al...
OPEN ACCESS ARTICLE
Select this article
Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...into specific environmentally responsive networks. However, we have very little understanding about what environmental signals these networks are sensing.In this study, we characterize bacterial metabolic variation as well as variation in nematode gene networks that respond to these bacteria. Applying a systems...
Select this article
Research: Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
- Yongqiang Liu,
- Junhua Niu,
- Fei Ye,
- Therese Solberg,
- Borong Lu,
- Chundi Wang,
- Mariusz Nowacki,
- and Shan Gao
Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
..., and enzyme activities, specifically protein–glycine ligase and acid–amino-acid ligase (Supplemental Fig. S5A). Notably, we also found genes associated with stress-response pathways to correlate with 6mA alterations, suggesting a direct involvement in cyst formation. For example, the down-regulation of genes...
Select this article
Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA...
OPEN ACCESS ARTICLE
Select this article
Research: Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity
- Alexander Crits-Christoph,
- Nicholas Bhattacharya,
- Matthew R. Olm,
- Yun S. Song,
- and Jillian F. Banfield
Genome Res. February 2021 31: 239-250; Published in Advance December 23, 2020, doi:10.1101/gr.268169.120
...by known metabolite functions. These networks used protein families from the Pfam database (Pfams) (El-Gebali et al. 2019) found in each BGC as features. They predicted activity labels of antibacterial, antifungal, cytotoxic, and inhibitor, with precisions of 36%, 47%, 61%, and 69% on each class...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Patel et al. 20 (7): 960.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: