AAPratama
In preparation
Viral ecology and dynamics across a temporal permafrost thaw gradient
Christine L. Sun*, Akbar Adjie Pratama*, Maria Consuelo Gazitúa, Ahmed A. Zayed, Dylan Cronin, Benjamin Bolduc, Dean R. Vik, Lindsey Solden, the IsoGenie Project Field Teams 2010-2017, the IsoGenie Project Coordinators, Virginia Rich, Matthew B. Sullivan. *Authors contributed equally. In preparation.
MArVDv2: a machine learning enhanced means for archaeal virus identification from metagenomic data
Dean Vik, Benjamin Bolduc, Simon Roux, Maria Consuelo Gazitúa, Christine Sun, Akbar Adjie Pratama, Mart Krupovic, Matthew B. Sullivan. Review in ISME Comm.
The global rumen virome: diversity and potential impact to rumen microbiome and functions
Ming Yan, Akbar Adjie Pratama, Zongjun Li, Yu Jiang, Matthew B. Sullivan, and Zhongtang Yu. Review in Nat. Comm.
Ecogenomics of soil RNA viruses along a permafrost thaw gradient
Akbar Adjie Pratama*, Guillermo Dominguez-Huerta*, Ahmed A. Zayed, Benjamin Bolduc, Funing Tian, James M. Wainaina, Jiarong Guo, Lindsey Solden and Matthew B. Sullivan. *Authors contributed equally. In preparation
2022
Diversity and ecological footprint of Global Ocean RNA viruses
Guillermo Dominguez-Huerta*, Ahmed A. Zayed*, James M. Wainaina, Jiarong Guo, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Mohamed Mohssen, Olivier Zablocki, Eric Pelletier, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Tara Oceans Coordinators, Chris Bowler, Damien Eveillard, Lionel Guidi, Eric Karsenti, Jens H. Kuhn, Hiroyuki Ogata, Patrick Wincker, Alexander Culley, Samuel Chaffron, and Matthew B. Sullivan. Science
Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome
Ahmed A. Zayed†, James M. Wainaina†, Guillermo Dominguez-Huerta†, Eric Pelletier, Jiarong Guo, Mohamed Mohssen, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Olivier Zablocki, Dylan Cronin, Lindsey Solden, Erwan Delage, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain, Hans-Joachim Ruscheweyh, Guillem Salazar, Elan Shatoff, Tara Oceans Coordinators, Ralf Bundschuh, Kurt Fredrick, Laura S. Kubatko, Samuel Chaffron, Alexander I. Culley, Shinichi Sunagawa, Jens H. Kuhn, Patrick Wincker, Matthew B. Sullivan. Science
2021
Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation
Akbar Adjie Pratama, Benjamin Bolduc, Ahmed A. Zayed, Zhi-Ping Zhong, Jiarong Guo , Dean R. Vik , Maria Consuelo Gazitúa, James M. Wainaina, Simon Roux and Matthew B. Sullivan (2021) PeerJ 9:e11447
-
Top 5 most viewed Bioinformatics, Microbiology and Virology article published in 2021 in PeerJ journal (with 2,648 views)
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
Jiarong Guo, Ben Bolduc, Ahmed A Zayed, Arvind Varsani, Guillermo Dominguez-Huerta, Tom O Delmont, Akbar Adjie Pratama, M Consuelo Gazitúa, Dean Vik, Matthew B Sullivan, Simon Roux (2021) Microbiome 9 (1), 1-13
2020
The role of rhizosphere bacteriophages in plant health
Akbar Adjie Pratama, Jurre Terpstra, Andre Luiz Martinez de Oliveria, Joana Falcão Salles (2020) Trends in microbiology, 28 (9): 709-718
Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features—Proposal for the Definition of a P. hospita Species Cluster
Akbar Adjie Pratama, Diego Javier Jiménez, Qian Chen, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Jan Dirk van Elsas (2020) Genome Biology and Evolution, 12 (4): 325–344
2019
Gene mobility in microbiomes of the mycosphere and mycorrhizosphere–role of plasmids and bacteriophages
Akbar Adjie Pratama and Jan Dirk van Elsas FEMS microbiology ecology (2019) 95 (5), fiz053
The viruses in soil-potential roles, activities, and impacts
Akbar Adjie Pratama and Jan Dirk van Elsas, Modern soil microbiology (third edition). Tylor&Francis: New York
Microbial interactions in soil
Jan Dirk van Elsas, Akbar Adjie Pratama, Welington Luiz de Araujoand Jack T. Trevors. Modern soil microbiology (third edition). Tylor&Francis: New York
2018
The ‘neglected’ soil virome–potential role and impact
Akbar Adjie Pratama, Jan Dirk van Elsas (2018) Trends in Microbiology 26 (8), 649-662
-
Most tweeted article in Trends in Microbiology journal in January 2018
Evolutionary history of bacteriophages in the genus Paraburkholderia
Akbar Adjie Pratama, Maryam Chaib De Mares, Jan Dirk Van Elsas (2018) Frontiers in microbiology 9, 835
2017
Draft genome sequences of three fungal-interactive Paraburkholderia terrae strains, BS007, BS110 and BS437
Akbar Adjie Pratama, Irshad Ul Haq, Rashid Nazir, Maryam Chaib De Mares, Jan Dirk van Elsas (2017) Standards in genomic sciences 12 (1), 1-14
A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437
Akbar Adjie Pratama, Jan Dirk van Elsas (2017) Scientific reports 7 (1), 1-14
2016
The significance of mutualistic phages for bacterial ecology and evolution
Nancy Obeng, Akbar Adjie Pratama, Jan Dirk van Elsas (2016) Trends in microbiology 24 (6), 440-449