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Minh awarded Highly Cited Researcher 2021

26 Nov 2021

Minh Bui was recognised as a highly cited researcher 2021, among nearly 6,700 scientists worldwide. In short, he is among the top 0.1% of researchers in the world, who have published many highly cited papers (in the top 1% papers) during the last 10 years.

Source: CECS academic cited 15,000 times, makes world’s ‘Highly Cited Researchers’ list by the College of Engineering and Computer Science, ANU.

When Dr Minh Bui started his research in bioinformatic methods, algorithms, and models to infer phylogenetic trees from large DNA sequencing data, he never imagined that his work would become essential in fighting a global pandemic, making him one of the most cited scientists in the world.

“My true aim is really just to publish some impactful research work that is potentially useful for many scientists,” said the Senior Lecturer of the ANU School of Computing, surprised to see himself on the 2021 list of Highly Cited Researchers.

Numbers speak for themselves when measuring how impactful Bui’s work is. According to analytics company Clarivate, his 44 publications were cited more than 15,000 times in the last decade, giving him a place on the list. His work with IQ-TREE, an open source software tool to help scientists synthesize enormous volumes of genetic data to map the evolutionary trees of biological entities, was cited more than 6,000 times. IQ-TREE (now in version 2.0) was downloaded more than 50,000 times in 2020, and the genomic data it produced contributed directly the identification of COVID-19 variants and the development of vaccines.

IQ-TREE “introduced a new and general method that every evolutionary biologist can use to analyse their data”, said the scientist. “I think the success is not only because IQ-TREE was already better than other state-of-the-art software at the time, but also it went a long way beyond research software: I applied a lot of industrial standards in software development to make it very user-friendly and also spent a large effort to support the user community. Therefore, IQ-TREE has quickly become a go-to software for many labs around the world.”

To improve the software, Bui and his research team were awarded a total of $464,000 as part of Chan Zuckerberg Initiative (CZI) Essential Open Source Software for Science (EOSS) program.

Pioneers in their fields over the last decade

Each year, Clarivate analyses thousands of scientific publications and identifies the world’s most influential researchers — the ones who have been most frequently cited by their peers over the last decade. In 2021, fewer than 6,700, or about 0.1%, of the world’s researchers, in 21 research fields and cross-fields, have earned this exclusive distinction.

The Highly Cited Researchers’ names are drawn from the publications that rank in the top 1% by citations for field and publication year in the Web of Science™ citation index, and the list identifies the research institutions and countries where they are based. Australia ranked fourth with 332 highly cited researchers, after the USA, China and the UK (see table below).

Bui was one of the 11 researchers with primary affiliation to The Australian National University to appear in 2021’s list. The institution with the highest concentration of Highly Cited Researchers in the world was Harvard University, home to 214 of the ranked academics.

Figure 1: Highly Cited Researchers by country or region

Rank	Country/Territory	Number HCRs	%
1	United States	2,622	39.7
2	China Mainland	935	14.2
3	United Kingdom	492	7.5
4	Australia	332	5
5	Germany	331	5
6	The Netherlands	207	3.1
7	Canada	196	3
8	France	146	2.2
9	Spain	109	1.7
10	Switzerland	102	1.5

Source: Clarivate

Joel Haspel, Senior Vice-president Strategy at Clarivate, said, “As well as documenting ‘Eureka!’ moments, this data tells the story of late nights spent filling in grant applications, poring over results in the lab, the unsung work of peer reviewing contemporaries’ manuscripts, and the many small failures that ultimately lead to bigger successes and accelerating innovation.”

Looking ahead: future computational challenges

Bui’s team is still working at full speed, as the COVID-19 pandemic sparked large sequencing efforts around the globe to study this virus. “Today there are already more than 5 million virus genomes available, up from just one in December 2019,” said Bui. “My team and I are currently focusing on solving computational challenges with such huge amount of data.”

As for long-term goals, Bui wants to develop next-generation methods and models for the post-genomic era. “One important direction is to use machine learning techniques to improve traditional phylogenetic methods. Whether or not it becomes a reference, you will know in 5 years,” said the scientist with a big smile.

Chan Zuckerberg Initiative 2021 award

03 Sep 2021

Chan-Zuckerberg Initiative generously provided a funding of US$ 339,000 for the IQ-TREE software project: “Real-time genomic epidemiology with IQ-TREE”.

This project aims to significantly speed up IQ-TREE to enable real-time genomic epidemiology during ongoing outbreaks such as COVID-19, and to introduce continuous integration and a testing framework to ease software maintenance for all developers.

We are looking for two people for this project!

The highlight news by the College of Engineering and Computer Science.

Details for IQ-TREE project from CZI website.

Full list of all funded projects here.

Minh's seminar for Vietnamese Bioinformatics Network

02 Mar 2021

Minh recently gave a seminar for the Vietnamese Bioinformatics Network about his work with IQ-TREE and challenges in COVID-19 data analysis. His recorded talk is now available on YouTube (in Vietnamese):

Nhan Trong Ly joins our group as a PhD student

04 Jan 2021

Welcome Nhan Trong Ly! Nhan just joined our group a PhD student. He will work on developing new effective methods for phylogenetic inference to deal with challenges from big biological data sets.

James Barbetti joins our group as software developer

01 Jun 2020

Welcome James Barbetti! James just joined our group a software developer. He will work on improving IQ-TREE for ultra-large genomic datasets, with a particular focus on COVID-19 data.

ARC discovery project 2020 award

04 Dec 2019

We have recently received an Australian Research Council discovery grant 2020, together with Prof. Allen Rodrigo (CI) and A/Prof. Rob Lanfear (co-CI), H/Prof. Lars Jermiin, and Prof. Matt Hahn. The value is $422,697 for a three-year Postdoc.

The topic is about Efficient phylogenetic methods that manage the curse of genomic complexity. This project aims to develop new methods and software to infer the evolutionary history of organisms using genomic data. These new phylogenomic methods need to take account of the complexity of evolutionary processes and/or patterns in time (along the evolutionary tree) and space (along the genome). This project is significant because these methods must merge mathematics and statistics with High-Performance Computing to handle the huge quantities of genetic data and the complexity of evolution itself. An important expected outcome of this project will be the development and release of freely-available software that incorporates these new methods. This project expects to benefit scientists who need to infer phylogenies from genomic data.

Full list of all funded projects here….

Chan Zuckerberg Initiative 2019 award

15 Nov 2019

We have recently received a prestigious grant funded by the Chan-Zuckerberg Initiative for essential open source software for Life Science. The project is entitled IQ-TREE for Ultra-Large Genomic Data: To develop an open standard and API for phylogenetic models and improve the speed and scalability of the IQ-TREE software for phylogenetic inference from ultra-large genomic data.

We are looking for a Software Engineer for this project!

The highlight news by the Research School of Computer Science.

Full list of all funded projects here.

Field Leader in Evolutionary Biology for Minh

29 Sep 2019

Congratulations to Minh, who has recently been named the Field Leader in Evolutionary Biology by The Australian.

The ANU has also been named the Lead Institution in two fields: Evolutionary Biology and Birds.