XiaLab at University of Ottawa

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Welcome to XiaLab!

We do research and teaching in molecular evolution and phylogenetics, bioinformatics, microbial genomics, transcriptomics, statistical modelling, evolutionary genetics and biomedical and biopharmaceutical sciences. You are welcome to join us, either as PhD, MSc or Honors students or visiting scientists

Research highlight:

Xia, X. 2020. A Mathematical Primer of Molecular Phylogenetics. New York: Apple Academic Press, pp. 380 (published on April 13, 2020).

Book reviews

“A highly effective volume ideal as textbook for an advanced undergraduate course or for seasoned biologists seeking deeper understanding of applying mathematical approaches to address fundamental questions in phylogeny and evolution. . . . In his latest book, Xia (Univ. of Ottawa) offers a treatment of phylogenetics deeply rooted in mathematical principles yet conversational in tone. Though the book is certainly best suited to an audience with background in mathematics and statistics, readers whose primary focus is molecular or evolutionary biology will find that chapter preambles offer an effective bridge between biological concepts and their mathematical treatment in phylogenetics. Xia’s frequent references to papers that use phylogenetic methods to resolve essential evolutionary questions also work to make the methods presented accessible to a broad readership. Though minimalist in presentation, Xia’s illustrations of concepts—including sequence alignment—successfully capture the essence of complex inference techniques. Moreover, rather than simply presenting mathematical expressions, Xia provides specific numeric examples, offering readers the opportunity to check their understanding by working through problems themselves. . . . Summing Up: Highly recommended. Upper-division undergraduates. Graduate students and faculty.”

CHOICE (publication of the Association of College and Research Libraries), review by D. P. Genereux, Broad Institute of Harvard University and Massachusetts Institute of Technology

“A nice job of presenting detailed worked analyses and of making strong connections to empirical settings, making it a useful reference for those wishing for a deeper description of these aspects. . . . Professor Xia has gone to considerable effort to provide examples that are based on empirical data, as well as worked details for the analyses performed on these data. These aspects of the book differ from many of the standard books on this topic, where toy examples and more abstract descriptions of the methodology are often provided instead.”

Systematic Biology, review by Laura Kubatko, Ohio State University, USA

“Gives the lay of the land in computing on DNA sequence data to reconstruct evolutionary history. The volume sensibly progresses from aligning raw sequences with one another to the models that describe their mutations and onwards to the construction of phylogenetic trees from these data, with the nuts and bolts of each method described and exemplified along the way. Professor Xia doesn’t shy away from challenging us; for example, where he treats the application of affine functions in alignment algorithms, he warns us that this is something ‘only a very good student can understand.‘ Yet his explanations are so concrete and laced with pseudocode and references to real-world implementations that they invite the reader to experiment and figure out what’s going on. The Primer is geared towards researchers who are familiar with the tools and methods of the field but who now, finally, want to know how they actually work and be able to implement them by themselves. For this audience, Xia’s work compares favorably where there is overlap in subject matter with Felsenstein’s Inferring Phylogenies. For example, where the Farris algorithm is described in prose by Felsenstein, Xia helpfully describes possible implementations (using bitmasks, as connoisseurs will understand). Along the way, the reader is treated to illustrative anecdotes and the occasional, charming Canadianism: the code samples in the book are provided in MAPLE, which, we are told, is ‘a beautiful Canadian product.‘ The same could be said about the Primer, and I wish it had been around when I was a graduate student.”

—Dr. Rutger Vos, Naturalis Biodiversity Center, The Netherlands

Other lab news

6/19/2024: Congratulations to Parisa Aris for a successful defense of her PhD thesis!

5/30/2024: Congratulations to Heba Faroochi for a successful defense of her MSc thesis!

5/17/2024: Congratulations to Alibek Kruglikov for a successful defense of his PhD thesis!

5/12/2024: Just noticed an update of the author citation indicator from Stanford University's Meta-Research Innovation Center. It is the only ranking index that takes author contribution into consideration, i.e., first author, single author and corresponding author are weighted more than other authors. In other citation impact indicators such as H index, an author in a 200-author paper is treated the same as an author in a single-author paper. The ranking of the scientists in the whole world is presented in two indices. The first is a career impact index, and the second is a recent single-year impact index, each ranked with or without self-citation. For the indices with self-citation excluded, I was ranked 19,767 in the career impact index (behind two retired departmental colleagues), and 7654 in the single-year (i.e., 2022) impact index (surprisingly ahead of all of my departmental colleagues).

5/10/2024: Congratulations to Mahbubeh for having published her thesis research: Askari Rad, M.; Kruglikov, A.; Xia, X. Three-Way Alignment Improves Multiple Sequence Alignment of Highly Diverged Sequences. Algorithms 2024, 17, 205.

4/18/2024: Congratulations to Mahbubeh for a successful thesis defense.

4/10/2024: Congratulations to Heba Faroohki for publishing her 26-page paper: Farookhi H, Xia X. 2024. Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species. Microorganisms 12(4):768.

3/1/2024: Nasser F, Gaudreau A, Lubega S, Zaker A, Xia X, Mer AS, D’Costa VM. 2024. Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter. Emerg Microbes Infect 13(1):2320929.

2/20/2024: Freeman A; Xia X. 2024 Phylogeographic Reconstruction to Trace the Source Population of Asian Giant Hornet Caught in Nanaimo in Canada and Blaine in the USA. Life 14(3), 283.

2/7/2024: Congratulations to Alibek Kruglikov for his new publication: Kruglikov, A.; Xia, X. 2024 Mesophiles vs. Thermophiles: Untangling the Hot Mess of Intrinsically Disordered Proteins and Growth Temperature of Bacteria. Int. J. Mol. Sci. 25, 2000.

1/16/2024: My software DAMBE was featured in Molecular Biology & Evoluition's 40-year celebration issue:

"Our journals have published other prominent software packages like DAMBE (Xia 2013), PAML (Yang 2007), IQ-TREE (Nguyen et al. 2015; Minh et al. 2020), and SEAVIEW (Gouy et al. 2010). DAMBE covers most of the major steps of phylogenetic inference, such as sequence alignment, model selection, and tree building, as well as analyses like codon bias detection and inferring the isoelectric point of a particular enzyme in a solution" (Claudia A M Russo, Adam Eyre-Walker, Laura A Katz, and Brandon S Gaut, 2024 Mol Biol Evol)

1/15/2024: Congratulations to Parisa Aris for her new publication: Aris, P.; Mohamadzadeh, M.; Zarei, M.; Xia, X. 2024 Computational Design of Novel Griseofulvin Derivatives Demonstrating Potential Antibacterial Activity: Insights from Molecular Docking and Molecular Dynamics Simulation. Int. J. Mol. Sci. 25, 1039.

8/25/2023: New paper published: Xia, X. 2023. Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis. Antibiotics 12, 1367

7/20/2023: New paper published: Xia, X. 2023. Identification of host receptors for viral entry and beyond: a perspective from the spike of SARS-CoV-2. Frontiers in Microbiology-Virology 14:1188249

4/28/2023: Congratulations to Parisa for winning the International OGS scholarship, one of only two in our Faculty of Science!

3/21/2023: New publication on optimization of therapeutic phages: Xia, X. Optimizing Protein Production in Therapeutic Phages against a Bacterial Pathogen, Mycobacterium abscessus. Drugs Drug Candidates 2023, 2, 189-209

3/5/2023: New publication on the origin of SARS-CoV-2: Xia, X. 2023 Rooting and Dating Large SARS-CoV-2 Trees by Modeling Evolutionary Rate as a Function of Time. Viruses 15, 684. Here is a Summary in simple terms.

3/4/2023: Congratulations to Parisa Aris and colleagues for their new publishing: Aris, P.; Mohamadzadeh, M.; Kruglikov, A.; Askari Rad, M.; Xia, X. In Silico Exploration of Microtubule Agent Griseofulvin and Its Derivatives Interactions with Different Human β-Tubulin Isotypes. Molecules 2023, 28, 2384.

12/19/2022: Alibek passed his PhD comprehensive exam.

12/09/2022: Significant advance in dating known SARS-CoV-2 genomes: Xia, X. 2022. Improved Method for Rooting and Tip-Dating a Viral Phylogeny. pp 397–410 In: Lu, H.HS., Schölkopf, B., Wells, M.T., Zhao, H. (eds) Handbook of Statistical Bioinformatics. Springer Handbooks of Computational Statistics. Springer, Berlin, Heidelberg.

What is special about the paper? Numerous dating studies have been carried out to date the most recent common ancestor of SARS-CoV-2 genomes. Although many methods allow different lineages to have different evolutionary rates by using the relaxed molecular clock, this is the only one that explicitly models the change of evolutionary rate over time. This dramatically improves dating accuracy. The method can be used with large viral trees (e.g., those released by NCBI) with a million or more leaves.

11/29/2022: Kerin Hudson successfully defended her MSc thesis

11/15/2022: Parisa passed her PhD comprehensive exam.

11/6/2022: Encoutered an interesting author citation indicator from Stanford University's Meta-Research Innovation Center. It is perhaps the first one to take author contribution into consideration. In other citation inpact indicators such as H index, an author in a 200-author paper is treated the same as an author in a single-author paper. With this new index from Stanford, I was ranked at 21716 for career impact in the world.

10/18/2022: Congratulation to Parisa and Yulong for their new publication: Aris, P.; Wei, Y.; Mohamadzadeh, M.; Xia, X. Griseofulvin: An Updated Overview of Old and Current Knowledge. Molecules 2022, 27, 7034. Molecules 27, 7034.

10/16/2022: Congratulation to Alibek and Yulong for their new publication: Kruglikov A, Wei Y, Xia X 2022. Proteins from Thermophilic Thermus thermophilus Often Do Not Fold Correctly in a Mesophilic Expression System Such as Escherichia coli. ACS Omega 7:37797–37806.

8/18/2022: Published a comprehensive review on Helicobacter pylori: Xia, X. 2022. Multiple regulatory mechanisms for pH homeostasis in the gastric pathogen, Helicobacter pylori. Advances in Genetics. Academic Press.

7/26/2022: Bosen Jia successfully defended his thesis.

7/11/2022: New publication by Bosen and others: Jia, B.; Conner, R.L.; Penner, W.C.; Zheng, C.; Cloutier, S.; Hou, A.; Xia, X.; You, F.M. Quantitative Trait Locus Mapping of Marsh Spot Disease Resistance in Cranberry Common Bean (Phaseolus vulgaris L.). Int. J. Mol. Sci. 2022, 23, 7639.

6/22/2022: New publication by Mohan and others: Rakesh, M., Aris-Brosou, S. & Xia, X. 2022. Testing alternative hypotheses on the origin and speciation of Hawaiian katydids. BMC Ecol Evo 22, 83.

6/20/2022: New publication by Parisa, Yulong and others: Aris, P.; Mohamadzadeh, M.; Wei, Y.; Xia, X. 2022 In Silico Molecular Dynamics of Griseofulvin and Its Derivatives Revealed Potential Therapeutic Applications for COVID-19. Int. J. Mol. Sci. 23, 6889

5/8/2022: Found an interesting site for citation ranking.

Congratulation to Parisa and Yulong for their new publication: Aris P, Yan L, Wei Y, Chang Y, Shi B, Xia X. 2021. Conservation of griseofulvin genes in the gsf gene cluster among fungal genomes. G3 Genes|Genomes|Genetics.

11/18/2021: Xia, X. 2021 Post-Alignment Adjustment and Its Automation. Genes, 12, 1809. https://doi.org/10.3390/genes12111809

9/24/2021: I participated in a discussion on differences in COVID-19 vaccine efficacy in TheScientist

9/8/2021: Xia X. 2021. Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes. Viruses 13(9),1790

9/8/2021: Congratulation to Bosen Jia for publishing in Agricultural Sciences:

Jia, B., Waldo, P., Conner, R., Moumen, I., Khan, N., Xia, X., Hou, A., You, F. (2021) Marsh Spot Disease and Its Causal Factor, Manganese Deficiency in Plants: A Historical and Prospective Review. Agricultural Sciences, 12, 928-948 doi: 10.4236/as.2021.129060

8/26/2021: Congratulations to Bosen Jia for publishing in the Crop Journal (Thanks to Dr. Frank You for doing the lion's share of supervision):

Jia B, Conner RL, Khan N, Hou A, Xia X, You FM. 2021. Inheritance of marsh spot disease resistance in cranberry common bean (Phaseolus vulgaris L.). The Crop Journal.

7/13/2021: Yulong Wei defended his PhD thesis. Congratulations! Yulong is moving to Yale University to be a postdoctoral fellow on viral research.

7/3/2021: Xia, X. 2021. Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines." Vaccines (Basel) 9(7).

6/21/2021: Full-text views of my 2021 Viruses paper exceeded 7000.

5/28/2021: Created a DAMBE forum to encourage discussion among DAMBE users

3/17/2021: Congratulations to Ali Tehfe and Talia Roseshter (two bright honors students) and Yulong Wei for their publication in Microorganisms:

Tehfe, A.; Roseshter, T.; Wei, Y.; Xia, X. Does Saccharomyces cerevisiae Require Specific Post-Translational Silencing against Leaky Translation of Hac1up? Microorganisms 2021, 9, 620.

3/8/2021: Kruglikov A, Rakesh M, Wei Y, Xia X. 2021. Applications of Protein Secondary Structure Algorithms in SARS-CoV-2 Research. " J Proteome Res 20:1457-1463.

1/18/2021: Wei Y, Aris P, Farookhi H & Xia X. 2021 Predicting mammalian species at risk of being infected by SARS‑CoV‑2 from an ACE2 perspective. Scientific Reports 11:1702

1/15,2021: Xia, X. 2021. Domains and Functions of Spike Protein in SARS-Cov-2 in the Context of Vaccine Design. Viruses 13(1), 109

12/22/2020: Wei Y, Silke J, Aris P & Xia X. Coronavirus genomes carry the signatures of their habitats. PLoS ONE 15(12): e0244025

Everything related to my 2020 MBE paper

If you come to me because of the media reports, please be informed that the paper has little similarity to what was reported by the media.

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