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Hi, this is Qingxiang (Allen) Guo, Ph.D. in Bioinformatics 👋

About •Research Focus •Publications & Patents •Tools & Skills •Contact

About myself

I received my Ph.D. in Bioinformatics at Huazhong Agricultural University, China in Jun 2021. With the generous guidance of Prof. Jerri Bartholomew, that experience sparked my lasting interest in host-parasite interactions and evolutionary genomics. My research background is in multi-omic insights (genomics, transcriptomics, and proteomics) into the early animal genome evolution and genetic basis of their phenotypic adaptation. And I am very interested in developing multimodal pipelines to discover fundamental principles that control phenotype.

During my PhD, I investigated the evolutionary genomics of the myxozoans, micro-meter sized parasitic cnidarians, and found a new model of parasite evolution – mosaic evolution (BMC Biology, 2022). I developed a customized comprehensive proteomic reference database (CCPRD) pipeline, which has greatly improved the efficiency and accuracy of proteomic research in non-model organisms. I also applied proteomics, algorithm development, and quantitative genetic analysis to demonstrate that nematocysts may be a key determinant of the adaptive success of cnidarians. I also modelled the relationship between the evolutionary mode of cnidarians and palaeo-environmental change and found that the diversification of cnidarians is predominantly uncoupled from palaeoclimate.

I have authored and co-authored 23 peer-reviewed publications on various biology journals, like BMC Biology, Biology, Journal of Experimental Biology, and Parasites & Vectors (seven papers are first author and three more in preparation).

My long-term goal is to become an independent academic researcher advancing the use ofmulti-omics and AI-driven methods in biomedical genomics. While my Ph.D. work focused on parasitic cnidarians, my current research as a postdoctoral fellow in Dr. Rendong Yang's lab at the Feinberg School of Medicine, Northwestern University, centers on the structural variations of cancer genomes and single-cell omics. I develop long-read and deep learning based tools to decode the regulatory complexity of cancer genomes, with the aim of enabling earlier detection, more precise target discovery, and personalized therapies - hoping that these approaches will help bridge the gap between genomic insights and practical tools for cancer diagnosis and treatment.

Structural Variants Analysis

Deep Learning in Genomics

Nanopore/PacBio Technologies

Multi-omics Integration

1. Guo Q, Atkinson SD, Xiao B, Zhai Y, Bartholomew JL, Gu Z. A myxozoan genome reveals mosaic evolution in a parasitic cnidarian.BMC Biol. 2022 Feb 18;20(1):51.
2. Guo Q, Whipps CM, Zhai Y, Li D, Gu Z. Quantitative insights into the contribution of nematocysts to the adaptive success of cnidarians based on proteomic analysis.Biology (Basel). 2022 Jan 7;11(1).
3. Guo Q, Liu Y, Zhai Y, Gu Z. A fast and effective method for dissecting parasitic spores: myxozoans as an example.J Exp Biol. 2020 Jan 1;223(10):jeb214916.
4. Guo Q, Li D, Zhai Y, Gu Z. CCPRD: A novel analytical framework for the comprehensive proteomic reference database construction of nonmodel organisms.ACS Omega. 2020 Jun 30;5(25):15370-15384.
5. Guo Q, Huang M, Liu Y, Zhang X, Gu Z. Morphological plasticity inMyxobolus Bütschli, 1882: a taxonomic dilemma case and renaming of a parasite species of the common carp.Parasit Vectors. 2018 Jul 9;11(1):399.
6. Guo Q, Zhai Y, Gu Z, Liu Y. Histopathological and ultrastructural studies ofMyxobolus turpisrotundus from allogynogenetic gibel carpCarassius auratus gibelio in China.Folia Parasitol (Praha). 2016 Oct 14;63.
7. Guo Q, Jia L, Qin J, Li H, Gu Z. Myxozoans and our dinner table: pathogenicity studies ofMyxobolus honghuensis (Myxosporea: Bivalvulida) using a suckling mice model.Foodborne Pathog Dis. 2015 Aug;12(8):653-60.

8. Yang Y, Wang TY, Li Q, Lu J, Ren Y, Weiner AB, Fry J, Liu Q, Yum C, Wang R,Guo Q, Wan Y, Zhe J, Dong X, Lotan TL, Schaeffer EM, Yang R, Cao Q. Androgen receptor–regulated lncRNA PRCAT71 promotes AR signaling through the interaction with KHSRP in prostate cancer.Sci Adv. 2025 Apr;11(15):eadk6989.
9. Schäfer RA,Guo Q, Yang R. ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations.Bioinformatics. 2023 Nov;39(11):btad659.
10. Zhang B,Guo Q, Tu X, Gu Z. Identification ofMyxobolus distalisensis n. sp. (Cnidaria: Myxozoa) infecting yellow catfishTachysurus fulvidraco (Richardson), with a supplement description ofM. voremkhai (Akhmerov, 1960) Landsberg and Lom, 1991.Syst Parasitol. 2023 Oct;100(5):473-485.
11. Xiao B,Guo Q, Zhai Y, Gu Z. Transcriptomic insights into the diversity and evolution of Myxozoa (Cnidaria, Endocnidozoa) toxin-like proteins.Mar Drugs. 2022 Apr 26;20(5).
12. Tahir UB,Guo Q, Gu Z. Fins infestation induced byMyxobolus xiantaoensis in yellow catfishTachysurus fulvidraco Richardson, 1846: Some pathophysiological and molecular insights.Microb Pathog. 2021 Apr;153:104772.
13. Wang S, Zhang B,Guo Q, Zhai Y, Gu Z. Molecular and light microscopy evidence for the transfer ofMyxobolus honghuensis fromCarassius auratus gibelio broodfish to progeny.J Fish Dis. 2020 Oct;43(10):1177-1184.
14. Zhang X, Liu Y, Whipps CM,Guo Q, Gu Z. Multiple evolutionary routes of the single polar capsule inThelohanellus species (Myxozoa; Myxobolidae).Int J Parasitol Parasites Wildl. 2019 Apr;8:56-62.
15. Tahir UB,Guo Q, Zhao D, Liu Y, Gu Z. Description ofMyxobolus xiantaoensis n. sp. from the fins of yellow catfish in China: a species previously attributed toMyxobolus physophilus Reuss, 1906 in Chinese records.Parasitol Res. 2019 Apr;118(4):1137-1146.
16. Shao J,Guo Q, Hu R, Gu Z. Comparative genomic insights into the taxonomy ofEdwardsiella tarda isolated from different hosts: marine, freshwater and migratory fish.Aquaculture Research. 2018 January;49(1):197-204.
17. Wang Z, Zhou T,Guo Q, Gu Z. Description of a new freshwater ciliateEpistylis wuhanensis n. sp. (Ciliophora, Peritrichia) from China, with a focus on phylogenetic relationships within family Epistylididae.Journal of Eukaryotic Microbiology. 2017;64(3):394-406.
18. Liu Y,Guo Q, Zhai Y, Gu Z. Effects of different preservation methods on morphology ofMyxobolus wulii spores.Journal of Huazhong Agricultural University. 2016;(4):87-92. (In Chinese with English abstract)
19. Zhai Y, Gu Z,Guo Q, Wu Z, Wang H, Liu Y. New type of pathogenicity ofThelohanellus kitauei Egusa & Nakajima, 1981 infecting the skin of common carpCyprinus carpio L.Parasitol Int. 2016 Feb;65(1):78-82.
20. Zhai Y, Whipps CM, Gu Z,Guo Q, Wu Z, Wang H, Liu Y. Intraspecific morphometric variation in myxosporeans.Folia Parasitol (Praha). 2016 Apr 1;63.
21. Deng Q,Guo Q, Zhai Y, Wang Z, Gu Z. First record ofChilodonella piscicola (Ciliophora: Chilodonellidae) from two endangered fishes,Schizothorax o'connori andOxygymnocypris stewartii in Tibet.Parasitol Res. 2015 Apr;114(8):3097-3103.
22. Jia L, Gu Z, Liu Y,Guo Q, Li D, Zhai Y. Preparation and characterization of polyclonal antibodies againstMyxobolus honghuensis (Myxosporea: Bivalvulida).Journal of Huazhong Agricultural University. 2015;(6):113-118. (In Chinese with English abstract)
23. Zhang JY, Gu ZM, Kalavati C, Costa Eiras J, Liu Y,Guo Q, Molnár K. Synopsis of the species ofThelohanellus Kudo, 1933 (Myxozoa: Myxosporea: Bivalvulida).Syst Parasitol. 2013 Nov;86(3):235-56.

24. Gu Z,Guo Q, Zhai Y, Liu Y. A method to isolate and purify the nematocyst ofMyxobolus honghuensis (Myxosporea: Bivalvulida).China Patent Application No. CN110055181B. 2022.
25. Gu Z,Guo Q, Zhai Y, Liu Y. A method to isolate and purify the shell valves ofMyxobolus wulii (Myxosporea: Bivalvulida).China Patent Application No. ZL CN110004104B. 2022.
26. Gu Z, Li D, Liu Y,Guo Q. A PCR method for simultaneous detection of multiple myxozoans in allogynogenetic gibel carpCarassius auratus gibelio.China Patent No. ZL201610051386.8. 2019.
27. Gu Z, Jia L, Liu Y, Zhai Y, Yuan J, Qin J, Li D,Guo Q. Preparation and application of polyclonal antibodies against the shell valves ofMyxobolus honghuensis (Myxosporea: Bivalvulida).China Patent No. CN103755806B. 2016.
28. Gu Z, Jia L, Liu Y, Zhai Y, Yuan J, Qin J, Li D,Guo Q. Preparation and application of polyclonal antibodies against the polar filaments ofMyxobolus honghuensis (Myxosporea: Bivalvulida).China Patent No. CN103880954B. 2015.

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