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

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

About me

I am a computational biologist and postdoctoral fellow in Dr. Rendong Yang’s lab at the Feinberg School of Medicine, Northwestern University. My research focuses on developing advanced bioinformatics algorithms, deep learning models, and multi-omic pipelines to decode the regulatory complexity of cancer genomes and transcriptomes. I am particularly passionate about leveraging third-generation long-read sequencing (e.g., Oxford Nanopore) and AI-driven methods to uncover novel structural variations and transcriptomic alterations that traditional methods often miss.

Currently, my work centers on building computational tools that address critical bottlenecks in biomedical genomics. As a lead developer, I created toolkits like OctopuSV (Bioinformatics) for automated, multi-sample structural variant analysis. Furthermore, I have enjoyed collaborating with excellent colleagues on various impactful projects. For instance, I contributed to the project of DeepChopper—a genomic language model published in Nature Communications designed to mitigate chimera artifacts in nanopore direct RNA sequencing. Additionally, I participated in developing analytical workflows for neoantigen detection (ScanNeo2, Bioinformatics) and supported the analysis for discovering novel cancer regulatory mechanisms (Science Advances).

My doctoral training provided a rigorous methodological foundation in algorithm design and multi-omic integration, which I further refined through independent computational development and cross-disciplinary collaborations. My scientific perspective was shaped during my studies at Oregon State University in 2014. I am grateful to Prof. Jerri Bartholomew for her mentorship, which sparked my interest in evolutionary genomics and laid the groundwork for my current research. To date, I have authored and co-authored 26 peer-reviewed publications, including works published in Nature Communications, Science Advances, Bioinformatics, BMC Biology, and Biology (eight papers as first author).

My long-term goal is to become an independent academic investigator advancing the intersection of AI and biomedical genomics. By designing specialized long-read and deep learning-based tools, I aim to bridge the gap between computational innovation and clinical application—ultimately enabling earlier cancer detection, precise target discovery, and the development of personalized therapies.

Structural Variants Analysis

Deep Learning in Genomics

Nanopore/PacBio Technologies

Multi-omics Integration

1. Guo Q, Li Y, Wang TY, Ramakrishnan A, Yang R. OctopuSV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. Bioinformatics. 2025;41(11):btaf599.
2. 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.
3. 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).
4. 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.
5. 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.
6. Guo Q, Huang M, Liu Y, Zhang X, Gu Z. Morphological plasticity in Myxobolus Bütschli, 1882: a taxonomic dilemma case and renaming of a parasite species of the common carp. Parasit Vectors. 2018 Jul 9;11(1):399.
7. Guo Q, Zhai Y, Gu Z, Liu Y. Histopathological and ultrastructural studies of Myxobolus turpisrotundus from allogynogenetic gibel carp Carassius auratus gibelio in China. Folia Parasitol (Praha). 2016 Oct 14;63.
8. Guo Q, Jia L, Qin J, Li H, Gu Z. Myxozoans and our dinner table: pathogenicity studies of Myxobolus honghuensis (Myxosporea: Bivalvulida) using a suckling mice model. Foodborne Pathog Dis. 2015 Aug;12(8):653-60.

9. Li Y, Wang TY, Guo Q, Ren Y, Lu X, Cao Q, Yang R. Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing. Nature Communications. 2026;17:1864.

10. 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.

11. 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.

12. Zhang B, Guo Q, Tu X, Gu Z. Identification of Myxobolus distalisensis n. sp. (Cnidaria: Myxozoa) infecting yellow catfish Tachysurus fulvidraco (Richardson), with a supplement description of M. voremkhai (Akhmerov, 1960) Landsberg and Lom, 1991. Syst Parasitol. 2023 Oct;100(5):473-485.

13. 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).

14. Tahir UB, Guo Q, Gu Z. Fins infestation induced by Myxobolus xiantaoensis in yellow catfish Tachysurus fulvidraco Richardson, 1846: Some pathophysiological and molecular insights. Microb Pathog. 2021 Apr;153:104772.

15. Wang S, Zhang B, Guo Q, Zhai Y, Gu Z. Molecular and light microscopy evidence for the transfer of Myxobolus honghuensis from Carassius auratus gibelio broodfish to progeny. J Fish Dis. 2020 Oct;43(10):1177-1184.

16. Zhang X, Liu Y, Whipps CM, Guo Q, Gu Z. Multiple evolutionary routes of the single polar capsule in Thelohanellus species (Myxozoa; Myxobolidae). Int J Parasitol Parasites Wildl. 2019 Apr;8:56-62.

17. Tahir UB, Guo Q, Zhao D, Liu Y, Gu Z. Description of Myxobolus xiantaoensis n. sp. from the fins of yellow catfish in China: a species previously attributed to Myxobolus physophilus Reuss, 1906 in Chinese records. Parasitol Res. 2019 Apr;118(4):1137-1146.

18. Shao J, Guo Q, Hu R, Gu Z. Comparative genomic insights into the taxonomy of Edwardsiella tarda isolated from different hosts: marine, freshwater and migratory fish. Aquaculture Research. 2018 January;49(1):197-204.

19. Wang Z, Zhou T, Guo Q, Gu Z. Description of a new freshwater ciliate Epistylis 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.

20. Liu Y, Guo Q, Zhai Y, Gu Z. Effects of different preservation methods on morphology of Myxobolus wulii spores. Journal of Huazhong Agricultural University. 2016;(4):87-92. (In Chinese with English abstract)

21. Zhai Y, Gu Z, Guo Q, Wu Z, Wang H, Liu Y. New type of pathogenicity of Thelohanellus kitauei Egusa & Nakajima, 1981 infecting the skin of common carp Cyprinus carpio L. Parasitol Int. 2016 Feb;65(1):78-82.

22. 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.

23. Deng Q, Guo Q, Zhai Y, Wang Z, Gu Z. First record of Chilodonella piscicola (Ciliophora: Chilodonellidae) from two endangered fishes, Schizothorax o'connori and Oxygymnocypris stewartii in Tibet. Parasitol Res. 2015 Apr;114(8):3097-3103.

24. Jia L, Gu Z, Liu Y, Guo Q, Li D, Zhai Y. Preparation and characterization of polyclonal antibodies against Myxobolus honghuensis (Myxosporea: Bivalvulida). Journal of Huazhong Agricultural University. 2015;(6):113-118. (In Chinese with English abstract)

25. Zhang JY, Gu ZM, Kalavati C, Costa Eiras J, Liu Y, Guo Q, Molnár K. Synopsis of the species of Thelohanellus Kudo, 1933 (Myxozoa: Myxosporea: Bivalvulida). Syst Parasitol. 2013 Nov;86(3):235-56.

26. Gu Z, Guo Q, Zhai Y, Liu Y. A method to isolate and purify the nematocyst of Myxobolus honghuensis (Myxosporea: Bivalvulida). China Patent Application No. CN110055181B. 2022.
27. Gu Z, Guo Q, Zhai Y, Liu Y. A method to isolate and purify the shell valves of Myxobolus wulii (Myxosporea: Bivalvulida). China Patent Application No. ZL CN110004104B. 2022.
28. Gu Z, Li D, Liu Y, Guo Q. A PCR method for simultaneous detection of multiple myxozoans in allogynogenetic gibel carp Carassius auratus gibelio. China Patent No. ZL201610051386.8. 2019.
29. 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 of Myxobolus honghuensis (Myxosporea: Bivalvulida). China Patent No. CN103755806B. 2016.
30. 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 of Myxobolus honghuensis (Myxosporea: Bivalvulida). China Patent No. CN103880954B. 2015.

Yangyang Li's website Tingyou Wang's Blog