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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 computational methods, machine learning models, and multi-omic pipelines to study the regulatory complexity of cancer genomes and transcriptomes. I am particularly interested in using third-generation long-read sequencing technologies, including Oxford Nanopore sequencing, together with AI-driven approaches to uncover structural variants and transcriptomic alterations that are difficult to resolve with conventional profiling methods.

My current work addresses key computational bottlenecks in biomedical genomics. As a lead developer, I engineered OctopuSV (Bioinformatics), an automated toolkit for multi-sample structural variant analysis. I also contribute to cross-disciplinary projects in long-read transcriptomics, cancer immunogenomics, and regulatory genomics, including DeepChopper, a genomic language model published in Nature Communications for mitigating chimera artifacts in nanopore direct RNA sequencing; ScanNeo2, a workflow for neoantigen detection (Bioinformatics); and multi-omic studies that supported the discovery of cancer regulatory mechanisms published in Science Advances.

My early academic training established a foundation in algorithm design, comparative genomics, and multi-omic integration. My scientific perspective was further shaped by my time at Oregon State University in 2014, where Prof. Jerri Bartholomew’s mentorship strengthened my interest in genomics, evolution, and data-driven biological discovery. To date, I have authored and co-authored 26 peer-reviewed publications, with works published in Nature Communications, Science Advances, Bioinformatics, BMC Biology, and Biology (eight papers as first author).

My long-term goal is lead an independent research program the intersection of AI, long-read sequencing, and biomedical genomics. By engineering specialized computational tools for complex genomic and transcriptomic events, I aim to advance mechanistic discovery in cancer biology and contribute to more precise approaches for biomarker discovery, therapeutic target identification, and translational genomics.

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.

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