Publications

Guillaume Marçais, Shane Elder, Carl Kingsford (2024). k-nonical space: sketching with reverse complements. bioRxiv.

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Guillaume Marçais, Dan DeBlasio, Carl Kingsford (2023). Sketching methods with small window guarantee using minimum decycling sets. arXiv.

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Hongyu Zheng, Guillaume Marçais, Carl Kingsford (2023). Creating and Using Minimizer Sketches in Computational Genomics. Journal of Computational Biology.

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Mihir Mongia, Chengze Shen, Arash Gholami Davoodi, Guillaume Marçais, Hosein Mohimani (2023). Large scale sequence alignment via efficient inference in generative models. Scientific Reports.

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Minh Hoang, Guillaume Marçais, Carl Kingsford (2022). Masked Minimizers: Unifying sequence sketching methods. bioRxiv.

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Trevor S. Frisby, Shawn J. Baker, Guillaume Marçais, Quang Minh Hoang, Carl Kingsford, Christopher J. Langmead (2021). Harvestman: a framework for hierarchical feature learning and selection from whole genome sequencing data. BMC BIoinformatics.

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Hongyu Zheng, Carl Kingsford, Guillaume Marçais (2020). Lower density selection schemes via small universal hitting sets with short remaining path length.

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Dan DeBlasio, Fiyinfoluwa Gbosibo, Carl Kingsford, Guillaume Marçais (2019). Practical universal $k$-mer sets for minimizer schemes.

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Guillaume Marçais, Brad Solomon, Rob Patro, Carl Kingsford (2019). Sketching and Sublinear Data Structures in Genomics. Anuual Review of Biomedical Data Science.

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Guillaume Marçais, Dan DeBlasio, Prashant Pandey, Carl Kingsford (2019). Locality sensitive hash for the edit distance.

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Guillaume Marçais, Dan DeBlasio, Carl Kingsford (2018). Asymptotically optimal minimizers schemes.

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Guillaume Marçais, Arthur L Delcher, Adam M Phillippy, Rachel Coston, Steven L Salzberg, Aleksey Zimin (2018). MUMmer4: a fast and versatile genome alignment system. PLoS Compbio.

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Y Orenstein, D Pellow, Guillaume Marçais, R Shamir, C Kingsford (2017). Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. PLoS Compbio.

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Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford (2017). Improving the performance of minimizers and winnowing schemes. Bioinformatics.

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Aleksey V. Zimin, Daniela Puiu, Ming-Cheng Luo, Tingting Zhu, Sergey Koren, Guillaume Marçais, James A. Yorke, Jan Dvořák, Steven L. Salzberg (2017). Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Research.

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Kristian A. Stevens, Jill L. Wegrzyn, Aleksey Zimin, Daniela Puiu, Marc Crepeau, Charis Cardeno, Robin Paul, Daniel Gonzalez-Ibeas, Maxim Koriabine, Ann E. Holtz-Morris, Pedro J. Martínez-García, Uzay U. Sezen, Guillaume Marçais, Kathy Jermstad, Patrick E. McGuire, Carol A. Loopstra, John M. Davis, Andrew Eckert, Pieter de Jong, James A. Yorke, Steven L. Salzberg, David B. Neale, Charles H. Langley (2016). Sequence of the Sugar Pine Megagenome. Genetics.

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Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford (2016). Compact Universal k-mer Hitting Sets. WABI 2016.

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Guillaume Marçais, James A. Yorke, Aleksey Zimin (2015). QuorUM: An Error Corrector for Illumina Reads. PLoS One.

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