Jekyll2025-06-14T14:57:57-07:00https://maxrossi91.com/feed.xmlMassimiliano Rossipersonal descriptionMassimiliano Rossimaxrossi91@gmail.comNew paper accepted at the Data Compression Conference 2022(DCC 22)2022-01-06T00:00:00-08:002022-01-06T00:00:00-08:00https://maxrossi91.com/posts/2022/07/DCCOur paper titled “Efficient CSTs for Terabyte-Sized Data” I co-authored with Marco Oliva, Davide Cenzato, Zsuzsanna Lipták, Travis Gagie, and Christina Boucher has been accepted at the Data Compression Conference 2022 (DCC 22).

]]>Massimiliano Rossimaxrossi91@gmail.comInvited speaker at Pangenomics Bio Hacking 20212021-11-23T00:00:00-08:002021-11-23T00:00:00-08:00https://maxrossi91.com/posts/2021/11/PangenomicsBio-HackingI will be an invited speaker at the Pangenomics Bio Hacking 2021 and I will talk about my recent work on pangenomics.

MONI is a pangenomic index for finding maximal exact matches (MEMs), that is built on top of the r-index but also includes auxiliary data structures to allow finding approximate matches on a pangenomic scale. It includes many open-source tools and data structures such as BigBWT, BigRePair, and SDSL. I will talk about MONI, which is written in C++ and freely available at https://github.com/maxrossi91/moni.

I will present the organization of the source code and the structural choices behind MONI, the challenges of integrating all third-party open-source components, and the data-structure designs and organization strategies we used for handling large-scale data. In particular I will show how functionally equivalent implementations of the same component may drastically affect performance, even though their asymptotic complexity is the same.

]]>Massimiliano Rossimaxrossi91@gmail.comNew paper accepted at the 28th International Symposium on String Processing and Information Retrieval (SPIRE 2021)2021-07-14T00:00:00-07:002021-07-14T00:00:00-07:00https://maxrossi91.com/posts/2021/07/SPIREOur paper titled “Computing the original eBWT faster, simpler, and with less memory” I co-authored with Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, and Marinella Sciortino has been accepted at the 28th International Symposium on String Processing and Information Retrieval (SPIRE 2021).

]]>Massimiliano Rossimaxrossi91@gmail.comNew paper published in iScience2021-06-25T00:00:00-07:002021-06-25T00:00:00-07:00https://maxrossi91.com/posts/2021/06/iScienceOur paper titled, “Pan-genomic Matching Statistics for Targeted Nanopore Sequencing” I co-authored with Omar Ahmed, Sam Kovaka, Michael C. Schatz, Travis Gagie, Christina Boucher, and Ben Langmead, has been published in iScience. [link]

]]>Massimiliano Rossimaxrossi91@gmail.comNew paper accepted at the RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-Seq 2021)2021-04-27T00:00:00-07:002021-04-27T00:00:00-07:00https://maxrossi91.com/posts/2021/04/RECOMB-SEQOur paper titled, “Pan-genomic Matching Statistics for Targeted Nanopore Sequencing” I co-authored with Omar Ahmed, Sam Kovaka, Michael C. Schatz, Travis Gagie, Christina Boucher, and Ben Langmead, has been accepted at the 11th RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-Seq 2021).

]]>Massimiliano Rossimaxrossi91@gmail.comNew paper published in the Journal of Experimental Algorithmics (JEA)2020-12-31T00:00:00-08:002020-12-31T00:00:00-08:00https://maxrossi91.com/posts/2020/12/JEAOur paper titled “Pattern Discovery in Colored Strings” I co-authored with Zsuzsanna Lipták and Simon J. Puglisi has been published in the Journal of Experimental Algorithmics (JEA). [link]

]]>Massimiliano Rossimaxrossi91@gmail.comNew paper accepted at the Data Compression Conference 2021(DCC 21)2020-12-30T00:00:00-08:002020-12-30T00:00:00-08:00https://maxrossi91.com/posts/2020/12/DCC/DCC-2Our paper titled “PHONI: Streamed Matching Statisticswith Multi-Genome References” I co-authored with Christina Boucher, Travis Gagie, Tomohiro I, Dominik Köppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, and Alejandro Pacheco has been accepted at the Data Compression Conference 2021 (DCC 21).

]]>Massimiliano Rossimaxrossi91@gmail.comNew paper accepted at the Data Compression Conference 2021(DCC 21)2020-12-30T00:00:00-08:002020-12-30T00:00:00-08:00https://maxrossi91.com/posts/2020/12/DCC/DCC-1Our paper titled “Efficiently Merging r-indexes” I co-authored with Marco Oliva, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, and Christina Boucher has been accepted at the Data Compression Conference 2021 (DCC 21).

]]>Massimiliano Rossimaxrossi91@gmail.comNew paper accepted at the 25th International Conference On Research In Computational Molecular Biology (RECOMB21)2020-12-21T00:00:00-08:002020-12-21T00:00:00-08:00https://maxrossi91.com/posts/2020/12/RECOMBOur paper titled “MONI: A Pangenomics Index for Finding MEMs” I co-authored with Christina Boucher, Travis Gagie, Ben Langmead, and Marco Oliva has been accepted at the 25th International Conference On Research In Computational Molecular Biology (RECOMB21).

]]>Massimiliano Rossimaxrossi91@gmail.comNew paper accepted at the SIAM Symposium on Algorithm Engineering and Experiments (ALENEX21)2020-10-07T00:00:00-07:002020-10-07T00:00:00-07:00https://maxrossi91.com/posts/2020/10/ALENEXOur paper titled “PFP Compressed Suffix Trees” I co-authored with Christina Boucher, Ondřej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, and Gonzalo Navarro has been accepted at the SIAM Symposium on Algorithm Engineering and Experiments (ALENEX21).

]]>Massimiliano Rossimaxrossi91@gmail.com