Search Results - "Comin, Matteo"

MetaCon: unsupervised clustering of metagenomic contigs with probabilistic k-mers statistics and coverage by Qian, Jia, Comin, Matteo

“…Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically…”
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MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures by Girotto, Samuele, Pizzi, Cinzia, Comin, Matteo

“…Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Taxonomic analysis of microbial…”
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Better quality score compression through sequence-based quality smoothing by Shibuya, Yoshihiro, Comin, Matteo

“…Current NGS techniques are becoming exponentially cheaper. As a result, there is an exponential growth of genomic data unfortunately not followed by an…”
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Benchmarking of alignment-free sequence comparison methods by Zielezinski, Andrzej, Girgis, Hani Z, Bernard, Guillaume, Leimeister, Chris-Andre, Tang, Kujin, Dencker, Thomas, Lau, Anna Katharina, Röhling, Sophie, Choi, Jae Jin, Waterman, Michael S, Comin, Matteo, Kim, Sung-Hou, Vinga, Susana, Almeida, Jonas S, Chan, Cheong Xin, James, Benjamin T, Sun, Fengzhu, Morgenstern, Burkhard, Karlowski, Wojciech M

“…Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed…”
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Efficient computation of spaced seed hashing with block indexing by Girotto, Samuele, Comin, Matteo, Pizzi, Cinzia

“…Spaced-seeds, i.e. patterns in which some fixed positions are allowed to be wild-cards, play a crucial role in several bioinformatics applications involving…”
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Fast alignment of reads to a variation graph with application to SNP detection by Monsu, Maurilio, Comin, Matteo

“…Sequencing technologies has provided the basis of most modern genome sequencing studies due to its high base-level accuracy and relatively low cost. One of the…”
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Higher recall in metagenomic sequence classification exploiting overlapping reads by Girotto, Samuele, Comin, Matteo, Pizzi, Cinzia

“…In recent years several different fields, such as ecology, medicine and microbiology, have experienced an unprecedented development due to the possibility of…”
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Alignment-free phylogeny of whole genomes using underlying subwords by Comin, Matteo, Verzotto, Davide

“…With the progress of modern sequencing technologies a large number of complete genomes are now available. Traditionally the comparison of two related genomes…”
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Special Issue of the 1st International Applied Bioinformatics Conference (iABC'21) by Allmer, Jens, Elloumi, Mourad, Comin, Matteo, Hofestädt, Ralf

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FSH: fast spaced seed hashing exploiting adjacent hashes by Girotto, Samuele, Comin, Matteo, Pizzi, Cinzia

“…Patterns with wildcards in specified positions, namely , are increasingly used instead of -mers in many bioinformatics applications that require indexing,…”
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Classification of protein sequences by means of irredundant patterns by Comin, Matteo, Verzotto, Davide

“…The classification of protein sequences using string algorithms provides valuable insights for protein function prediction. Several methods, based on a variety…”
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Filtering Degenerate Patterns with Application to Protein Sequence Analysis by Comin, Matteo, Verzotto, Davide

“…In biology, the notion of degenerate pattern plays a central role for describing various phenomena. For example, protein active site patterns, like those…”
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Enhanced Compression of k-Mer Sets with Counters via de Bruijn Graphs by Rossignolo, Enrico, Comin, Matteo

“…An essential task in computational genomics involves transforming input sequences into their constituent k -mers. The quest for an efficient representation of…”
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ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs by Cavattoni, Margherita, Comin, Matteo

“…Current technologies allow the sequencing of microbial communities directly from the environment without prior culturing. One of the major problems when…”
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K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification by Storato, Davide, Comin, Matteo

“…The major problem when analyzing a metagenomic sample is to taxonomically annotate its reads to identify the species they contain. Most of the methods…”
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Covid-19 Pandemic’s Enduring Impact on Urban Mobility: The Case of Free-Floating Bike Sharing in Padova, Italy by Cavattoni, Margherita, Comin, Matteo, Silvestri, Francesco

“…The spread of the Covid-19 virus all around the globe drastically changed our lifestyles and our habits. Among all aspects affected by the pandemic, mobility…”
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Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns by Comin, Matteo, Schimd, Michele

“…With the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available,…”
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MetaProb 2: Metagenomic Reads Binning Based on Assembly Using Minimizers and K-Mers Statistics by Andreace, Francesco, Pizzi, Cinzia, Comin, Matteo

“…Current technologies allow the sequencing of microbial communities directly from the environment without prior culturing. One of the major problems when…”
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Mining, compressing and classifying with extensible motifs by Apostolico, Alberto, Comin, Matteo, Parida, Laxmi

“…Motif patterns of maximal saturation emerged originally in contexts of pattern discovery in biomolecular sequences and have recently proven a valuable notion…”
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SPRISS: approximating frequent k-mers by sampling reads, and applications by Santoro, Diego, Pellegrina, Leonardo, Comin, Matteo, Vandin, Fabio

“…Abstract Motivation The extraction of k-mers is a fundamental component in many complex analyses of large next-generation sequencing datasets, including reads…”
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