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  1. No Access

    Article

    Gene trajectory inference for single-cell data by optimal transport metrics

    Single-cell RNA sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typica...

    Rihao Qu, **uyuan Cheng, Esen Sefik, Jay S. Stanley III… in Nature Biotechnology (2024)

  2. Article

    Open Access

    Identifying peaks in *-seq data using shape information

    Peak calling is a fundamental step in the analysis of data generated by ChIP-seq or similar techniques to acquire epigenetics information. Current peak callers are often hard to parameterise and may therefore ...

    Francesco Strino, Michael Lappe in BMC Bioinformatics (2016)

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  3. No Access

    Article

    FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

    Screening of cells transduced with a lentivirus library harboring nucleosome-free regions of mammalian genomes identifies cis elements that regulate transcription.

    Matthew Murtha, Zeynep Tokcaer-Keskin, Zuojian Tang, Francesco Strino… in Nature Methods (2014)

  4. No Access

    Article

    Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity

    The identification of glycan epitopes such as the histo-blood group ABH determinants as docking sites for bacterial/viral infections and signals in growth regulation fuels the interest to develop non-hydrolysa...

    Francesco Strino, Jenn-Huei Lii… in Journal of Computer-Aided Molecular Design (2010)

  5. No Access

    Article

    Computational studies on the interaction of ABO-active saccharides with the norovirus VA387 capsid protein can explain experimental binding data

    Norovirus strains are known to cause recurring epidemics of winter vomiting disease. The crystal structure of the capsid protein of VA387, a representative of the clinically important GII.4 genocluster, was re...

    Chaitanya A. K. Koppisetty, Waqas Nasir… in Journal of Computer-Aided Molecular Design (2010)

  6. No Access

    Article

    Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics

    Histo-blood group ABH antigens serve as recognition sites for infectious microorganisms and tissue lectins in intercellular communication, e.g. in tumor progression. Thus, they are of interest as a starting po...

    Francesco Strino, Jenn-Huei Lii… in Journal of Computer-Aided Molecular Design (2009)