Publication

Chemical approach for the study of the 'kissing complex' of Moloney murine leukaemia Virus

Publications associées (28)

An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

ASSOC COMPUTING MACHINERY2019

Toward a Dynamic Threshold for Quality-Score Distortion in Reference-Based Alignment

Marco Mattavelli, Claudio Paolo Alberti, Ana Angelica Hernandez Lopez

The intrinsic high entropy metadata, known as quality scores, are largely the cause of the substantial size of sequence data files. Yet, there is no consensus on a viable reduction of the resolution of the quality score scale, arguably because of collatera ...

2019

On the relevance of quality score metadata in genomic sequence data for omics applications

Ana Angelica Hernandez Lopez

High-throughput sequencing of DNA molecules has revolutionized biomedical research by enabling the quantitative analysis of the genome to study its function, structure and dynamics. It is driving sequencing-based experiments in life sciences as evidenced b ...

EPFL2019

A sequence-dependent coarse-grain model of B-DNA with explicit description of bases and phosphate groups parametrised from large scale Molecular Dynamics simulations

Alessandro Samuele Patelli

We introduce a sequence-dependent coarse-grain model of double-stranded DNA with an explicit description of both the bases and the phosphate groups as interacting rigid-bodies. The model parameters are trained on extensive, state-of-the-art large scale mol ...

EPFL2019

High level synthesis of Smith-Waterman dataflow implementations

Marco Mattavelli, Endri Bezati, Simone Casale Brunet

The paper presents the results of design explorations for the implementation of the Smith-Waterman (S-W) algorithm executing DNA and protein sequences alignment. Both design explorations studies and the corresponding FPGA implementations are obtained by wr ...

2017

Persona: A High-Performance Bioinformatics Framework

Edouard Bugnion, Christos Kozyrakis, Sam David Whitlock, James Richard Larus, Stuart Anthony Byma

Next-generation genome sequencing technology has reached a point at which it is becoming cost-effective to sequence all patients. Biobanks and researchers are faced with an oncoming deluge of genomic data, whose processing requires new and scalable bioinfo ...

2017

PROPER: global protein interaction network alignment through percolation matching

Matthias Grossglauser, Seyed Hamed Hassani, Ehsan Kazemi, Hasan Pezeshgi Modarres

Background The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological know ...

2016

Network Alignment: Theory, Algorithms, and Applications

Ehsan Kazemi

Networks are central in the modeling and analysis of many large-scale human and technical systems, and they have applications in diverse fields such as computer science, biology, social sciences, and economics. Recently, network mining has been an active a ...

EPFL2016