Timeline

Rayan Chikhi

Head of Structure

01 Dec 2024

publication

Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes.

24 Mar 2024

event

Pr[AI]rie Scientific Workshop

30 Nov 2023

publication

Comparing methods for constructing and representing human pangenome graphs

17 Nov 2023

publication

aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.

06 Nov 2023

publication

decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.

30 Jun 2023

publication

Efficient mapping of accurate long reads in minimizer space with mapquik.

22 Dec 2022

publication

SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.

18 Nov 2022

publication

Mapping-friendly sequence reductions: Going beyond homopolymer compression.

29 Jul 2022

publication

The K-mer File Format: a standardized and compact disk representation of sets of k-mers

06 Oct 2021

event

2021 Computational Biology Department Days

14 Sep 2021

publication

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.

26 Jul 2021

news

Strainberry: automated strain separation in low-complexity metagenomes using long reads

23 Jul 2021

publication

Strainberry: automated strain separation in low-complexity metagenomes using long reads.

27 May 2021

event

DCB Seminar- C. Titus Brown: “Lightweight and large scale (meta)genome analysis: chasing strain variation across a million genomes!”

25 Aug 2020

publication

A Graph-Theoretic Barcode Ordering Model for Linked-Reads

24 Jun 2019

publication

Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

26 May 2019

publication

Parallel decompression of gzip-compressed files and random access to DNA sequences

03 May 2019

event

[C3BI Seminar]- Eran Halperin: New computational tools for the analysis of microbiome dynamics

27 Mar 2019

publication

Graph analysis of fragmented long-read bacterial genome assemblies

15 Jan 2019

team

A little guide for advanced search:

Timeline

Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes.

Pr[AI]rie Scientific Workshop

Comparing methods for constructing and representing human pangenome graphs

aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.

decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.

Efficient mapping of accurate long reads in minimizer space with mapquik.

SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.

Mapping-friendly sequence reductions: Going beyond homopolymer compression.

The K-mer File Format: a standardized and compact disk representation of sets of k-mers

2021 Computational Biology Department Days

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.

Strainberry: automated strain separation in low-complexity metagenomes using long reads

Strainberry: automated strain separation in low-complexity metagenomes using long reads.

DCB Seminar- C. Titus Brown: “Lightweight and large scale (meta)genome analysis: chasing strain variation across a million genomes!”

A Graph-Theoretic Barcode Ordering Model for Linked-Reads

Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

Parallel decompression of gzip-compressed files and random access to DNA sequences

[C3BI Seminar]- Eran Halperin: New computational tools for the analysis of microbiome dynamics

Graph analysis of fragmented long-read bacterial genome assemblies

Sequence Bioinformatics