Molecular sequence analysis

alexeigurevich — Mon, 31 Mar 2014 08:31:40 +0000

Дата:

28 Mar 2014, Fri, 17:00

Докладчик:

Sergey Nurk

String Graph Assembly For Diploid Genomes With Long Reads (PacBio)

alexeigurevich — Thu, 20 Mar 2014 14:11:49 +0000

Дата:

21 Mar 2014, Fri, 16:00

Докладчик:

Dmitry Antipov

RECOMB talk rehearsal

alexeigurevich — Mon, 31 Mar 2014 12:32:46 +0000

Дата:

14 Mar 2014, Fri, 16:00

Докладчик:

Yana Safonova, Anton Bankevich

HyDA: Efficient synergistic single-cell genome assembly

alexeigurevich — Thu, 20 Mar 2014 14:18:52 +0000

Дата:

7 Mar 2014, Fri, 16:00

Докладчик:

Ira Vasilinec

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

alexeigurevich — Thu, 20 Mar 2014 14:15:42 +0000

Дата:

28 Feb 2014, Fri, 16:00

Докладчик:

Vlad Saveliev

Assembly of million nucleotides long reads

alexeigurevich — Tue, 11 Feb 2014 14:50:07 +0000

Дата:

12 Feb 2014, Wed, 20:00

Докладчик:

Andrey Prjibelski

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome.

Mugsy: fast multiple alignment of closely related whole genomes

alexeigurevich — Tue, 11 Feb 2014 14:47:33 +0000

Дата:

7 Feb 2014, Fri, 15:00

Докладчик:

Alexey Gurevich

Readjoiner: a fast and memory efficient string graph-based sequence assembler

alexeigurevich — Wed, 29 Jan 2014 12:27:17 +0000

Дата:

30 Jan 2014, Thu, 14:00

Докладчик:

Sergey Nurk

Understanding of antibody repertoires from sequencing data

alexeigurevich — Mon, 23 Dec 2013 05:59:16 +0000

Дата:

19 Dec 2013, Thu, 14:00

Докладчик:

Yana Safonova

- The Application of Next Generation Sequencing to the Understanding of Antibody Repertoires [review]

- IgM Repertoire Biodiversity is Reduced in HIV-1 Infection and Systemic Lupus Erythematosus

- The past, present, and future of immune repertoire biology – the rise of next-generation repertoire analysis [review]

- Sequencing antibody repertoires. The next generation [review]

- Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes.

Ragout - a tool for assisted assembly using multiple references

alexeigurevich — Wed, 04 Dec 2013 16:19:36 +0000

Дата:

5 Dec 2013, Thu, 14:00

Докладчик:

Mikhail Kolmogorov

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach

alexeigurevich — Sat, 23 Nov 2013 08:27:21 +0000

Дата:

15 Nov 2013, Fri, 16:00

Докладчик:

Alexey Gurevich

Partial order alignment

alexeigurevich — Tue, 29 Oct 2013 12:43:32 +0000

Дата:

1 Nov 2013, Fri, 14:00

Докладчик:

Dmitry Antipov

Smart pointers

alexeigurevich — Tue, 29 Oct 2013 13:10:20 +0000

Дата:

31 Oct 2013, Thu, 14:00

Докладчик:

Alexey Gurevich

HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data

alexeigurevich — Thu, 17 Oct 2013 13:51:15 +0000

Дата:

24 Oct 2013, Thu, 14:00

Докладчик:

Yana Safonova

HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data

Haplotype assembly in polyploid genomes and identical by descent shared tracts

Exact pattern matching with feed-forward bloom filters

alexeigurevich — Mon, 07 Oct 2013 13:01:11 +0000

Дата:

17 Oct 2013, Thu, 14:00

Докладчик:

Sergey Nurk

SPA: a short peptide assembler for metagenomic data

alexeigurevich — Mon, 07 Oct 2013 13:00:28 +0000

Дата:

11 Oct 2013, Fri, 14:00

Докладчик:

Andrey Prjibelski

"SRmapper: a fast and sensitive genome-hashing alignment tool" and "A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data"

alexeigurevich — Sat, 28 Sep 2013 04:50:42 +0000

Дата:

3 Oct 2013, Thu, 14:00

Докладчик:

Ira Vasilinec

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

alexeigurevich — Fri, 20 Sep 2013 13:23:58 +0000

Дата:

27 Sep 2013, Fri, 15:00

Докладчик:

Anton Bankevich

The MaSuRCA genome assembler

alexeigurevich — Fri, 20 Sep 2013 13:19:08 +0000

Дата:

20 Sep 2013, Fri, 15:00

Докладчик:

Alexey Gurevich

Uncovering the roles of rare variants in common disease through whole-genome sequencing

alexeigurevich — Wed, 22 May 2013 13:40:39 +0000

Дата:

16 May 2013, Thu, 16:00

Докладчик:

Ksenia Krasheninnikova

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs

alexeigurevich — Wed, 24 Apr 2013 14:38:18 +0000

Дата:

25 Apr 2013, Thu, 16:00

Докладчик:

Vlad Saveliev

Reference-assisted chromosome assembly

alexeigurevich — Thu, 28 Mar 2013 12:48:43 +0000

Дата:

4 Apr 2013, Thu, 12:30

Докладчик:

Dmitry Antipov

Next generation sequencing for TCR repertoire profiling: platform—specific features and correction algorithms

alexeigurevich — Tue, 19 Mar 2013 14:32:15 +0000

Дата:

21 Mar 2013, Thu, 12:30

Докладчик:

Yana Safonova

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

alexeigurevich — Wed, 13 Mar 2013 18:57:39 +0000

Дата:

14 Mar 2013, Thu, 12:30

Докладчик:

Alexey Gurevich

Ray, Telescoper, and PE assembler.

alexeigurevich — Wed, 20 Feb 2013 14:08:48 +0000

Дата:

21 Feb 2013, Thu, 13:00

Докладчик:

Andrey Prjibelski

CGAL: computing genome assembly likelihoods

alexeigurevich — Wed, 13 Feb 2013 13:48:32 +0000

Дата:

14 Feb 2013, Thu, 13:00

Докладчик:

Alexander Sirotkin

ALLPATHS-LG

alexeigurevich — Wed, 06 Feb 2013 13:42:17 +0000

Дата:

7 Feb 2013, Thu, 13:00

Докладчик:

Dmitry Antipov

Metagenomics

alexeigurevich — Thu, 24 Jan 2013 08:55:38 +0000

Дата:

24 Jan 2013, Thu, 13:00

Докладчик:

ABLab and ITMO

De novo co-assembly of bacterial genomes from multiple single cells

alexeigurevich — Fri, 18 Jan 2013 08:46:41 +0000

Дата:

17 Jan 2013, Thu, 13:00

Докладчик:

Sergey Nurk

Genovo: De Novo Assembly for Metagenomes

alexeigurevich — Wed, 12 Dec 2012 15:08:18 +0000

Дата:

13 Dec 2012, Thu, 12:30

Докладчик:

Alexander Sirotkin

Abstract. Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A Chinese restaurant process prior accounts for the unknown number of genomes in the sample. Inference is made by applying a series of hill-climbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs across one synthetic dataset and eight metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo’s reconstructions cover more bases and recover more genes than the other methods, and yield a higher assembly score.

EULER-AIR and GraphLab

alexeigurevich — Wed, 21 Nov 2012 14:20:43 +0000

Дата:

22 Nov 2012, Thu, 12:30

Докладчик:

Sergey Nikolenko

Novel applications of nanobodies for in vivo bio-imaging of inflamed tissues in inflammatory diseases and cancer

alexeigurevich — Wed, 06 Nov 2013 09:06:32 +0000

Дата:

8 Nov 2012, Thu, 14:00

Докладчик:

Kira Vyatkina

Meta-IDBA and Meta-Velvet, assemblers for metagenome datasets

alexeigurevich — Wed, 24 Oct 2012 12:44:03 +0000

Дата:

25 Oct 2012, Thu, 14:00

Докладчик:

Dmitry Antipov

Stem cells and bioinformatics challenges

Nikolay Vyahhi — Fri, 12 Oct 2012 07:04:50 +0000

Дата:

12 Oct 2012, Fri, 14:00

Докладчик:

Prof. Kiselev S.L. Moscow, The Vavilov Institute of General Genetics (VIGG)

Pluripotent stem cells are the cells that can differentiate into any cell type of the body. There are two sources for human pluripotent stem cells: embryonic stem (ES) cells derived from surplus early preimplantation embryos created for in vitro fertilization and induced pluripotent stem (iPS) cells generated by genetic reprogramming of somatic cells. ES cells have been an area of intense research during the last decade and two clinical trials have been recently approved. iPS cells were created only recently and most of the research has been focused on the iPS generation protocols and investigation of mechanisms of direct reprogramming. iPS technology makes possible to derive pluripotent stem cells from any patient. However there is a number of hurdles to be overcome before iPS cells will find a niche in practice. The important question is how close iPS cells are to their natural analogue ES cells in their genetic and epigenetic properties. To address this issue we recently established a system allowing human ES cells differentiation to any particular cell type followed by reverse procedure of reprogramming to the pluripotent state. Isogenic “forth and back” system makes possible to perform genome-wide detailed comparison of human pluripotent cells and to distinguish traces of the reprogramming process from the genetic and epigenetic differences between various allogenic cell lines.

Despite the equivalency of induced pluripotent and embryonic stem cells it is still an unresolved issue, we have generated a number of iPS cell lines from the patients with various disorders for disease modeling and new therapies development.

Growing numbers of genome-wide sequencing approaches, versions of microarrys and batch-to-batch variations as well as the amount of already collected data complicate output data analysis.

Stem cells and bioinformatics challenges

alexeigurevich — Wed, 10 Oct 2012 13:04:08 +0000

Дата:

12 Oct 2012, Fri, 14:00

Докладчик:

Prof. Kiselev S.L., Moscow, The Vavilov Institute of General Genetics (VIGG)

Growing numbers of genome-wide sequencing approaches, versions of microarrys and batch-to-batch variations as well as the amount of already collected data complicate output data analysis.

Note: the talk will be in room 206!!!

A proteomics approach for the identification and cloning of monoclonal antibodies from serum

Nikolay Vyahhi — Wed, 03 Oct 2012 09:49:23 +0000

Дата:

4 Oct 2012, Thu, 12:30

Докладчик:

Nikolay Vyahhi

Molecular sequence analysis

String Graph Assembly For Diploid Genomes With Long Reads (PacBio)

RECOMB talk rehearsal

HyDA: Efficient synergistic single-cell genome assembly

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

Assembly of million nucleotides long reads

Mugsy: fast multiple alignment of closely related whole genomes

Readjoiner: a fast and memory efficient string graph-based sequence assembler

Understanding of antibody repertoires from sequencing data

Ragout - a tool for assisted assembly using multiple references

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach

Partial order alignment

Smart pointers

HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data

Exact pattern matching with feed-forward bloom filters

SPA: a short peptide assembler for metagenomic data

"SRmapper: a fast and sensitive genome-hashing alignment tool" and "A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data"

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

The MaSuRCA genome assembler

Uncovering the roles of rare variants in common disease through whole-genome sequencing

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs

Reference-assisted chromosome assembly

Next generation sequencing for TCR repertoire profiling: platform—specific features and correction algorithms

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

Ray, Telescoper, and PE assembler.

CGAL: computing genome assembly likelihoods

ALLPATHS-LG

Metagenomics

De novo co-assembly of bacterial genomes from multiple single cells

Genovo: De Novo Assembly for Metagenomes

EULER-AIR and GraphLab

Novel applications of nanobodies for in vivo bio-imaging of inflamed tissues in inflammatory diseases and cancer

Meta-IDBA and Meta-Velvet, assemblers for metagenome datasets

Stem cells and bioinformatics challenges

Stem cells and bioinformatics challenges

A proteomics approach for the identification and cloning of monoclonal antibodies from serum

The cactus graph

Determinism and stochasticity during maturation of the zebrafish antibody repertoire.

Hybrid Error Correction and De Novo Assembly of Single-Molecule Sequencing Reads

Hapsembler

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Disease (Ulitsky, Shamir et al)

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes

organelles; central dogma special cases.

GASV Software

Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi

Chromosomal Basis of Heredity, Meiosis and Gametogenesis

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

Reconstructing cancer genomes from paired-end sequencing data

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Journal Club: Assisted assembly

Journal Club: A high-resolution map of human evolutionary constraint using 29 mammals

Proteomics BootCamp (LAB projects in Computational Proteomics)

Genome Rearrangement Bootcamp

Peptide Sequence TagsPeptide Sequence Tags: Generation and Applications

Opera and MIP scaffolders

Metagenomic discovery of biomass-degrading genes and genomes from cow rumen (Science, 2011 Jan).

Genome Rearrangement - Introduction

Path-set: novel approach to repeat resolving

Structural variation in two human genomes using de novo assembly

Protein identificaion be spectral network analysis

A ranking-based scoring function for peptide-spectrum matches, part 2

A ranking-based scoring function for peptide-spectrum matches, part 1

Aligners + visualizers

Talk by Son

Journal Club

Tech talk - git, tmux

С++ talking

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De Novo peptide sequencing (Dancik et al., 1999 and Frank, 2009)

Peptide spectrum matching

С++ talking

Blocked Pattern Matching: Open problems

Target-Decoy Search in MS: When things may go wrong

Spectral probabilities and spectral dictionaries

Intro to computational MS

New possibilities of high-resolution mass-spectrometry at top-down and bottom up proteomics

Seaweeds

C++ talking

Methods for finding frequent items in data stream