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List of works by Alexej Abyzov

A comprehensive analysis of non-sequential alignments between all protein structures

scientific article (publication date: 16 November 2007)

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

scientific article published on 18 April 2016

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

scientific article

Active site prediction for comparative model structures with thematics

scientific article

AlleleSeq: analysis of allele-specific expression and binding in a network framework

scientific article published on 2 August 2011

An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces

scientific article

An integrated map of structural variation in 2,504 human genomes

scientific article

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets

scientific article

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms ⬇️

scientific article published on June 2015

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

scientific article (publication date: December 2013)

Annual Research Review: The promise of stem cell research for neuropsychiatric disorders

scientific article

Architecture of the human regulatory network derived from ENCODE data

scientific article (publication date: 6 September 2012)

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

scientific article

Child development and structural variation in the human genome

scientific article published on 13 January 2013

Chromatin organization modulates the origin of heritable structural variations in human genome

scientific article published on 01 April 2019

Colorectal Cancer with Residual Polyp of Origin: A Model of Malignant Transformation

scientific article published on 09 July 2016

Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection

scientific article published on 28 November 2019

Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans.

scientific article

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

scientific article published on 08 February 2019

Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues Using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide Variants

scientific article published on 01 January 2018

Different mutational rates and mechanisms in human cells at pregastrulation and neurogenesis.

scientific article published on 7 December 2017

Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis.

scientific article

Erratum: Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

scientific article published in Nature Communications

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders

scientific article (publication date: 16 July 2015)

Friend, an integrated analytical front-end application for bioinformatics

scientific article published on 2 August 2005

Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms

scientific article

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2

scientific article published on 01 May 2019

Human induced pluripotent stem cells for modelling neurodevelopmental disorders.

scientific article

Inferring modes of evolution from colorectal cancer with residual polyp of origin.

scientific article published on 26 December 2017

Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions

scientific article published on 15 September 2011

Integrative annotation of variants from 1092 humans: application to cancer genomics

scientific article

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network

scientific article

Landscape and variation of novel retroduplications in 26 human populations.

scientific article

MSB: a mean-shift-based approach for the analysis of structural variation in the genome

scientific article published on 26 November 2008

Mapping copy number variation by population-scale genome sequencing

scientific article

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

scientific article published on 10 April 2015

Molecular characterization of colorectal adenomas with and without malignancy reveals distinguishing genome, transcriptome and methylome alterations

scientific article published on 16 February 2018

Molecular signatures of multiple myeloma progression through single cell RNA-Seq

scientific article published on 03 January 2019

Neurological safety of oxaliplatin in patients with uncommon variants in Charcot-Marie-tooth disease genes

scientific article published on 14 January 2020

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.

scientific article

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

scientific article (publication date: 23 February 2009)

Regulatory element copy number differences shape primate expression profiles.

scientific article

RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes

scientific article published in February 2010

SCELLECTOR: ranking amplification bias in single cells using shallow sequencing

scientific article published on 12 November 2020

Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors.

scientific article published on 29 December 2015

Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells

scientific article

Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point

scientific article

Structural exon database, SEDB, mapping exon boundaries on multiple protein structures

scientific article published on 26 February 2004

Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways

scientific article published on 30 May 2007

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method

scientific article

Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance)

scientific article

The PsychENCODE project

scientific article

Transcriptome and epigenome landscape of human cortical development modeled in organoids

scientific article

UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB.

scientific article published on December 2007

Understanding genome structural variations

scientific article published on 7 December 2015

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

scientific article published on 17 December 2014

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