List of works - Can Alkan

A Draft Sequence of the Neandertal Genome

scientific article

A burst of segmental duplications in the genome of the African great ape ancestor

scientific article published on February 2009

A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD

scientific article

A high-coverage genome sequence from an archaic Denisovan individual

scientific article

A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk

scientific article

A robust benchmark for detection of germline large deletions and insertions

scientific article published on 15 June 2020

Accelerating read mapping with FastHASH.

scientific article

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells

scientific article published on 14 January 2015

Alu repeat discovery and characterization within human genomes

scientific article

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

scientific article

Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome

scientific article

Annotated features of domestic cat - Felis catus genome

scientific article

Author Correction: A robust benchmark for detection of germline large deletions and insertions

scientific article published on 22 July 2020

Author Correction: Comparative and demographic analysis of orang-utan genomes

correction of a scholarly article

Building and Improving Reference Genome Assemblies

Can you Really Anonymize the Donors of Genomic Data in Today’s Digital World?

Characterization of missing human genome sequences and copy-number polymorphic insertions

scientific article

Characterization of segmental duplications and large inversions using Linked-Reads

Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools

scientific article published on 05 August 2019

Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X.

scientific article

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

scientific article published on 15 May 2009

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

scientific article

Comparative and demographic analysis of orang-utan genomes

scientific article

Complete Khoisan and Bantu genomes from southern Africa

scientific article

Copy number variation of individual cattle genomes using next-generation sequencing

scientific article published on 2 February 2012

Death and resurrection of the human IRGM gene

scientific article published in March 2009

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

scientific article

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

scientific article

Detection of structural variants and indels within exome data

scientific article

Determining the origin of synchronous multifocal bladder cancer by exome sequencing.

scientific article published on 9 November 2015

Discovery and genotyping of novel sequence insertions in many sequenced individuals

scientific article published on July 2017

Discovery of large genomic inversions using long range information

scientific article

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

scientific article published on 01 October 2019

Diversity of human copy number variation and multicopy genes

scientific article

Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair

scientific article published on 24 April 2014

Erratum: A burst of segmental duplications in the genome of the African great ape ancestor

scientific article published in Nature

Evaluation of genome scaffolding tools using pooled clone sequencing

scientific article published on 10 December 2018

Fast and accurate mapping of Complete Genomics reads

scientific article

GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

scientific article published on 9 May 2018

GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping

scientific article published on 31 May 2017

Genetic history of an archaic hominin group from Denisova Cave in Siberia

scientific article

Genome sequencing highlights the dynamic early history of dogs

scientific article published in January 2014

Genome structural variation discovery and genotyping

scientific article published on March 2011

Genome-wide characterization of centromeric satellites from multiple mammalian genomes

scientific article (publication date: 2011)

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

scientific article

Great ape genetic diversity and population history

scientific article published on 03 July 2013

Haplotype-resolved genome sequencing of a Gujarati Indian individual.

scientific article

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

scientific article published on 01 November 2018

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas

scientific article published on 9 September 2011

Insights into hominid evolution from the gorilla genome sequence

scientific article

Inter-varietal structural variation in grapevine genomes

scientific article published on 15 July 2016

Limitations of next-generation genome sequence assembly

scientific article

Manipulating multiple sequence alignments via MaM and WebMaM

scientific article

Mapping and sequencing of structural variation from eight human genomes

scientific article

Mapping copy number variation by population-scale genome sequencing

scientific article

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

scientific article published on 2 April 2018

New insights into centromere organization and evolution from the white-cheeked gibbon and marmoset

scientific article

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

scientific article

On genomic repeats and reproducibility

scientific article published on 11 March 2016

Optimal design of oligonucleotide microarrays for measurement of DNA copy-number

article by Andrew J. Sharp et al published 28 August 2007 in Human Molecular Genetics

Optimal seed solver: optimizing seed selection in read mapping.

scientific article published on 14 November 2015

Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data

scientific article

Personalized copy number and segmental duplication maps using next-generation sequencing.

scientific article

Rates and patterns of great ape retrotransposition

scientific article published on 24 July 2013

Realizing the potential of blockchain technologies in genomics

scientific article published on 03 August 2018

Reconstructing complex regions of genomes using long-read sequencing technology

scientific article published on 13 January 2014

Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder

scientific article

Robustness of Massively Parallel Sequencing Platforms

scientific article published on 18 September 2015

SCALCE: boosting sequence compression algorithms using locally consistent encoding

scientific article

Sensitive and fast mapping of di-base encoded reads

scientific article

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

scientific article

Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping

scientific article published on 10 January 2015

Shouji: a fast and efficient pre-alignment filter for sequence alignment

scientific article published on 01 November 2019

Targeting PLK1 overcomes T-DM1 resistance via CDK1-dependent phosphorylation and inactivation of Bcl-2/xL in HER2-positive breast cancer.

scientific article published on 2 February 2018

The bonobo genome compared with the chimpanzee and human genomes

scientific article

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild

scientific article

The structure and evolution of centromeric transition regions within the human genome

scientific article published on 01 August 2004

Toolkit for automated and rapid discovery of structural variants

scientific article published on 2 June 2017

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa

scientific article

Whole-Genome Shotgun Sequence CNV Detection Using Read Depth

scientific article published on 01 January 2018

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications

scientific article

mrsFAST: a cache-oblivious algorithm for short-read mapping.

scientific article

taveRNA: a web suite for RNA algorithms and applications

scientific article published on 8 May 2007

List of works by Can Alkan

A Draft Sequence of the Neandertal Genome

A burst of segmental duplications in the genome of the African great ape ancestor

A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD

A high-coverage genome sequence from an archaic Denisovan individual

A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk

A robust benchmark for detection of germline large deletions and insertions

Accelerating read mapping with FastHASH.

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells

Alu repeat discovery and characterization within human genomes

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

Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome

Annotated features of domestic cat - Felis catus genome

Author Correction: A robust benchmark for detection of germline large deletions and insertions

Author Correction: Comparative and demographic analysis of orang-utan genomes

Building and Improving Reference Genome Assemblies

Can you Really Anonymize the Donors of Genomic Data in Today’s Digital World?

Characterization of missing human genome sequences and copy-number polymorphic insertions

Characterization of segmental duplications and large inversions using Linked-Reads

Characterizing microsatellite polymorphisms using assembly-based and mapping-based tools

Clcn4-2 genomic structure differs between the X locus in Mus spretus and the autosomal locus in Mus musculus: AT motif enrichment on the X.

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

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Comparative and demographic analysis of orang-utan genomes

Complete Khoisan and Bantu genomes from southern Africa

Copy number variation of individual cattle genomes using next-generation sequencing

Death and resurrection of the human IRGM gene

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

Detection of structural variants and indels within exome data

Determining the origin of synchronous multifocal bladder cancer by exome sequencing.

Discovery and genotyping of novel sequence insertions in many sequenced individuals

Discovery of large genomic inversions using long range information

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

Diversity of human copy number variation and multicopy genes

Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair

Erratum: A burst of segmental duplications in the genome of the African great ape ancestor

Evaluation of genome scaffolding tools using pooled clone sequencing

Fast and accurate mapping of Complete Genomics reads

GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping

Genetic history of an archaic hominin group from Denisova Cave in Siberia

Genome sequencing highlights the dynamic early history of dogs

Genome structural variation discovery and genotyping

Genome-wide characterization of centromeric satellites from multiple mammalian genomes

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Great ape genetic diversity and population history

Haplotype-resolved genome sequencing of a Gujarati Indian individual.

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

Hercules: a profile HMM-based hybrid error correction algorithm for long reads

Identification and validation of a novel mature microRNA encoded by the Merkel cell polyomavirus in human Merkel cell carcinomas

Insights into hominid evolution from the gorilla genome sequence

Inter-varietal structural variation in grapevine genomes

Limitations of next-generation genome sequence assembly

Manipulating multiple sequence alignments via MaM and WebMaM

Mapping and sequencing of structural variation from eight human genomes

Mapping copy number variation by population-scale genome sequencing

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

New insights into centromere organization and evolution from the white-cheeked gibbon and marmoset

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

On genomic repeats and reproducibility

Optimal design of oligonucleotide microarrays for measurement of DNA copy-number

Optimal seed solver: optimizing seed selection in read mapping.

Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data

Personalized copy number and segmental duplication maps using next-generation sequencing.

Rates and patterns of great ape retrotransposition

Realizing the potential of blockchain technologies in genomics

Reconstructing complex regions of genomes using long-read sequencing technology

Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder

Robustness of Massively Parallel Sequencing Platforms

SCALCE: boosting sequence compression algorithms using locally consistent encoding

Sensitive and fast mapping of di-base encoded reads

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping

Shouji: a fast and efficient pre-alignment filter for sequence alignment

Targeting PLK1 overcomes T-DM1 resistance via CDK1-dependent phosphorylation and inactivation of Bcl-2/xL in HER2-positive breast cancer.

The bonobo genome compared with the chimpanzee and human genomes

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild

The structure and evolution of centromeric transition regions within the human genome