List of works - Inanc Birol

A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations.

scientific article

A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance.

scientific article published on 15 January 2017

A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations.

scientific article published on 8 February 2018

A search for νμ→ντ oscillation

article

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.

scientific article

ABySS: a parallel assembler for short read sequence data

scientific article (publication date: June 2009)

ARCS: scaffolding genome drafts with linked reads.

scientific article published on 23 October 2017

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

scientific article

Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles

scientific article published in Scientific Reports

Approximately conserved quantity in the Hénon-Heiles problem

scientific article published on 01 November 1995

Assembling genomes using short-read sequencing technology.

scientific article published on 28 January 2010

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

scientific article

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

scientific article

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies

scientific article

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.

scientific article

Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

scientific article published in January 2023

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

scientific article published on 29 December 2017

Circos: an information aesthetic for comparative genomics

scientific article (publication date: September 2009)

Complete Chloroplast Genome Sequence of a Black Spruce (Picea mariana) from Eastern Canada

scientific article published on 24 September 2020

Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease

scientific article published on 14 September 2017

Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers

scientific article

DIDA: Distributed Indexing Dispatched Alignment.

scientific article published on 29 April 2015

De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

scientific article published on 29 June 2015

De novo assembly and analysis of RNA-seq data.

scientific article

De novo assembly of the ringed seal (Pusa hispida) blubber transcriptome: A tool that enables identification of molecular health indicators associated with PCB exposure

scientific article published on 03 February 2017

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

scientific article

De novo transcriptome assembly with ABySS.

scientific article

Dissect: detection and characterization of novel structural alterations in transcribed sequences

scientific article

Divergent clonal selection dominates medulloblastoma at recurrence

scientific article published on 13 January 2016

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

scientific article

Effect of environment partitioning on the survival and coexistence of autocatalytic replicators.

scientific article

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors

scientific article

Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size

scientific article

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

scientific article

GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies

scientific article published on 01 November 2021

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia

scientific article

Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen

scientific article

Genome sequence of Mycoplasma capricolum subsp. capripneumoniae strain M1601.

scientific article

Genome sequences of six Phytophthora species threatening forest ecosystems.

scientific article published on 3 October 2016

Genome-Enhanced Detection and Identification (GEDI) of plant pathogens.

scientific article published on 22 February 2018

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

scientific article published on 11 September 2008

Genomic analysis of a rare human tumor

scientific article published on 23 July 2010

Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98.

scientific article published on 31 August 2017

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

scientific article

Hive plots--rational approach to visualizing networks.

scientific article published on 9 December 2011

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline.

scientific article published on 28 May 2013

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

scientific article published on 28 May 2015

Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art

scientific article

Insights into conifer giga-genomes

scientific article

JAGuaR: junction alignments to genome for RNA-seq reads

scientific article

Konnector v2.0: pseudo-long reads from paired-end sequencing data

scientific article

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.

scientific article published on 4 August 2015

Large-scale profiling of microRNAs for The Cancer Genome Atlas.

scientific article published on 13 August 2015

Linear time complexity de novo long read genome assembly with GoldRush

scientific article published on 22 May 2023

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

scientific article

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce

scientific article published on 27 January 2024

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage

scientific article published in 2022

Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters

scientific article published on 08 July 2020

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing

scientific article published on 22 May 2013

NanoSim: nanopore sequence read simulator based on statistical characterization

scientific article

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

scientific article published on 8 December 2015

RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes

scientific article published on 17 August 2020

Recurrent targets of aberrant somatic hypermutation in lymphoma

scientific article

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

scientific article published on 13 July 2018

Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis

scientific article

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

scientific article published on 22 May 2023

Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs

scientific article published on 01 October 2019

Retrospective in silico HLA predictions from COVID-19 patients reveal alleles associated with disease prognosis

scientific article published on 02 November 2020

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.

scientific article published in March 2011

Sealer: a scalable gap-closing application for finishing draft genomes.

scientific article published on 25 July 2015

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

scientific article

Spruce giga‐genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes

scientific article published in 2022

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

scientific article

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data

scientific article published on 10 September 2018

The CHORUS experiment to search for νμ → ντ oscillation

article

The Genome of the Beluga Whale (Delphinapterus leucas).

scientific article published on 11 December 2017

The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis

article

The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).

scientific article published on 11 December 2017

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.

scientific article

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

scientific article (publication date: 4 April 2012)

The genetic landscape of high-risk neuroblastoma

scientific article published on 20 January 2013

The genome of the forest insect pest <i>Pissodes strobi</i> reveals genome expansion and evidence of a <i>Wolbachia</i> endosymbiont

scientific article published in 2022

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

scientific article

Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data

scientific article published on 01 June 2020

UniqTag: Content-derived unique and stable identifiers for gene annotation

article

Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees

scientific article

Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii

scientific article published in 2013

Whole-genome sequencing and social-network analysis of a tuberculosis outbreak

scientific article (publication date: 24 February 2011)

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

scientific article

ntCard: a streaming algorithm for cardinality estimation in genomics data

scientific article

ntHash: recursive nucleotide hashing

scientific article published on 16 July 2016

List of works by Inanc Birol

A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations.

A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance.

A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations.

A search for νμ→ντ oscillation

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.

ABySS: a parallel assembler for short read sequence data

ARCS: scaffolding genome drafts with linked reads.

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

Antimicrobial peptides from Rana [Lithobates] catesbeiana: Gene structure and bioinformatic identification of novel forms from tadpoles

Approximately conserved quantity in the Hénon-Heiles problem

Assembling genomes using short-read sequencing technology.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.

Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Circos: an information aesthetic for comparative genomics

Complete Chloroplast Genome Sequence of a Black Spruce (Picea mariana) from Eastern Canada

Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease

Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers

DIDA: Distributed Indexing Dispatched Alignment.

De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

De novo assembly and analysis of RNA-seq data.

De novo assembly of the ringed seal (Pusa hispida) blubber transcriptome: A tool that enables identification of molecular health indicators associated with PCB exposure

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

De novo transcriptome assembly with ABySS.

Dissect: detection and characterization of novel structural alterations in transcribed sequences

Divergent clonal selection dominates medulloblastoma at recurrence

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

Effect of environment partitioning on the survival and coexistence of autocatalytic replicators.

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors

Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies

Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia

Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen

Genome sequence of Mycoplasma capricolum subsp. capripneumoniae strain M1601.

Genome sequences of six Phytophthora species threatening forest ecosystems.

Genome-Enhanced Detection and Identification (GEDI) of plant pathogens.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

Genomic analysis of a rare human tumor

Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98.

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

Hive plots--rational approach to visualizing networks.

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline.

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism

Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art

Insights into conifer giga-genomes

JAGuaR: junction alignments to genome for RNA-seq reads

Konnector v2.0: pseudo-long reads from paired-end sequencing data

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.

Large-scale profiling of microRNAs for The Cancer Genome Atlas.

Linear time complexity de novo long read genome assembly with GoldRush

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene βglu-1 with large variations in white spruce but not Norway spruce

Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage

Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters

Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing

NanoSim: nanopore sequence read simulator based on statistical characterization

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation

RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes

Recurrent targets of aberrant somatic hypermutation in lymphoma

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs

Retrospective in silico HLA predictions from COVID-19 patients reveal alleles associated with disease prognosis

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.

Sealer: a scalable gap-closing application for finishing draft genomes.

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

Spruce giga‐genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes

Subgroup-specific structural variation across 1,000 medulloblastoma genomes

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data

The CHORUS experiment to search for νμ → ντ oscillation

The Genome of the Beluga Whale (Delphinapterus leucas).

The Genome of the North American Brown Bear or Grizzly: Ursus arctos ssp. horribilis

The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).

The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.