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Papers
Our software is frequently cited
in independent research papers and
published in Nature, Science, and PLoS,
as well as other high-impact journals.
Selected papers
Papers citing CLC bio
2013
- Doubly heterozygous LMNA and TTN mutations revealed by exome sequencing in a severe form of dilated cardiomyopathy
- Molecular Phylogeny and Evolution of the Proteins Encoded by Coleoid (Cuttlefish, Octopus, and Squid) Posterior Venom Glands
- Metabolic model for the filamentous ‘Candidatus Microthrix parvicella’ based on genomic and metagenomic analyses
- Identification of genetic markers linked to anthracnose resistance in sorghum using association analysis
- Interpretation, Stratification and Evidence for Sequence Variants Affecting mRNA Splicing in Complete Human Genome Sequences
2012
- Multistrain genome analysis identifies candidate vaccine antigens of Anaplasma marginale
- RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus
- RNA-seq Analysis Reveals That an ECF σ Factor, AcsS, Regulates Achromobactin Biosynthesis in Pseudomonas syringae pv. syringae B728a
- Opsins in Onychophora (Velvet Worms) Suggest a Single Origin and Subsequent Diversification of Visual Pigments in Arthropods
- First draft genome sequence of the Japanese eel, Anguilla japonica
- A physical, genetic and functional sequence assembly of the barley genome
- Evidence for Lettuce big-vein associated virus as the causal agent of a syndrome of necrotic rings and spots in lettuce
- A framework for human microbiome research
- Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade
- Phylogenetic Analysis of the Complete Mitochondrial Genome of Madurella mycetomatis Confirms Its Taxonomic Position within the Order Sordariales
- Chimeric piggyBac transposases for genomic targeting in human cells
- Human ESC/iPSC-based ‘omics’ and bioinformatics for translational research
- Using ESTs database to predict and validate single polymorphisms at the HLA system
- Whole-Genome Sequencing and Genetic Variant Analysis of a Quarter Horse Mare
- Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock
- Genome Sequence of Staphylococcus aureus Strain 11819-97, an ST80-IV European Community-Acquired Methicillin-Resistant Isolate
- Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing
- Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.)
- Short Reads, Circular Genome: Skimming SOLiD Sequence to Construct the Bighorn Sheep Mitochondrial Genome
- Carriage of an ACME II Variant may have contributed to MRSA ST239-like Strain Replacement in Liverpool Hospital, Sydney, Australia
- Computational Prediction and Molecular Characterization of an Oomycete Effector and the Cognate Arabidopsis Resistance Gene
- RNA-Seq Analysis of Developing Nasturtium Seeds (Tropaeolum majus): Identification and Characterization of an additional Galactosyltransferase Involved in Xyloglucan Biosynthesis
- High-throughput molecular diagnosis of von Willebrand disease by next generation sequencing methods
- Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant
- Ion Torrent Personal Genome Machine Sequencing for Genomic Typing of Neisseria meningitidis for Rapid Determination of Multiple Layers of Typing Information
- Deep Sequencing Reveals Minor Protease Resistance Mutations in Patients Failing a Protease Inhibitor Regimen
- TRAPPC9-related autosomal recessive intellectual disability: report of a new mutation and clinical phenotype
- Global analysis of DNA methylation in early-stage liver fibrosis
- Targeted exome sequencing in clear cell renal cell carcinoma tumors suggests aberrant chromatin regulation as a crucial step in ccRCC development
- Applications of next-generation sequencing in plant biology
- Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions
- Agammaglobulinemia and absent B lineage cells in a patient lacking the p85α subunit of PI3K
- Application of Genomic Tools in Plant Breeding
- High Prevalence of Respiratory Ciliary Dysfunction in Congenital Heart Disease Patients With Heterotaxy
- Bioinformatic analysis to discover putative drug targets against diarrheal causative agents
- Down-regulation of ANAPC13 and CLTCL1: Early Events in the Progression of Preinvasive Ductal Carcinoma of the Breast
- Characterization of the Tawgar Gene Mapped to the Intragenic HUMARA Gene in Benign Prostate Tissue-Derived Human Prostate Cancer Cell Line
- Characterization of mtDNA variation in a cohort of South African paediatric patients with mitochondrial disease
- Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
- Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny
- Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing
2011
- Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens
- Tight control of mycotoxin biosynthesis gene expression in Aspergillus flavus by temperature as revealed by RNA-Seq
- RNA-Seq Reveals an Integrated Immune Response in Nucleated Erythrocytes
- Second messenger role for Mg2+ revealed by human T-cell immunodeficiency
- A cryptic deletion in 5q31.2 provides further evidence for a minimally deleted region in myelodysplastic syndromes
- Absence of Common Somatic Alterations in Genes on 1p and 19q in Oligodendrogliomas
- Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1 causing citrus bacterial spot and related strains provides insights into virulence and host-specificity
- Complete Genome Sequence of Propionibacterium acnes Type IB strain 6609
- HDAC inhibitors and decitabine are highly synergistic and associated with unique gene expression and epigenetic profiles in models of DLBCL
- Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
- Second messenger role for Mg2+ revealed by human T-cell immunodeficiency
- Everything at once: Comparative analysis of the genomes of bacterial pathogens
- Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses
- A Selectable and Excisable Marker System for the Rapid Creation of Recombinant Poxviruses
- Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species
- Damage-induced localized hypermutability
- Screening for antimicrobial resistance genes and virulence factors via genome sequencing
- Next-generation sequencing and its applications in molecular diagnostics
- Molecular diagnosis for heterogeneous genetic diseases with targeted high-throughput DNA sequencing applied to retinitis pigmentosa
- A comparison of analog and Next-generation transcriptomic tools for mammalian studies
- The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus
- Directed Culturing of Microorganisms Using Metatranscriptomics
- Unraveling the Evolution of Auxin Signaling
- Elucidation of the Regulon and cis-Acting Regulatory Element of HrpB, the AraC-Type Regulator of a Plant Pathogen-Like Type III Secretion System in Burkholderia pseudomallei
- Genomic Stability over 9 Years of an Isoniazid Resistant Mycobacterium tuberculosis Outbreak Strain in Sweden
- Next-Generation Sequencing: A Revolutionary Tool for Toxicogenomics
- Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy
- Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs
- Fluorescent-antibody staining assays for human Cryptosporidium detect oocysts of Cryptosporidium molnari from fish
- Detection of small RNAs in Bordetella pertussis and identification of a novel repeated genetic element
- Stimulating denitrification in a stream mesocosm with elemental sulfur as an electron donor
- Antennal transcriptome of Manduca sexta
- Prevalence and dispersal of a facultative bacterial symbiont associated with an endemic metazoan host
- Cloning Argonaute-Associated Small RNAs from Caenorhabditis elegans
- The C1q domain containing proteins of the Mediterranean mussel Mytilus galloprovincialis: A widespread and diverse family of immune-related molecules
- Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium
- Genetic variability of human metapneumovirus amongst an all ages population in Cambodia between 2007 and 2009
- Expression of three galactinol synthase isoforms in Coffea arabica L. and accumulation of raffinose and stachyose in response to abiotic stresses
- Mutation analysis in Bardet–Biedl syndrome by DNA pooling and massively parallel resequencing in 105 individuals
- Genetic diversity of Phytophthora infestans in the Northern-Andean region
- Characterizing homologues of crop domestication genes in poorly described wild relatives by high-throughput sequencing of whole genomes
- HIV-1 nucleotide mixture detection in the virco®TYPE HIV-1 genotyping assay: A comparison between Sanger sequencing and 454 pyrosequencing
- Genetic characterization of bulgarian rotavirus isolates and detection of rotavirus variants: challenges for the rotavirus vaccine program?
- Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids
- Description of Psychrobacter sanguinis sp. nov. recovered from four clinical specimens in New York State over a 4-year period
- The Cluster 1 Type VI Secretion System is a Major Virulence Determinant in Burkholderia pseudomallei
- From L-Dopa to Dihydroxyphenylacetaldehyde: A Toxic Biochemical Pathway Plays a Vital Physiological Function in Insects
- Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana
- Molecular epidemiology of Orientia tsutsugamushi in Cambodia and Central Vietnam reveals a broad region-wide genetic diversity
- Draft Genome Sequence of a Dominant Multidrug-resistant Neisseria gonorrhoeae strain TCDC-NG08107 from Sexual Network at High Risk of Acquiring Human Immunodeficiency Virus and Syphilis
- Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen
- Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata)
- Mayday SeaSight: Combined Analysis of Deep Sequencing and Microarray Data
- Tracing the Domestication of a Biofilm-Forming Bacterium
- Characterization of genomic sequence showing strong association with polyembryony among diverse Citrus species and cultivars, and its synteny with Vitis and Populus
- Aphid genome expression reveals host–symbiont cooperation in the production of amino acids
- Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq
- OrchidBase: A Collection of Sequences of the Transcriptome Derived from Orchids
- Genetic Basis for Daptomycin Resistance in Enterococci
- Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids
- Mutation analysis of the tyrosine phosphatase PTPN2 in Hodgkin lymphoma and T-cell non-Hodgkin lymphoma
- Targeted Next-Generation Sequencing for the Molecular Genetic Diagnostics of Cardiomyopathies
- Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens
- Dynamic growth program regulated by LANCEOLATE enables flexible leaf patterning
- Beta hydroxylation of glycolipids from Ustilago maydis and Pseudozyma flocculosa is done by a NADPH dependent β hydroxylase
- Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array
- Novel, Divergent Simian Hemorrhagic Fever Viruses in a Wild Ugandan Red Colobus Monkey Discovered Using Direct Pyrosequencing
- Hyaloperonospora arabidopsidis ATR1 effector is a repeat protein with distributed recognition surfaces
- Variant Plasmodium ovale isolated from a patient infected in Ghana
- De Novo Assembly of Expressed Transcripts and Global Analysis of the Phalaenopsis aphrodite Transcriptome
- Disproportionate Distribution of Androgen Receptor Mutations Allocated by the Race/Ethnicity of Prostate Cancer Patients
- Multiple Reassortment between Pandemic (H1N1) 2009 and Endemic Infl uenza Viruses in Pigs
- De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification
- The persistence of antibiotic resistance: evaluation of a probiotic approach using antibiotic-sensitive Megasphaera elsdenii strains to prevent colonization of swine by antibiotic-resistant strains
- Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics
- Identification of two novel CAKUT-causing genes by massively parallel exon resequencing of candidate genes in patients with unilateral renal agenesis
- Characterization of expression dynamics of WOX homeodomain transcription factors during somatic embryogenesis in Vitis vinifera
- High levels of genetic variation within core Helicoverpa armigera nucleopolyhedrovirus genes
- Molecular cloning and characterization of Izumo1 gene from sheep and cashmere goat reveal alternative splicing
- Transcriptomes of Frankia sp. strain CcI3 in growth transitions
- Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation
- Multilocus VNTR analysis of Mycobacterium ulcerans strains isolated in Côte d’Ivoire
- Selection in Coastal Synechococcus (Cyanobacteria) Populations Evaluated from Environmental Metagenomes
- Microviridae Goes Temperate: Microvirus-Related Proviruses Reside in the Genomes of Bacteroidetes
- Detecting signatures of positive selection in partial sequences generated on a large scale: pitfalls, procedures and resources
- Identification at the larval stage of four Curculio species coexisting on oak trees using PCR-RFLP
- Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River
- Rapid identification of mutations in GJC2 in primary lymphoedema using whole exome sequencing combined with linkage analysis with delineation of the phenotype
- Transcriptome Profiling of Bovine Milk Oligosaccharide Metabolism Genes Using RNA-Sequencing
- Insights into the bacterial diversity in a freshwater-deprived permanently open Eastern Cape estuary, using 16S rRNA pyrosequencing analysis
- Evaluation of a rapid detection method of clarithromycin resistance genes in Mycobacterium avium complex isolates
- Identification of immunogenic proteins in Treponema phagedenis-like strain V1 from digital dermatitis lesions by phage display
- Bacterial glyoxalase enzymes
- Transcriptome characterization of the South African abalone Haliotis midae using sequencing-by-synthesis
- Characterization and Transcriptome Analysis of Mycobacterium tuberculosis Persisters
- Differential Growth-Related Gene Expression in Abalone (Haliotis midae)
- Expression of recombinant Streptokinase from local Egyptian Streptococcus sp. SalMarEg
- A novel homozygous missense mutation (c.610G>A, p.Gly204Ser) in the WNT7A gene causes tetra-amelia in two Saudi families
- Genome Sequence of the Campylobacter jejuni strain 327, a turkey strain isolated from a slaughterhouse
- Gene Discovery and Tissue-specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development
- Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome
- Diversity Arrays Technology (DArT) and next-generation sequencing combined: genome-wide, high throughput, highly informative genotyping for molecular breeding of Eucalyptus
- Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum
- Assessing the Performance of Assembly Tools on Simulated Sequencing Data and Their Sensitivity to GC Content
- Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse
- Exome capture and massively parallel sequencing identifies a novel HPSE2 mutation in a Saudi Arabian child with Ochoa (urofacial) syndrome
- Genome Sequences of Two Stress-Tolerant Campylobacter jejuni Poultry Strains, 305 and DFVF1099
- Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation
- Deep sequencing of voodoo lily (Amorphophallus konjac): an approach to identify relevant genes involved in the synthesis of the hemicellulose glucomannan
- Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper
- Discovery and Initial Analysis of Novel Viral Genomes in the Soybean Cyst Nematode
- High-quality genome sequence of Pichia pastoris CBS7435
- Molecular and Biochemical Characterization of the 5-Nitroanthranilic Acid Degradation Pathway in Bradyrhizobium sp. Strain JS329
- Gene and genome construction in yeast
- GENOMIC SEQUENCE OF LACTOBACILLUS RUMINIS SPM0211 ISOLATED FROM A FECAL SAMPLE FROM A HEALTHY KOREAN
- Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes
- Identification and characterisation of seed storage protein transcripts from Lupinus angustifolius
- Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1
- Whole genome sequencing and phenotypic analysis of mutations found in Bacillus subtilis following evolution under relaxed selection for sporulation
- Draft Genome Sequence of Paenibacillus polymyxaType Strain (ATCC 842T), a Plant Growth-Promoting Bacterium
- Identification of the First Human Gyrovirus, a Virus Related to Chicken Anemia Virus
- Chromatin occupancy of transcription factor 7-like 2 (TCF7L2) and its role in hepatic glucose metabolism
- Single Virus Genomics: A New Tool for Virus Discovery
- Genome sequence of Listeria monocytogenes Scott A, a clinical isolate from a foodborne listeriosis outbreak
- Full length MHC IIβ exon 2 primers for salmonids: a new resource for next generation sequencing
- Genome Sequencing and Analysis of Yersina pestis KIM D27, an Avirulent Strain Exempt from Select Agent Regulation
- Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation
- Massively Parallel Amplicon Sequencing Reveals Isotype-Specific Variability of Antimicrobial Peptide Transcripts in Mytilus galloprovincialis
2010
- Comparative Analysis Of Bovine Milk And Mammary Gland Transcriptome Using RNA-Seq
- The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
- Genetic Analysis of Baker’s Yeast Msh4-Msh5 Reveals a Threshold Crossover Level for Meiotic Viability
- The Aspartate-Semialdehyde Dehydrogenase of Edwardsiella ictaluri and Its Use as Balanced-Lethal System in Fish Vaccinology
- Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)
- The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution
- PLUNC Is a Novel Airway Surfactant Protein with Anti-Biofilm Activity
- Fis Is Essential for Capsule Production in Pasteurella multocida and Regulates Expression of Other Important Virulence Factors
- Genome Sequences of Lactococcus lactis MG1363 (Revised) and NZ9000 and Comparative Physiological Studies
- Deep sequencing analysis of mutations resulting from the incorporation of dNTP analogs
- SNP discovery in the bovine milk transcriptome using RNA-Seq technology
- De novo assembly of short sequence reads
- Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic Bacteroidetes
- Genome-wide model for the normal eukaryotic DNA replication fork
- Ultra High Throughput Sequencing in Human DNA Variation Detection: A Comparative Study on the NDUFA3-PRPF31 Region
- The Genome of a Pathogenic Rhodococcus: Cooptive Virulence Underpinned by Key Gene Acquisitions
- GAMES identifies and annotates mutations in next-generation sequencing projects
- Mutation analysis of 18 nephronophthisis associated ciliopathy disease genes using a DNA pooling and next generation sequencing strategy
- Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing
- A Molecular Mechanism for Eflornithine Resistance in African Trypanosomes
- Arbovirus Detection in Insect Vectors by Rapid, High-Throughput Pyrosequencing
- The mtDNA Mutation Spectrum of the Progeroid Polg Mutator Mouse Includes Abundant Control Region Multimers
- Molecular diagnosis for heterogeneous genetic diseases with targeted high-throughput DNA sequencing applied to retinitis pigmentosa
- Polymorphisms in the Tlr4 and Tlr5 Gene Are Significantly Associated with Inflammatory Bowel Disease in German Shepherd Dogs
- A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNA-Seq for Stem Cell and Regeneration Biology
- Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola
- Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets
2009
- Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sour
- Evolutionary History of the HAP2/GCS1 Gene and Sexual Reproduction in Metazoans
- Identification and Expression Analysis of Ras Gene in Silkworm, Bombyx mori
- Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line
- Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant pathology
- Comparative Transcriptional Profiling of Bacillus cereus Sensu Lato Strains during Growth in CO2-Bicarbonate and Aerobic Atmospheres
- Recombination between Polioviruses and Co-Circulating Coxsackie A Viruses: Role in the Emergence of Pathogenic Vaccine-Derived Polioviruses
- Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa
- Managing and Analyzing Next-Generation Sequence Data
- Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing
- Evidence of Recombination and Genetic Diversity in Human Rhinoviruses in Children with Acute Respiratory Infection
- Mapping Accuracy of Short Reads from Massively Parallel Sequencing and the Implications for Quantitative Expression Profiling
- Comparative SNP diversity among four Eucalyptusspecies for genes from secondary metabolite biosynthetic pathways
- Differential Regulation of Type I Interferon and Epidermal Growth Factor Pathways by a Human Respirovirus Virulence Factor
- CGI-58/ABHD5 is a coenzyme A-dependent lysophosphatidic acid acyltransferase
- Characterization of Genes Encoding Poly(A) Polymerases in Plants: Evidence for Duplication and Functional Specialization
2008
- Promoter-Wide Hypermethylation of the Ribosomal RNA Gene Promoter in the Suicide Brain
- The cytoplasmic C2A domain of synaptotagmin shows sequence specific interaction with its own mRNA
- Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa
2007
- A Family of Chemoreceptors in Tribolium castaneum (Tenebrionidae: Coleoptera)
Selected books
Books citing CLC bio
2011
- Epigenetics in Male Reproduction: A Practical Introduction to the Informatics of Next Generation Sequencing
- Next Generation Sequencing and Whole Genome Selection in Aquaculture
- Epigenetics in Male Reproduction: A Practical Introduction to the Informatics of Next Generation Sequencing
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