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List of works by Vladimir Benes

"Doublex" fluorescent DNA sequencing: two independent sequences obtained simultaneously in one reaction with internal labeling and unlabeled primers.

scientific article

3' Uridylation controls mature microRNA turnover during CD4 T-cell activation.

scientific article published on 28 March 2017

A cautionary tale of sense-antisense gene pairs: independent regulation despite inverse correlation of expression

scientific article published on 20 October 2017

A genomic switch at the transition from cell proliferation to terminal differentiation in the Drosophila eye.

scientific article published in October 2002

A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation

scientific article published on 20 July 2000

A novel method to identify Post-Aire stages of medullary thymic epithelial cell differentiation

scientific article published on 26 August 2020

A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing

scientific journal article

A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA)

scientific article

A severe connatal form of Pelizaeus Merzbacher disease in a Czech boy caused by a novel mutation (725C>A, Ala242Glu) at the 'jimpy(msd) codon' in the PLP gene.

scientific article published in February 2002

AXL Inhibition in Macrophages Stimulates Host-versus-Leukemia Immunity and Eradicates Naïve and Treatment-Resistant Leukemia

publication published on 08 June 2021

Accounting for technical noise in single-cell RNA-seq experiments.

scientific article published on 22 September 2013

Actin-binding protein regulation by microRNAs as a novel microbial strategy to modulate phagocytosis by host cells: the case of N-Wasp and miR-142-3p

scientific article published on 5 June 2013

Adhesion of hematopoietic progenitor cells to human mesenchymal stem cells as a model for cell−cell interaction

article

Aging and replicative senescence have related effects on human stem and progenitor cells

scientific article

Aire-expressing ILC3-like cells in the lymph node display potent APC features

scientific article published on 27 March 2019

Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing

scientific article published on 01 July 2019

Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions.

scientific article

Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells.

scientific article

An assessment of air as a source of DNA contamination encountered when performing PCR

scientific article published on December 2009

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

scientific article published on 7 January 2013

An efficient method for genome-wide polyadenylation site mapping and RNA quantification.

scientific article

An estimate of large-scale sequencing accuracy

scientific article published on July 2000

Analysis of 1.9 Mb of contiguous sequence from chromosome 4 ofArabidopsis thaliana

scientific article published in Nature

Analysis of microribonucleic acid expression by quantitative real-time polymerase chain reaction

Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines

scientific article published on June 2000

Apoptotic Cell Exclusion and Bias-Free Single-Cell Selection Are Important Quality Control Requirements for Successful Single-Cell Sequencing Applications

scientific article published on 11 October 2019

Aspirin impairs acetyl-coenzyme A metabolism in redox-compromised yeast cells

scientific article published on 16 April 2019

Automated cycle sequencing with Taquenase: protocols for internal labeling, dye primer and "doublex" simultaneous sequencing

scientific article published on August 1, 1997

BAC engineering for the generation of ES cell-targeting constructs and mouse transgenes

scientific article published in January 2004

BAC trimming: minimizing clone overlaps

scientific article published in February 2000

Bacteriophage B103: complete DNA sequence of its genome and relationship to other Bacillus phages

scientific article published on October 1997

Bacteriophage φ29 early protein p17 is conditionally required for the first rounds of viral DNA replication1Published in conjunction with A Wisconsin Gathering Honoring Waclaw Szybalski on the occasion of his 75th year and 20years of Editorship-in-C

scientific article published on 01 November 1998

Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing

scientific article published on July 2015

CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

scientific article

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

scientific article published on 6 August 2010

Cautionary note on contamination of reagents used for molecular detection of SARS-CoV-2

scientific article published on 07 September 2020

Characterization of Two Historic Smallpox Specimens from a Czech Museum

scientific article

Characterization of an Escherichia coli elaC deletion mutant.

scientific article

Cloning and developmental expression of amphioxus Dachschund

scientific article published in March 2003

Co-translational assembly orchestrates competing biogenesis pathways

scientific article published on 09 March 2022

Comparison of 3 fusion techniques in the treatment of the degenerative cervical spine disease. Is stand-alone autograft really the "gold standard?": prospective study with 2-year follow-up

scientific article

Consequences of the loss of the Grainyhead-like 1 gene for renal gene expression, regulation of blood pressure and heart rate in a mouse model.

scientific article published on 21 April 2015

Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers

scientific article published on 4 January 2018

Corrigendum: Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network

scientific article published on 26 February 2015

Cyclical DNA methylation of a transcriptionally active promoter

scientific article

DELLY: structural variant discovery by integrated paired-end and split-read analysis

scientific article

DNA binding and transactivating properties of the paired and homeobox protein Pax4.

scientific article published in June 1999

DNA sequencing and analysis of 130 kb from yeast chromosome XV.

scientific article

Decompressive surgery for malignant supratentorial infarction remains underutilized after guideline publication

scientific article published on 24 March 2011

Developmentally regulated switching of titin size alters myofibrillar stiffness in the perinatal heart

scientific article published on 26 February 2004

Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin

scientific article (publication date: November 2012)

Differentially expressed genes associated with human limbal epithelial phenotypes: new molecules that potentially facilitate selection of stem cell-enriched populations

scientific article

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli

scientific article published on 21 November 2010

Direct primer walking on P1 plasmid DNA

scientific article published on 01 July 1997

Direct regulation of microRNA biogenesis and expression by estrogen receptor beta in hormone-responsive breast cancer

scientific article published on 9 January 2012

Disruption of EXOC6B in a patient with developmental delay, epilepsy, and a de novo balanced t(2;8) translocation

scientific article published on 20 February 2013

Dissecting the genomic complexity underlying medulloblastoma

scientific article

Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone.

scientific article

Diverse roles of hnRNP L in mammalian mRNA processing: a combined microarray and RNAi analysis

scientific article published on 11 December 2007

Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS.

scientific article published on 19 April 2004

Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network

scientific article

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

scientific article

Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease.

scientific article

Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources

scientific article

ET recombination: DNA engineering using homologous recombination in E. coli

scientific article published in January 2004

Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein

scientific article

Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles.

scientific article published on 10 March 2003

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics

scientific article published on 24 January 2022

Epigenetic program and transcription factor circuitry of dendritic cell development

scientific article

Exhausted phenotype of follicular CD8 T cells in CVID

scientific article published on 10 March 2020

Exome sequencing identifies MRPL3 mutation in mitochondrial cardiomyopathy

scientific article

Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available

scientific article published on 28 January 2010

Extensive 5'-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast

scientific article published on 02 November 2020

Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression

scientific article published on 04 February 2019

Functional equivalency of amphioxus and vertebrate Pax258 transcription factors suggests that the activation of mid-hindbrain specific genes in vertebrates occurs via the recruitment of Pax regulatory elements

scientific article published on January 2002

Geminin deletion increases the number of fetal hematopoietic stem cells by affecting the expression of key transcription factors.

scientific article published on January 2015

Genetic Labeling of Nuclei-Specific Thalamocortical Neurons Reveals Putative Sensory-Modality Specific Genes

scientific article

Genetic code expansion for multiprotein complex engineering.

scientific article

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

scientific article

Genome-wide RNAi screening identifies human proteins with a regulatory function in the early secretory pathway

Genomic Analysis and Isolation of RNA Polymerase II Dependent Promoters from Spodoptera frugiperda

scientific article published on 11 August 2015

Genomic insights into the pathogenesis of Epstein-Barr virus-associated diffuse large B-cell lymphoma by whole-genome and targeted amplicon sequencing

scientific article published on 26 May 2021

Genomic locus and promoter region of rat Smad7, an important antagonist of TGFbeta signaling

scientific article published in February 2000

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

scientific article published on 6 June 2012

Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment

scientific article

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

scientific article

Global miRNA and mRNA expression profiles identify miRNA-26a-2-3p-dependent repression of IFN signature in systemic sclerosis human monocytes

scientific article published on 22 February 2020

Heme oxygenase-1 deficiency triggers exhaustion of hematopoietic stem cells

scientific article published on 29 December 2019

Hfe deficiency impairs pulmonary neutrophil recruitment in response to inflammation

scientific article

HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing

scientific article

Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba <i>Pelomyxa schiedti</i>

scientific article published on 26 August 2023

Identification of MiR-21-5p as a Functional Regulator of Mesothelin Expression Using MicroRNA Capture Affinity Coupled with Next Generation Sequencing

scientific article

Identification of a genetically defined ultra-high-risk group in relapsed pediatric T-lymphoblastic leukemia

scientific article published on 3 February 2017

Identification of cytokine-induced modulation of microRNA expression and secretion as measured by a novel microRNA specific qPCR assay.

scientific article published on 25 June 2015

Identification of novel follicular dendritic cell sarcoma markers, FDCSP and SRGN, by whole transcriptome sequencing.

scientific article published on 27 January 2017

Identification of novel sequence variations in microRNAs in chronic lymphocytic leukemia

scientific article

Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs

scientific article

Inhibition of aurora kinases for tailored risk-adapted treatment of multiple myeloma

scientific article published on 26 January 2009

Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer

scientific article

Intracellular microRNA profiles form in the Xenopus laevis oocyte that may contribute to asymmetric cell division

scientific article published on 10 June 2015

Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by iron regulatory proteins

scientific article published on 22 September 2011

Isolation of Open Chromatin Identifies Regulators of Systemic Acquired Resistance

scientific article published on 23 July 2019

Isolation, biochemical characterization and crystallization of the p15gag proteinase of myeloblastosis associated virus expressed in E. coli

scientific article published in February 1992

Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis

scientific article

Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster

scholarly article

Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods

scientific article published on 01 September 2020

Lymphocyte gene expression signatures from patients and mouse models of hereditary hemochromatosis reveal a function of HFE as a negative regulator of CD8+ T-lymphocyte activation and differentiation in vivo

scientific article

M13 and pUC vectors with new unique restriction sites for cloning

scientific article

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

scientific article published in 2021

MicroRNA miR-34a downregulates FOXP1 during DNA damage response to limit BCR signalling in chronic lymphocytic leukaemia B cells

scientific article published on 15 August 2018

MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer

scientific article

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions

scientific article published on 27 February 2019

Microcontact printing of DNA molecules

scientific article published in March 2004

Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme

scientific article published on 18 March 2019

Modular proteins from the Drosophila sallimus (sls) gene and their expression in muscles with different extensibility

scientific article published on 27 January 2007

Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo

scientific article published on 01 December 2020

Molecular characterization of two high affinity sulfate transporters in Saccharomyces cerevisiae.

scientific article

Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis

scientific journal article

Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor alpha, in response to deacetylase inhibition by valproic acid and trichostatin A.

scientific article

Natural course of pineal cysts-a radiographic study

scientific article published on 11 December 2018

Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy

scientific article published on 16 August 2011

Nucleotide sequence of the right early region of Bacillus phage phi 15 and comparison with related phages: reorganization of gene 17 during evolution

scientific article published on February 1989

On the current status of Phakopsora pachyrhizi genome sequencing

scientific article

Optimization of extraction of circulating RNAs from plasma--enabling small RNA sequencing

scientific article

P55-S Genomic Profile in Asthma

scientific article published in February 2007

Pax-Six-Eya-Dach network during amphioxus development: conservation in vitro but context specificity in vivo

scientific article

Pediatric T-cell lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation

scientific article

Potential of fecal microbiota for early-stage detection of colorectal cancer

scientific article

Potential protective role of Grainyhead-like genes in the development of clear cell renal cell carcinoma.

scientific article

Primate genome architecture influences structural variation mechanisms and functional consequences

scientific article

Primer sequence disclosure: a clarification of the MIQE guidelines.

scientific article

Protein-induced bending or flexing at the 5′-end of the duck βA-globin promoter

scientific article published on 01 April 1995

Publisher Correction: Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme

scientific article published on 01 June 2019

Quantitative real-time RT-PCR--a perspective.

scientific article

RDML-Ninja and RDMLdb for standardized exchange of qPCR data

scientific article

RNA degradation compromises the reliability of microRNA expression profiling

scientific article

RNA splicing regulated by RBFOX1 is essential for cardiac function in zebrafish

scientific article

RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation

scientific article

RNA-Sequencing as Useful Screening Tool in the Combat against the Misuse of Anabolic Agents

scientific article published in 2012

Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites

scientific article

Replicative senescence of mesenchymal stem cells: a continuous and organized process

scientific article

Reprogramming of the ERRα and ERα target gene landscape triggers tamoxifen resistance in breast cancer

scientific article

Role of CXCL13 in Asthma

scientific article published on 20 October 2011

SUMOylation regulates the chromatin occupancy and anti-proliferative gene programs of glucocorticoid receptor

scientific article published on 4 November 2013

Sec61beta, a subunit of the protein translocation channel, is required during Drosophila development

scientific article published in December 1999

Senescence-associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells

scientific article published on 26 October 2016

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

scientific article

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

scientific article

Sequence and expression of the kettin gene in Drosophila melanogaster and Caenorhabditis elegans

scientific article published in February 2000

Sequencing 39,350 bp of Saccharomyces cerevisiae chromosome XII utilizing ordered shotgun libraries.

scientific article published on January 1996

Sequencing and analysis of 51 kb on the right arm of chromosome XV from Saccharomyces cerevisiae reveals 30 open reading frames

scientific article published on March 1996

Sequencing of a patient with balanced chromosome abnormalities and neurodevelopmental disease identifies disruption of multiple high risk loci by structural variation

scientific article

Single-Virus Droplet Microfluidics for High-Throughput Screening of Neutralizing Epitopes on HIV Particles

scientific article

Single-cell analysis of structural variations and complex rearrangements with tri-channel processing

scientific article published on 23 December 2019

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states

scientific article published on 19 March 2021

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states

scientific article published on 22 November 2021

Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition

scientific article published on 29 January 2020

Standardization of protocols in cDNA microarray analysis

scientific article published in May 2003

Strawberry vein banding virus--definitive member of the genus Caulimovirus

scientific article published on January 1998

Systematic gain-of-function genetics in Drosophila.

scientific article published in March 1998

TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data

scientific article published on 01 October 2020

Targeted mutagenesis of the murine IRP1 and IRP2 genes reveals context-dependent RNA processing differences in vivo.

scientific article published in July 2004

Telomerase stimulates ribosomal DNA transcription under hyperproliferative conditions

scientific article published on 13 August 2014

Tetracycline Antibiotics Induce Host-Dependent Disease Tolerance to Infection

scientific article published on 08 October 2020

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

scientific article

The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments

scientific article (publication date: April 2009)

The Slicer Activity of ARGONAUTE1 Is Required Specifically for the Phasing, Not Production, of Trans-Acting Short Interfering RNAs in Arabidopsis.

scientific article

The differential expression of alternatively polyadenylated transcripts is a common stress-induced response mechanism that modulates mammalian mRNA expression in a quantitative and qualitative fashion

scientific article published on 12 July 2016

The digital MIQE guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments

scientific article

The genomic response of the Drosophila embryo to JNK signaling

scientific article published in October 2001

The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice

scientific article

The molecular elasticity of the insect flight muscle proteins projectin and kettin

scholarly article

The need for transparency and good practices in the qPCR literature.

scientific article published in November 2013

The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.

scientific article published in May 1997

The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.

scientific article

The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.

scientific article published in May 1997

Thyrotroph embryonic factor regulates light-induced transcription of repair genes in zebrafish embryonic cells

scientific article

ToTem: a tool for variant calling pipeline optimization.

scientific article

Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files

scientific article published on 14 March 2020

Transcriptional complexes engaged by apo-estrogen receptor-alpha isoforms have divergent outcomes

scientific article published on 02 September 2004

Transcriptome profiling of estrogen-regulated genes in human primary osteoblasts reveals an osteoblast-specific regulation of the insulin-like growth factor binding protein 4 gene

scientific article

Transient cyclical methylation of promoter DNA.

scientific article

Translational control mediated by hnRNP K links NMHC IIA to erythroid enucleation

scientific article published on 28 January 2016

Treatment for brain arteriovenous malformation in the 1998-2011 period and review of the literature.

scientific article published on 13 December 2012

Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging

Unreliable real-time PCR analysis of human endogenous retrovirus-W (HERV-W) RNA expression and DNA copy number in multiple sclerosis.

scientific article

VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing

scientific article published on 01 February 2020

Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii

scientific article

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.

scientific article published on 3 May 2017

Widespread estrogen-dependent repression of micrornas involved in breast tumor cell growth

scientific article published on 13 October 2009

gga-miRNOME, a microRNA-sequencing dataset from chick embryonic tissues

publication published on 31 January 2022

miChip: A microarray platform for expression profiling of microRNAs based on locked nucleic acid (LNA) oligonucleotide capture probes

miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes

scientific article from 2008

miRNAs in multiple myeloma--a survival relevant complex regulator of gene expression

scientific article published on 12 October 2015

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