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Vybrané publikace/výsledky

Human Treponema pallidum 11q/j isolate belongs to subsp. endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively (2017)
Eudiplozoon nipponicum (Monogenea: Diplozoidae): Comparative study of transcriptome and secretome of fish parasite (2017)
The impact of choice of reference gene annotation (2017)
Eudiplozoon nipponicum (Polyopisthocotylea: Diplozoidae): transcriptome and secretome analyses of hematophagous fish parasite (2017)
Epigenetic Control Of Aging In Response To Caloric Restriction (2017)
Analysis of gene expression and protein synthesis related to hypobiosis of Teladorsagia circumcincta (2017)
Candidate gene molecular markers as tools for analyzing genetic susceptibility to Morbillivirus infection in stranded Cetaceans (2017)
Formation of Staphylococcus aureus biofilm in the presence of sub-lethal concentrations of disinfectants: a transcriptomic analysis using RNA-seq (2017)
MicroRNA induced by DNA damage response regulate the expression of FOXP1 and therapy response in CLL (2017)
Could nanopore sequencing help us improve genome assembly of Eudiplozoon nipponicum (Polyopisthocotylea, Diplozoidae)? (2017)
MicroRNA induced by DNA damage response regulates the expression of FOXP1 and therapy response in CLL (2017)
Low-burden TP53 mutations in chronic phase of myeloproliferative neoplasms: association with age, hydroxyurea administration, disease type and JAK2 mutational status (2018)
The clinical impact of targeted „next-generation“ sequencing in molecular diagnostics of intellectual disabilities and multiple congenital abnormalities (2017)
Chromothripsis 18 in multiple myeloma patient with rapid extramedullary relapse (2018)
Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes (2018)
The clinical utility of array-CGH and targeted NGS in idiopathic intellectual disabilities and developmental delays: a case report of SCN2A p.Ala263Val variant (2017)
Parazitičtí jednorodí (Monogenea) - stále neznámé organismy (2018)
Worldwide Protein Data Bank validation information: usage and trends (2018)
Validation of ligands in macromolecular structures determined by X-ray crystallography (2018)
Liver regeneration during the associating liver partition and portal vein ligation for staged hepatectomy procedure in Sus scrofa is positively modulated by stem cells (2018)
Bringing validation information closer to the user (2018)
Monogeneans in the pores (2018)
Identifikace mikrobiomu kolorektálního karcinomu z RNAseq dat nádorové tkáně a jeho korelace s klinickými proměnnými a molekulárními podtypy (2018)
Validation information in the Protein Data Bank: What is it and why should you care? (2018)
Connection of glycoinformatics databases with Pubchem (2018)
Empirical methods for calculation of partial atomic charges – applicability for proteins? (2018)
The influence of mutational status and biological characteristics of acute myeloid leukemia on xenotransplantation outcomes in NOD SCID gamma mice (2018)
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update) (2018)
bio.tools Sum – tool for exploration of summary information about bioinformatics services in bio.tools (2018)
PITHYA (2018)
Monogenea, fish parasites and their unknown molecules (2018)
Molecular evolution and diversification of the SMXL gene family (2018)
ToTem: a tool for variant calling pipeline optimization (2018)
CD20 supports BCR signaling in an intra clonal aggressive chronic lymphocytic leukemia subpopulation of cells and rituximab primarily targets these BCR proficient B cells in vivo (2018)
CD20 reguluje signalizaci přes B-buněčný receptor v mikroprostředí chronické lymfocytární leukémie (2018)
CD20 is a direct regulator of B-cell receptor signaling in the microenvironment of chronic lymphocytic leukemia (2018)
Secondary Structure Elements-Annotations and Schematic 2D Visualizations Stable for Individual Protein Families (2018)
Annotation of protein secondary structure elements for whole protein families (2018)
Sequencing of Treponema pallidum subsp pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material (2018)
Bioinformatická platforma pro rutinní využití v diagnostice pacientů s chronickou lymfocytární leukémií (2018)
CCL - Charge Calculation Language (2018)
Rituximab primarily targets an intra-clonal BCR signaling proficient CLL subpopulation characterized by high CD20 levels (2018)
ValTrendsDB: Viewing structure quality from macro and micro perspective (2018)
Analýza rozsáhlých přestaveb genomu u chronické lymfocytární leukémie (2018)
Bioinformatics platform for routine diagnsotics of chronic lymphocytic leukemia patients (2018)
microRNA – are you real? (2018)
microRNA – are you real? (2018)
Complete genome sequences of two strains of Treponema pallidum subsp pertenue from Indonesia: Modular structure of several treponemal genes (2018)
Global microRNA analysis in cerebrospinal fluid in glioblastoma patients. (2018)
SugarSketcher: Quick and Intuitive Online Glycan Drawing (2018)
miR-150 downregulation contributes to the high-grade transformation of follicular lymphoma by upregulating FOXP1 levels (2018)
Hladiny vybraných plazmatických mikroRNA u pacientů po srdeční transplantaci odrážejí probíhající celulární rejekci štěpu - primární výsledky sekvenací (2018)
Použití sekvenování nové generace při hledání kandidátních mikroRNA jako biomarkerů rekurence fibrilace síní po katetrové ablaci - pilotní data (2018)
MicroRNA miR-34a downregulates FOXP1 during DNA damage response to limit BCR signalling in chronic lymphocytic leukaemia B cells (2019)
Encyclopedia of CLL Subsets: An Online Knowledgebase forSubsets of CLL Cases with Stereotyped B Cell Receptors (2018)
Bioinformatics platform for routine diagnostics of chronic lymphocytic leukemia patients (2018)
Promoter methylation of ROR1 ligand WNT5A associates with its expression in CLL (2018)
Activation-induced deaminase and its splice variants associate with trisomy 12 in chronic lymphocytic leukemia (2019)
Bioinformatic analysis of microRNAs and long non-coding RNAs in malignant B cells (2018)
Advances in the cellular structural biology of nucleic acids (2018)
CDK12 kinase activity controls G1/S progression by regulating optimal transcription of core DNA replication genes (2018)
Protein Data Bank: the single global archive for 3D macromolecular structure data (2019)
Automated family-wide annotation of secondary structure elements (2019)
Novel de novo frameshift variant in the ASXL3 gene in a child with microcephaly and global developmental delay (2019)
ValTrendsDB: bringing Protein Data Bank validation information closer to the user (2019)
Interactive exploration of trends in biomacromolecule structure quality with ValTrendsDB (2019)
ValTrendsDB: bringing Protein Data Bank validation information closer to the user (2019)
ValTrendsDB: Database of biomacromolecular structure validation trends (2019)
The bio.tools registry of software tools and data resources for the life sciences (2019)
Testing of library preparation methods for transcriptome sequencing of real life glioblastoma and brain tissue specimens: A comparative study with special focus on long non-coding RNAs (2019)
Barbaric Robustness Monitoring Revisited for STL* in Parasim (2019)
Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants (2019)
Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS (2019)
Halančíci jako nový model pro studium věkem podmíněné spontánní karcinogeneze (2019)
Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway (2019)
AtomicChargeCalculator II (2019)
Partial atomic charges for proteins (2019)
Exploring trends in quality and features of biomacromolecular complexes with ValTrendsDB (2019)
ValTrendsDB: Enabling comparison of quality and features of biomacromolecular complexes to the global trend (2019)
Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study (2019)
Encyklopedie subsetů CLL – unikátní bioinformatický nástroj a databáze pro analýzu subsetů stereotypních B buněčných receptorů u CLL (2019)
Analýza dlouhých nekódujících RNA v tkáni multiformního glioblastomu a jejich asociace s celkovým přežíváním (2019)
Family-wide annotation and schematic 2D visualization of secondary structure elements (2018)
Protein family based 2D Diagrams of Secondary Structure Elements (2018)
Automated Annotation of Secondary Structure Elements for Entire Protein Families (2018)
Creation and visualization of secondary structure consensus for protein families (2019)
Mechanism of leukemia cell adaptation to targeted therapy in chronic lymphocytic leukemia (2019)
The surprising role of microRNAs in the DNA damage and B cell receptor signalling in malignant B cells (2019)
The use of CRISPR/Cas9 technology in the study of chronic lymphocytic leukemia (2019)
CRISPR/Cas9 gene editing and functional screening in chronic lymphocytic leukemia (2019)
B Cell Receptor Signalling Regulation by Non-coding RNAs. (2019)
CD20 in the context of microenvironmental interactions of malignant B cells: Implications for targeted therapy. (2019)
Encyklopedie subsetů CLL – Unikátní bio informatický nástroj a databáze pro analýzu subsetů stereotypních B buněčných receptorů u CLL (2019)
Promoter Methylation of ROR1 Ligand WNT5A associates with Its Expression in Chronic Lymphocytic Leukemia (2019)
A Simple RNA Target Capture NGS Strategy for Fusion Genes Assessment in the Diagnostics of Pediatric B-cell Acute Lymphoblastic Leukemia (2019)
The major histocompatibility complex of Old World camelids: Class I and class I-related genes (2019)
Dicier: a Fine-tuned Bioinformatics Pipeline to Detect Micro-RNA Chimeric Reads (2019)
First evidence of a paediatric patient with Cornelia de Lange syndrome with acute lymphoblastic leukaemia (2019)
Lesson development for Open Source Software best practices adoption (2018)
Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA (2020)
Interactive 3D Macromolecular Structure Data Mining with MolQL and Litemol Suite (2018)
CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells (2020)
Genome-wide CRISPR/Cas9 screening reveals novel target genes, whose inactivation is able to upregulate surface expression of immunotherapy target CD20 (2020)
Analysis mutational landscape in systemic anaplastic large cell lymphoma identifies novel prognostic markers (2020)
HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids (2020)
The use of CRISPR/Cas9 technology in the study of chronic lymphocytic leukemia. (2020)
High throughput sequencing data analysis of IG/TR rearranged genes in leukemie clinical research. (2020)
Mutational landscape analysis in systematic anaplastic large cell lymphoma identifies novel prognostic markers. (2020)
CRISPR/CAS9 technology: a useful tool in the study of chronic lymphocytic leukemia (2020)
High-throughput sleep phenotyping produces robust and heritable traits in Diversity Outbred mice and their founder strains (2020)
PENGUINN: Precise Exploration of Nuclear G-Quadruplexes Using Interpretable Neural Networks (2020)
STAT3 and TP53 mutations associate with poor prognosis in anaplastic large cell lymphoma (2021)
WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis (2021)
Histopathology of laboratory-reared Nothobranchius fishes: Mycobacterial infections versus neoplastic lesions (2021)
microRNA – are you real?! (2018)
Fosforylace proteinu p53: vliv na aktivitu dráhy p53 po poškození DNA u chronické lymfocytární leukémie. (2021)
Phosphorylation patterns of tumor suppressor P53 and their impact on the P53 pathway activity in chronic lymphocytic leukemia. (2021)
Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements (2021)
ENNGene: an Easy Neural Network model building tool for Genomics (2022)
Noncanonical small RNA chimeras identified by AGO2-CLASH (2022)
miRBind: a Deep Learning method for miRNA binding classification (2022)
PENGUINN-RNA: prediction of RNA G-quadruplexes using interpretable Neural Networks (2022)
Genomic Benchmarks: A Collection of Datasets for Genomic Sequence Classification (2022)
Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in circumjacent pathways activation upon DNA damage (2022)
Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in circumjacent pathways activation upon DNA damage (2022)
KMT2C methyltransferase domain regulated INK4A expression suppresses prostate cancer metastasis (2022)
Registry-based analysis of Icatibant and C1-inhibitor use in treatment of laryngeal attacks of hereditary angioedema (2022)
GDF11 inhibits adipogenesis and improves mature adipocytes metabolic function via WNT/beta-catenin and ALK5/SMAD2/3 pathways (2022)
Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in the activation of circumjacent pathways upon DNA damage (2023)
Increased occurrence of Treponema spp. and double-species infections in patients with Alzheimer's disease (2022)
Memory B-cell like chronic lymphocytic leukaemia is associated with specific methylation profile of WNT5A promoter and undetectable expression of WNT5A gene (2022)
Distinct p53 phospohrylation patterns in chronic lymphocytic leukemia patients are reflected in circumjacent pathways activation upon DNA damage. (2022)
CRISPR/Cas9 knockout screening revealed genes involved in CD20 regulation. (2022)
Výsledky celoexomového sekvenování germinální DNA u dětských pacientů se solidními tumory (2022)
Genic and chromosomal components of Prdm9-driven hybrid male sterility in mice (Mus musculus) (2022)
CF Day Meeting (2022)
Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling (2022)
miRBind: A Deep Learning Method for miRNA Binding Classification (2022)
Toll-Like Receptor 3 Overexpression Induces Invasion of Prostate Cancer Cells, whereas Its Activation Triggers Apoptosis (2022)
The mechanical regulation of RNA binding protein hnRNPC in the failing heart (2022)
Using relational graphs for exploratory analysis of network traffic data (2023)
SeqUIa: Softwarová platforma pro zpracování sekvenování nové generace skrze grafické rozhraní (2022)
From fish to cells: Establishment of continuous cell lines from embryos of annual killifish Nothobranchius furzeri and N. kadleci (2023)
Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus. (2023)
Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth (2024)
Genomic benchmarks: a collection of datasets for genomic sequence classification (2023)
Výsledky celoexomového sekvenování germinální DNA u dětských pacientů se solidními tumory (2023)
Transcriptome Profile Analyses of Head Kidney in Roach (Rutilus rutilus), Common Bream (Abramis brama) and Their Hybrids: Does Infection by Monogenean Parasites in Freshwater Fish Reveal Differences in Fish Vigour among Parental Species and Their Hybrids? (2023)
Clonal competition and disrupted molecular processes in chronic lymphocytic leukemia. (2023)
Calc-X and Calcformers: Empowering Arithmetical Chain-of-Thought through Interaction with Symbolic Systems (2023)
Heterosis versus breakdown in cyprinid hybrids associated with SVCV infection revealed by transcriptome profile analysis of head kidney (2024)
CRISPR/Cas9 technology as a useful tool in the study of chornic lymphocytic leukemia. (2023)
Distinct p53 Phosphorylation Patterns in Chronic Lymphocytic Leukemia: Where They Come from and How They Affect p53 Function. (2023)
CRISPR/Cas9 technology as a useful tool in the study of chronic lymphocytic leukemia. (2023)
iReenCAM: automated imaging system for kinetic analysis of photosynthetic pigment biosynthesis at high spatiotemporal resolution during early deetiolation (2023)
Proteogenomic Classification of Triple-Negative Breast Cancer for Prognosis and Targeted Therapy (2023)
Unraveling Epigenetic Changes in A. thaliana Calli: Impact of HDAC Inhibitors (2023)
The SAP domain of Ku facilitates its efficient loading onto DNA ends (2023)
Mimicking Tumor Cell Heterogeneity of Colorectal Cancer in a Patient-derived Organoid-Fibroblast Model (2023)
TeloBase: a community-curated database of telomere sequences across the tree of life (2024)
RNA Summer School 2023 (2023)
Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation (2023)
Radiogenomic markers enable risk stratification and inference of mutational pathway states in head and neck cancer (2023)
Toll-Like Receptor 3 Overexpression Induces Invasion of Prostate Cancer Cells, whereas Its Activation Triggers Apoptosis (2022)
Self-Training Language Models in Arithmetic Reasoning (2024)
Stromal cells engineered to express T cell factors induce robust CLL cell proliferation in vitro and in PDX co-transplantations allowing the identification of RAF inhibitors as anti-proliferative drug (2024)
Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model (2024)
Cytokinins regulate spatially specific ethylene production to control root growth in Arabidopsis (2024)
Reproduction-associated pathways in females of gibel carp (Carassius gibelio) shed light on the molecular mechanisms of the coexistence of asexual and sexual reproduction (2024)
Trematode Diplostomum pseudospathaceum inducing differential immune gene expression in sexual and gynogenetic gibel carp (Carassius gibelio): parasites facilitating the coexistence of two reproductive forms of the invasive species (2024)
Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics (2024)
JUN mediates the senescence associated secretory phenotype and immune cell recruitment to prevent prostate cancer progression (2024)
Transmembrane glycoprotein GPNMB is a candidate predictive biomarker and potentially a therapeutic target in metastatic renal cell carcinoma (2024)

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