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Articles by Peter Chovanec
Robust Chromosome Segmentation in Sparse Single-Cell Whole-Genome Sequencing Using a k-Segment Constrained Hidden Markov Model
Abstract Genome integrity is essential for cellular and organismal fitness. Loss of heterozygosity (LOH), which eliminates the buffering effect of heterozygosity and can expose deleterious recessive alleles, is an important form of somatic genome alteration associated with aging and tumorigenesis. To characterize LOH across cell populations, we use sci-L3, a high-throughput combinatorial-indexing approach for single-cell whole-genome sequencing (WGS).
Terabyte scale dataset for partial discharge detection in covered conductors via contact galvanic method
Abstract This article introduces a dataset designed for the detection of partial discharges in transmission power lines using covered conductors through a contact galvanic method, sourced from real environments across 23 different power lines in various locations. Though partially introduced in a Kaggle competition (only 3% of data), its full extent is disclosed here for the first time.
High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq
Abstract Despite the many advances in single cell genomics, detecting structural rearrangements in single cells, particularly error-free sister-chromatid exchanges, remains challenging. Here we describe sci-L3-Strand-seq, a combinatorial indexing method with linear amplification for DNA template strand sequencing that cost-effectively scales to millions of single cells, as a platform for mapping mitotic crossover and resulting genome instability events.
High-throughput linear amplification for single-cell template strand sequencing with sci-L3-Strand-seq
Abstract Despite the advances in single cell whole genome sequencing, the ability to detect structural variations from mitotic crossovers remains challenging, while sister chromatid exchanges remain undetectable. Here we describe sci-L3-Strand-seq, a combinatorial indexing method with linear amplification for DNA template strand sequencing that cost-effectively scales to millions of single cells.
VH-replacement shapes the antibody repertoire by targeting non-pairing heavy-chains
Abstract The diversity of antibodies underpins robust immune responses. During the formation of the antibody repertoire in early bone marrow B-cells, random antibody heavy-chain proteins are generated from recombined V, D and J gene-segments. Many are non-functional and are negatively selected. Critically, this phase of development is impacted by ageing and inflammation.
Kazachstan: výstredné hlavné mesto a sovietska minulosť
Písmo: A- | A+ Diskusia (0) Z kirgizského hlavného mesta Biškeku na neďalekú hranicu s Kazachstanom som šiel taxíkom značky Lada. Toto auto bolo staršie, nie ako tie najnovšie typy - ešte malo elektrické sťahovanie okien. Ale popravde, taxikár by mal radšej mechanické. Otvorené okienko sa mu samovoľne každých päť minút zatváralo, čo vždy komentoval šťavnatými ruskými nadávkami. Hraničný prechod vyzeral štandardne, predsa len je najdôležitejší medzi týmito krajinami. Ale aj tu sú zvláštne procesy.
Hory a jurty Kirgizska
Písmo: A- | A+ Diskusia (0) Uzbekistan a Kirgizsko sa veľmi nemajú radi, a tak aj vyzerá hraničný priechod medzi týmito krajinami. Vybral som si menej významný prechod Madaniyat, cez ktorý sa dá do druhej krajiny prejsť len peši. Treba si ho predstaviť ako ostnatý plot na konci zaprášenej dediny, v ktorom je vŕzgavá plechová bránička a za ňou ozbrojenec.
Mestá a vlaky Uzbekistanu
Písmo: A- | A+ Diskusia (0) Po prehliadke Taškentu, sovietskeho mesta s širokými bulvármi a peknými parkami, som druhý deň ráno ešte pred raňajkami stihol presun o tisíc kilometrov. Ráno som prišiel na vnútroštátny terminál letiska v Taškente – veľkú halu bez funkčnej informačnej tabule a vypnutými obrazovkami pri bránach k lietadlám. Jediným zdrojom informácií bol nezrozumiteľný chrchlavý reproduktor.
Srí Lankou na mopede
A hneď prvý víkend roka som sa rozhodol, že idem na to. Zistil som si aktuálne cestovné obmedzenia a Srí Lanka bola v poriadku. V pondelok som vybavil víza, PCR test a musel som si kúpiť akési lokálne covid poistenie za 12 dolárov, v utorok som kúpil letenku a vo štvrtok ráno som letel. Po príjazde do Kolomba som si chcel niekde nechať kufor a pozrieť si centrum, ale úschovňa tam nebola a žiadny obchod nebol ochotný postrážiť na dve hodiny batožinu.
Network analysis of promoter interactions reveals the hierarchical differences in genome organisation between human pluripotent states
SUMMARY A complex and poorly understood interplay between 3D genome organisation, transcription factors and chromatin state underpins cell identity. To gain a systems-level understanding of this interplay, we generated a high-resolution atlas of annotated chromatin interactions in naïve and primed human pluripotent stem cells and developed a network-graph approach to examine the atlas at multiple spatial scales.
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