Igor Mandric
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View article: Comparative transcriptome analysis of Peromyscus leucopus and C3H mice infected with the Lyme disease pathogen
Comparative transcriptome analysis of Peromyscus leucopus and C3H mice infected with the Lyme disease pathogen Open
Lyme disease (LD), the most prevalent tick-borne disease of humans in the Northern Hemisphere, is caused by the spirochetal bacterium of Borreliella burgdorferi ( Bb ) sensu lato complex. In nature, Bb spirochetes are continuously transmit…
View article: In vitro atlas of dorsal spinal interneurons reveals Wnt signaling as a critical regulator of progenitor expansion
In vitro atlas of dorsal spinal interneurons reveals Wnt signaling as a critical regulator of progenitor expansion Open
Restoring sensation after injury or disease requires a reproducible method for generating large quantities of bona fide somatosensory interneurons. Toward this goal, we assess the mechanisms by which dorsal spinal interneurons (dIs; dI1-dI…
View article: Assembly, quantification, and downstream analysis for high trhoughput sequencing data
Assembly, quantification, and downstream analysis for high trhoughput sequencing data Open
Next Generation Sequencing is a set of relatively recent but already well-established technologies with a wide range of applications in life sciences. Despite the fact that they are constantly being improved, multiple challenging problems …
View article: Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data
Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data Open
In this article, we present our novel pipeline for analysis of metabolic activity using a microbial community's metatranscriptome sequence data set for validation. Our method is based on expectation-maximization (EM) algorithm and provides…
View article: Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development
Single Cell Transcriptomic Analyses Reveal the Impact of bHLH Factors on Human Retinal Organoid Development Open
The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of bHLH factors ATOH7 and Neurog…
View article: Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis
Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis Open
Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and simultaneously measure cellular composition and state, which can otherwise only be estimated by applying deconvolution methods to bulk RNA-Seq estimates. Howev…
View article: Single cell transcriptomic analyses reveal the impact of bHLH factors ATOH7 and Neurog2 on human retinal organoid development
Single cell transcriptomic analyses reveal the impact of bHLH factors ATOH7 and Neurog2 on human retinal organoid development Open
The developing retina expresses multiple bHLH transcription factors. Their precise functions and interactions in uncommitted retinal progenitors remain to be fully elucidated. Here, we investigate the roles of bHLH factors ATOH7 and Neurog…
View article: Rrp6 Moonlights in an RNA Exosome-Independent Manner to Promote Cell Survival and Gene Expression during Stress
Rrp6 Moonlights in an RNA Exosome-Independent Manner to Promote Cell Survival and Gene Expression during Stress Open
The nuclear RNA exosome is essential for RNA processing and degradation. Here, we show that the exosome nuclear-specific subunit Rrp6p promotes cell survival during heat stress through the cell wall integrity (CWI) pathway, independently o…
View article: Benchmarking of computational error-correction methods for next-generation sequencing data
Benchmarking of computational error-correction methods for next-generation sequencing data Open
Background Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data sti…
View article: Gerrymandering and fair districting in parallel voting systems
Gerrymandering and fair districting in parallel voting systems Open
Switching from one electoral system to another one is frequently criticized by the opposition and is viewed as a means for the ruling party to stay in power. In particular, when the new electoral system is a parallel voting (or a single-me…
View article: BATMAN: fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching
BATMAN: fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching Open
Single-cell RNA-Sequencing (scRNA-Seq) is a set of technologies used to profile gene expression at the level of individual cells. Although the throughput of scRNA-Seq experiments is steadily growing in terms of the number of cells, large d…
View article: Datasets (raw and true reads) supporting the study "Benchmarking of computational error-correction methods for next-generation sequencing data"
Datasets (raw and true reads) supporting the study "Benchmarking of computational error-correction methods for next-generation sequencing data" Open
We used both simulated and experimental datasets derived from human genomic DNA, human T cell receptor repertoires, and intra-host viral populations. Next, we summarize datasets shared here, i.e., D1, D2, D3, D4, and D5. More details can b…
View article: Datasets (raw and true reads) supporting the study "Benchmarking of computational error-correction methods for next-generation sequencing data"
Datasets (raw and true reads) supporting the study "Benchmarking of computational error-correction methods for next-generation sequencing data" Open
We used both simulated and experimental gold standard datasets derived from human genomic DNA, human T cell receptor repertoires, and intra-host viral populations. Next, we summarize datasets shared here, i.e., D1, D2, D3, and D5. More det…
View article: Datasets (raw and true reads) supporting the study "Benchmarking of computational error-correction methods for next-generation sequencing data"
Datasets (raw and true reads) supporting the study "Benchmarking of computational error-correction methods for next-generation sequencing data" Open
We used both simulated and experimental datasets derived from human genomic DNA, human T cell receptor repertoires, and intra-host viral populations. Next, we summarize datasets shared here, i.e., D1, D2, D3, D4, and D5. More details can b…
View article: Optimal design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis
Optimal design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis Open
Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to simultaneously measure cellular composition and state which is impossible with bulk profiling approaches. However, it has not yet become a widely used tool in population-sc…
View article: MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples Open
MiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, …
View article: MiCoP: Microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
MiCoP: Microbial community profiling method for detecting viral and fungal organisms in metagenomic samples Open
Background
\nHigh throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods b…
View article: Solving scaffolding problem with repeats
Solving scaffolding problem with repeats Open
One of the most important steps in genome assembly is scaffolding. Increasing the length of sequencing reads allows assembling short genomes but assembly of long repeat-rich genomes remains one of the most interesting and challenging probl…
View article: Repeat-aware evaluation of scaffolding tools
Repeat-aware evaluation of scaffolding tools Open
Summary Genomic sequences are assembled into a variable, but large number of contigs that should be scaffolded (ordered and oriented) for facilitating comparative or functional analysis. Finding scaffolding is computationally challenging d…
View article: MiCoP: Microbial Community Profiling method for detecting viral and fungal organisms in metagenomic samples
MiCoP: Microbial Community Profiling method for detecting viral and fungal organisms in metagenomic samples Open
Background High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods bas…
View article: QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data Open
Motivation Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks for inference of transmission history from viral genomic data often do not consider intra-host di…
View article: Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data
Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data Open
Summary This note presents IsoEM2 and IsoDE2, new versions with enhanced features and faster runtime of the IsoEM and IsoDE packages for expression level estimation and differential expression. IsoEM2 estimates fragments per kilobase milli…
View article: ScaffMatch: scaffolding algorithm based on maximum weight matching
ScaffMatch: scaffolding algorithm based on maximum weight matching Open
Motivation: Next-generation high-throughput sequencing has become a state-of-the-art technique in genome assembly. Scaffolding is one of the main stages of the assembly pipeline. During this stage, contigs assembled from the paired-end rea…