Marcin Tabaka
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View article: Presynaptic Changes in Mouse Rod Photoreceptors During Early Retinitis Pigmentosa
Presynaptic Changes in Mouse Rod Photoreceptors During Early Retinitis Pigmentosa Open
Rod degeneration induces molecular changes in the P23H/Gnat2-/- mouse rods that suggest synaptic plasticity and strengthening of rod-rod bipolar cell synaptic transmission in early RP.
View article: Ocelli: an open-source tool for the analysis and visualization of developmental multimodal single-cell data
Ocelli: an open-source tool for the analysis and visualization of developmental multimodal single-cell data Open
The recent expansion of single-cell technologies has enabled simultaneous genome-wide measurements of multiple modalities in the same single cell. The potential to jointly profile such modalities as gene expression, chromatin accessibility…
View article: Referee report. For: SCUBA implements a storage format-agnostic API for single-cell data access in R [version 2; peer review: 2 approved, 1 approved with reservations]
Referee report. For: SCUBA implements a storage format-agnostic API for single-cell data access in R [version 2; peer review: 2 approved, 1 approved with reservations] Open
View article: A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models
A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models Open
Inherited retinopathies are devastating diseases that in most cases lack treatment options. Disease-modifying therapies that mitigate pathophysiology regardless of the underlying genetic lesion are desirable due to the diversity of mutatio…
View article: Conditional deletion of miR-204 and miR-211 in murine retinal pigment epithelium results in retinal degeneration
Conditional deletion of miR-204 and miR-211 in murine retinal pigment epithelium results in retinal degeneration Open
MicroRNAs (miRs) are short, evolutionarily conserved noncoding RNAs that canonically downregulate expression of target genes. The miR family composed of miR-204 and miR-211 is among the most highly expressed miRs in the retinal pigment epi…
View article: Restoring retinal polyunsaturated fatty acid balance and retina function by targeting ceramide in AdipoR1-deficient mice
Restoring retinal polyunsaturated fatty acid balance and retina function by targeting ceramide in AdipoR1-deficient mice Open
Mutations in the adiponectin receptor 1 gene (AdipoR1) lead to retinitis pigmentosa and are associated with age-related macular degeneration. This study explores the effects of AdipoR1 gene deficiency in mice, revealing a striking decline …
View article: Distinct mouse models of Stargardt disease display differences in pharmacological targeting of ceramides and inflammatory responses
Distinct mouse models of Stargardt disease display differences in pharmacological targeting of ceramides and inflammatory responses Open
Mutations in many visual cycle enzymes in photoreceptors and retinal pigment epithelium (RPE) cells can lead to the chronic accumulation of toxic retinoid byproducts, which poison photoreceptors and the underlying RPE if left unchecked. Wi…
View article: Ocelli: an open-source tool for the visualization of developmental multimodal single-cell data
Ocelli: an open-source tool for the visualization of developmental multimodal single-cell data Open
The recent expansion of single-cell technologies has enabled simultaneous genome-wide measurements of multiple modalities in the same single cell. The potential to jointly profile such modalities as gene expression, chromatin accessibility…
View article: spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content
spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content Open
View article: Stress resilience-enhancing drugs preserve tissue structure and function in degenerating retina via phosphodiesterase inhibition
Stress resilience-enhancing drugs preserve tissue structure and function in degenerating retina via phosphodiesterase inhibition Open
Chronic, progressive retinal diseases, such as age-related macular degeneration (AMD), diabetic retinopathy, and retinitis pigmentosa, arise from genetic and environmental perturbations of cellular and tissue homeostasis. These disruptions…
View article: spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content
spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content Open
Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RN…
View article: A newly-recognized population of residual neural crest cells in the adult leptomeninges is re-activated for vascular repair
A newly-recognized population of residual neural crest cells in the adult leptomeninges is re-activated for vascular repair Open
Summary The neural crest (NC) is a transient structure in vertebrate embryogenesis comprising highly migratory multipotent stem cells that give rise to a diverse array of cell types in organs throughout the body, including initiating neuro…
View article: Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function
Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function Open
Dendritic cells (DCs) sense environmental cues and adopt either an immune-stimulatory or regulatory phenotype, thereby fine-tuning immune responses. Identifying endogenous regulators that determine DC function can thus inform the developme…
View article: Inhibition of ceramide accumulation in AdipoR1–/– mice increases photoreceptor survival and improves vision
Inhibition of ceramide accumulation in AdipoR1–/– mice increases photoreceptor survival and improves vision Open
Adiponectin receptor 1 (ADIPOR1) is a lipid and glucose metabolism regulator that possesses intrinsic ceramidase activity. Mutations of the ADIPOR1 gene have been associated with nonsyndromic and syndromic retinitis pigmentosa. Here, we sh…
View article: Blood and immune development in human fetal bone marrow and Down syndrome
Blood and immune development in human fetal bone marrow and Down syndrome Open
View article: Cycling cancer persister cells arise from lineages with distinct programs
Cycling cancer persister cells arise from lineages with distinct programs Open
View article: Intrinsic and extrinsic regulation of human fetal bone marrow haematopoiesis and perturbations in Down syndrome
Intrinsic and extrinsic regulation of human fetal bone marrow haematopoiesis and perturbations in Down syndrome Open
Throughout postnatal life, haematopoiesis in the bone marrow (BM) maintains blood and immune cell production. Haematopoiesis first emerges in human BM at 12 post conception weeks while fetal liver (FL) haematopoiesis is still expanding. Ye…
View article: TIM-3 restrains anti-tumour immunity by regulating inflammasome activation
TIM-3 restrains anti-tumour immunity by regulating inflammasome activation Open
View article: Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells
Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells Open
View article: Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq
Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq Open
View article: Cycling cancer persister cells arise from lineages with distinct transcriptional and metabolic programs
Cycling cancer persister cells arise from lineages with distinct transcriptional and metabolic programs Open
Non-genetic mechanisms have recently emerged as important drivers of therapy failure in cancer (Salgia and Kulkarni, 2018), where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment (Vallette et …
View article: Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes
Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes Open
View article: Single cell profiling of immature human postnatal thymocytes resolves the complexity of intra-thymic lineage differentiation and thymus seeding precursors
Single cell profiling of immature human postnatal thymocytes resolves the complexity of intra-thymic lineage differentiation and thymus seeding precursors Open
During postnatal life, thymopoiesis depends on the continuous colonization of the thymus by bone marrow derived hematopoietic progenitors that migrate through the bloodstream. In human, the nature of these thymus immigrants has remained un…
View article: Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq
Cumulus: a cloud-based data analysis framework for large-scale single-cell and single-nucleus RNA-seq Open
Massively parallel single-cell and single-nucleus RNA-seq (sc/snRNA-seq) have opened the way to systematic tissue atlases in health and disease, but as the scale of data generation is growing, so does the need for computational pipelines f…
View article: Decoding human fetal liver haematopoiesis
Decoding human fetal liver haematopoiesis Open
View article: Genetic predisposition to myeloproliferative neoplasms implicates hematopoietic stem cell biology
Genetic predisposition to myeloproliferative neoplasms implicates hematopoietic stem cell biology Open
Myeloproliferative neoplasms (MPNs) are blood cancers characterized by excessive production of mature myeloid cells that result from the acquisition of somatic driver mutations in hematopoietic stem cells (HSCs) 1 . While substantial progr…
View article: Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses
Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses Open
View article: A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia
A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia Open
View article: Decoding the development of the blood and immune systems during human fetal liver haematopoiesis
Decoding the development of the blood and immune systems during human fetal liver haematopoiesis Open
Summary Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells/multipotent progenitors (HSC/MPPs), yet remains poorly defined in humans. Using single cell transcriptome profiling…
View article: A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia
A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia Open