Nikita R. Dsouza
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View article: Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants
Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants Open
Clinical genomics sequencing is rapidly expanding the number of variants that need to be functionally elucidated. Interpreting genetic variants (i.e., mutations) usually begins by identifying how they affect protein-coding sequences. Still…
View article: MARK2 variants cause autism spectrum disorder via the downregulation of WNT/β-catenin signaling pathway
MARK2 variants cause autism spectrum disorder via the downregulation of WNT/β-catenin signaling pathway Open
View article: <i>MARK2</i>variants cause autism spectrum disorder<i>via</i>the downregulation of WNT/β-catenin signaling pathway
<i>MARK2</i>variants cause autism spectrum disorder<i>via</i>the downregulation of WNT/β-catenin signaling pathway Open
MARK2 , a member of the evolutionarily conserved PAR1/MARK serine/threonine kinase family, has been identified as a novel risk gene for autism spectrum disorder (ASD) based on the enrichment of de novo loss-of-function (Lof) variants in la…
View article: Structural and Dynamic Analyses of Pathogenic Variants in PIK3R1 Reveal a Shared Mechanism Associated among Cancer, Undergrowth, and Overgrowth Syndromes
Structural and Dynamic Analyses of Pathogenic Variants in PIK3R1 Reveal a Shared Mechanism Associated among Cancer, Undergrowth, and Overgrowth Syndromes Open
The PI3K enzymes modify phospholipids to regulate cell growth and differentiation. Somatic variants in PI3K are recurrent in cancer and drive a proliferative phenotype. Somatic mosaicism of PIK3R1 and PIK3CA are associated with vascular an…
View article: Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants
Assessing Protein Surface-Based Scoring for Interpreting Genomic Variants Open
Clinical genomics sequencing is rapidly expanding the number of variants that need to be functionally elucidated. Interpreting genetic variants (i.e., mutations) usually begins by identifying how they affect protein-coding sequences. Still…
View article: SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors
SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors Open
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variati…
View article: Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome
Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome Open
Background Genomics enables individualized diagnosis and treatment, but large challenges remain to functionally interpret rare variants. To date, only one causative variant has been described for KCNK9 imprinting syndrome (KIS). The genoty…
View article: Additional file 2 of Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome
Additional file 2 of Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome Open
Additional file 2: Table S1. KCNK9 variants, impact summary, and ACMG classification.
View article: <i>De novo</i> coding variants in the <i>AGO1</i> gene cause a neurodevelopmental disorder with intellectual disability
<i>De novo</i> coding variants in the <i>AGO1</i> gene cause a neurodevelopmental disorder with intellectual disability Open
Background High-impact pathogenic variants in more than a thousand genes are involved in Mendelian forms of neurodevelopmental disorders (NDD). Methods This study describes the molecular and clinical characterisation of 28 probands with ND…
View article: Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics
Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics Open
In the current study, we report computational scores for advancing genomic interpretation of disease-associated genomic variation in members of the RAS family of genes. For this purpose, we applied 31 sequence- and 3D structure-based compu…
View article: Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1‐like ( <i>DOT1L</i> ) and partnering complexes involved in leukemogenesis
Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1‐like ( <i>DOT1L</i> ) and partnering complexes involved in leukemogenesis Open
Disruptor of telomeric silencing 1‐like ( DOT1L ) is the only non‐SET domain histone lysine methyltransferase (KMT) and writer of H3K79 methylation on nucleosomes marked by H2B ubiquitination. DOT1L has elicited significant attention becau…
View article: Correction to: Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction
Correction to: Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction Open
View article: <i>SASH3</i>variants cause a novel form of X-linked combined immunodeficiency with immune dysregulation
<i>SASH3</i>variants cause a novel form of X-linked combined immunodeficiency with immune dysregulation Open
Sterile alpha motif (SAM) and Src homology-3 (SH3) domain-containing 3 (SASH3), also called SH3-containing lymphocyte protein (SLY1), is a putative adaptor protein that is postulated to play an important role in the organization of signali…
View article: Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction
Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction Open
View article: <i>De novo</i>coding variants in the<i>AGO1</i>gene cause a neurodevelopmental disorder with intellectual disability
<i>De novo</i>coding variants in the<i>AGO1</i>gene cause a neurodevelopmental disorder with intellectual disability Open
High-impact pathogenic variants in more than 1,000 protein-coding genes cause Mendelian forms of neurodevelopmental disorders (NDD), including the newly reported AGO2 gene. This study describes the molecular and clinical characterization o…
View article: Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations
Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations Open
Motivation Protein-coding genetic alterations are frequently observed in Clinical Genetics, but the high yield of variants of uncertain significance remains a limitation in decision making. RAS-family GTPases are cancer drivers, but only 5…
View article: Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder
Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder Open
View article: POLD1 Deficiency Reveals a Role for POLD1 in DNA Repair and T and B Cell Development
POLD1 Deficiency Reveals a Role for POLD1 in DNA Repair and T and B Cell Development Open
View article: Impairment of the mitochondrial one-carbon metabolism enzyme SHMT2 causes a novel brain and heart developmental syndrome
Impairment of the mitochondrial one-carbon metabolism enzyme SHMT2 causes a novel brain and heart developmental syndrome Open
View article: A homozygous missense variant in UBE2T is associated with a mild Fanconi anemia phenotype
A homozygous missense variant in UBE2T is associated with a mild Fanconi anemia phenotype Open
A homozygous missense variant in UBE2T is associated with a mild Fanconi anemia phenotype
View article: Interaction between Mas1 and AT1RA contributes to enhancement of skeletal muscle angiogenesis by angiotensin-(1-7) in Dahl salt-sensitive rats
Interaction between Mas1 and AT1RA contributes to enhancement of skeletal muscle angiogenesis by angiotensin-(1-7) in Dahl salt-sensitive rats Open
The heptapeptide angiotensin-(1-7) (Ang-(1-7)) is protective in the cardiovascular system through its induction of vasodilator production and angiogenesis. Despite acting antagonistically to the effects of elevated, pathophysiological leve…
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Discovery, expression, cellular localization, and molecular properties of a novel, alternative spliced HP1γ isoform, lacking the chromoshadow domain Open
View article: Novel <i>KLHL26</i> variant associated with a familial case of Ebstein’s anomaly and left ventricular noncompaction
Novel <i>KLHL26</i> variant associated with a familial case of Ebstein’s anomaly and left ventricular noncompaction Open
Background Ebstein's anomaly (EA) is a rare congenital heart disease of the tricuspid valve and right ventricle. Patients with EA often manifest with left ventricular noncompaction (LVNC), a cardiomyopathy. Despite implication of cardiac s…
View article: Novel biallelic variants in <i>MSTO1</i> associated with mitochondrial myopathy
Novel biallelic variants in <i>MSTO1</i> associated with mitochondrial myopathy Open
Mitochondrial disorders are caused by nuclear and mitochondrial pathogenic variants leading to defects in mitochondrial function and cellular respiration. Recently, the nuclear-encoded mitochondrial fusion gene MSTO1 (Misato 1) has been im…
View article: Integration of Multi-level Molecular Scoring for the Interpretation of RAS-Family Genetic Variation
Integration of Multi-level Molecular Scoring for the Interpretation of RAS-Family Genetic Variation Open
Protein-coding genetic variants are the first considered in most studies and Precision Medicine workflows, but their interpretation is primarily driven by DNA sequence-based analytical tools and annotations. Thus, more specific and mechani…
View article: A case of Coffin–Siris syndrome with severe congenital heart disease and a novel <i>SMARCA4</i> variant
A case of Coffin–Siris syndrome with severe congenital heart disease and a novel <i>SMARCA4</i> variant Open
Coffin–Siris syndrome (CSS) is a developmental disability, caused by genomic variants in the gene SMARCA4 , in addition to other known genes, but the full spectrum of SMARCA4 variants that can cause CSS is unknown with 40% of cases not hav…
View article: Discovery, Expression, Cellular Localization, and Molecular Properties of a Novel, Alternative Spliced HP1γ Isoform, Lacking the Chromoshadow Domain
Discovery, Expression, Cellular Localization, and Molecular Properties of a Novel, Alternative Spliced HP1γ Isoform, Lacking the Chromoshadow Domain Open
By reading the H3K9Me3 mark through their N-terminal chromodomain (CD), HP1 proteins play a significant role in cancer-associated processes, including cell proliferation, differentiation, chromosomal stability, and DNA repair. Here, we use…
View article: Discovery of small molecule inhibitors of adenovirus by disrupting E3-19K/HLA-A2 interactions
Discovery of small molecule inhibitors of adenovirus by disrupting E3-19K/HLA-A2 interactions Open
View article: Strategies for Identification of Small Molecule Inhibitors of Ad2 E3-19K/HLA-A2 Binding Interaction
Strategies for Identification of Small Molecule Inhibitors of Ad2 E3-19K/HLA-A2 Binding Interaction Open
Adenovirus (Ad) infections are widespread in the human population, and causes infections linked to many gastrointestinal, respiratory and ocular illnesses. In vitro and in vivo studies have shown that the binding of the adenovirus protein …