Priyatama Pandey
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View article: Laser Cooling Positronium with Broadband Laser Pulses
Laser Cooling Positronium with Broadband Laser Pulses Open
The first successful demonstration of broadband laser cooling of positronium (Ps) atoms, obtained within the AEgIS experiment at CERN, is presented here. By employing a custom-designed pulsed alexandrite laser system at 243 nm featuring lo…
View article: Development of the normalization method for the first large field-of-view plastic-based PET Modular scanner
Development of the normalization method for the first large field-of-view plastic-based PET Modular scanner Open
In positron emission tomography acquisition (PET), sensitivity along a line of response can vary due to crystal geometrical arrangements in the scanner and/or detector inefficiencies, leading to severe artefacts in the reconstructed image.…
View article: Nanoporosity imaging by positronium lifetime tomography
Nanoporosity imaging by positronium lifetime tomography Open
Positron Annihilation Lifetime Spectroscopy (PALS) is a well-established non-destructive technique used for nanostructural characterization of porous materials. It is based on the annihilation of a positron and an electron. Mean positron l…
View article: Investigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia
Investigating DNA methylation as a mediator of genetic risk in childhood acute lymphoblastic leukemia Open
Genome-wide association studies have identified a growing number of single nucleotide polymorphisms (SNPs) associated with childhood acute lymphoblastic leukemia (ALL), yet the functional roles of most SNPs are unclear. Multiple lines of e…
View article: Accelerated epigenetic aging in newborns with Down syndrome
Accelerated epigenetic aging in newborns with Down syndrome Open
Accelerated aging is a hallmark of Down syndrome (DS), with adults experiencing early‐onset Alzheimer's disease and premature aging of the skin, hair, and immune and endocrine systems. Accelerated epigenetic aging has been found in the blo…
View article: Epigenome-wide association study of acute lymphoblastic leukemia in children with Down syndrome
Epigenome-wide association study of acute lymphoblastic leukemia in children with Down syndrome Open
Down syndrome (DS) is caused by constitutional trisomy of chromosome 21 and is associated with an up to 30-fold increased risk of acute lymphoblastic leukemia (ALL). 1,2While DS is associated with alterations in epigenetic markers, includi…
View article: Development of a Droplet Digital™ PCR DNA Methylation Detection and Quantification Assay of Prenatal Tobacco Exposure
Development of a Droplet Digital™ PCR DNA Methylation Detection and Quantification Assay of Prenatal Tobacco Exposure Open
DNA methylation is a labile modification associated with gene expression control and environmental adaptations. High throughput, scalable and quantitative assessments of specific DNA methylation modifications in complex genomic regions for…
View article: Lysine acetylation regulates the interaction between proteins and membranes
Lysine acetylation regulates the interaction between proteins and membranes Open
View article: Epigenetic Biomarkers of Prenatal Tobacco Smoke Exposure Are Associated with Gene Deletions in Childhood Acute Lymphoblastic Leukemia
Epigenetic Biomarkers of Prenatal Tobacco Smoke Exposure Are Associated with Gene Deletions in Childhood Acute Lymphoblastic Leukemia Open
Background: Parental smoking is implicated in the etiology of acute lymphoblastic leukemia (ALL), the most common childhood cancer. We recently reported an association between an epigenetic biomarker of early-life tobacco smoke exposure at…
View article: <i>In utero</i> and early-life exposure to thirdhand smoke causes profound changes to the immune system
<i>In utero</i> and early-life exposure to thirdhand smoke causes profound changes to the immune system Open
Acute lymphoblastic leukemia (ALL) is the most common cancer in children. Thirdhand smoke (THS) is the residual tobacco contamination that remains after the smoke clears. We investigated the effects of THS exposure in utero and during earl…
View article: The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis
The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis Open
View article: iMutSig: a web application to identify the most similar mutational signature using shiny
iMutSig: a web application to identify the most similar mutational signature using shiny Open
There are two frameworks for characterizing mutational signatures which are commonly used to describe the nucleotide patterns that arise from mutational processes. Estimated mutational signatures from fitting these two methods in human can…
View article: iMutSig: a web application to identify the most similar mutational signature using shiny
iMutSig: a web application to identify the most similar mutational signature using shiny Open
There are two frameworks for characterizing mutational signatures which are commonly used to describe the nucleotide patterns that arise from mutational processes. Estimated mutational signatures from fitting these two methods in human can…
View article: Mutational signatures in colon cancer
Mutational signatures in colon cancer Open
Objective Recently, many tumor sequencing studies have inferred and reported on mutational signatures, short nucleotide patterns at which particular somatic base substitutions appear more often. A number of signatures reflect biological pr…
View article: HiLDA: a statistical approach to investigate differences in mutational signatures
HiLDA: a statistical approach to investigate differences in mutational signatures Open
We propose a hierarchical latent Dirichlet allocation model (HiLDA) for characterizing somatic mutation data in cancer. The method allows us to infer mutational patterns and their relative frequencies in a set of tumor mutational catalogs …
View article: HiLDA: a statistical approach to investigate differences in mutational signatures
HiLDA: a statistical approach to investigate differences in mutational signatures Open
We propose a hierarchical latent Dirichlet allocation model (HiLDA) for characterizing somatic mutation data in cancer. The method allows us to infer mutational patterns and their relative frequencies in a set of tumor mutational catalogs …
View article: De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski
De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski Open
Many trematode parasites cause infection in humans and are thought to be a major public health problem. Their ecological diversity in different regions provides challenging questions on evolution of these organisms. In this report, we perf…
View article: <i>De novo</i> genome and transcriptome analyses provide insights into the biology of the trematode human parasite <i>Fasciolopsis buski</i>
<i>De novo</i> genome and transcriptome analyses provide insights into the biology of the trematode human parasite <i>Fasciolopsis buski</i> Open
Many trematode parasites cause infection in humans and are thought to be a major public health problem. Their ecological diversity in different regions provides challenging questions on evolution of these organisms. In this report, we perf…
View article: The 17-residue-long N terminus in huntingtin controls stepwise aggregation in solution and on membranes via different mechanisms
The 17-residue-long N terminus in huntingtin controls stepwise aggregation in solution and on membranes via different mechanisms Open
Aggregation of huntingtin protein arising from expanded polyglutamine (polyQ) sequences in the exon-1 region of mutant huntingtin plays a central role in the pathogenesis of Huntington's disease. The huntingtin aggregation pathways are of …
View article: A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
We generated high-quality transcriptome sequence data from H. indica IJs for the first time. The transcripts showed high similarity with the parasitic nematodes, M. hapla, and A. suum as opposed to C. elegans, a species to which H. indica …
View article: Additional file 11: Table S8. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 11: Table S8. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
Orthologs of members of C. elegans gene classes present in H. indica at â Ľ25% identity and query coverage. (XLSX 37 kb)
View article: Additional file 7: Table S5b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 7: Table S5b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
MEROPS analysis of H. indica transcripts to identify secreted peptidases, proteases, and peptides. (XLSX 11 kb)
View article: Additional file 4: Table S3. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 4: Table S3. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
KEGG Pathways represented by transcripts with FPKM value of â Ľ100 and â Ľ1000. (XLSX 20 kb)
View article: Additional file 6: Table S5a. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 6: Table S5a. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
H. indica secretome prediction by SignalP. (XLSX 90 kb)
View article: Additional file 12: of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 12: of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
H. indica assembled sequences. (TXT 14804 kb)
View article: Additional file 1: Table S1a. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 1: Table S1a. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
Blast, KOG and PRK analysis of the H. indica IJ transcripts. (XLSX 2073 kb)
View article: Additional file 3: Table S2. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 3: Table S2. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
Transcript abundance of H. Indica transcripts along with KOG analysis of transcripts showing FPKM values ≥ 100 and ≥ 1000. (XLSX 486 kb)
View article: Additional file 2: Table S1b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 2: Table S1b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
Standalone blast of H. indica IJ transcripts against H. bacteriophora genome. (XLSX 336 kb)
View article: Additional file 10: Table S7. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 10: Table S7. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
RNAi effector pathway genes in H. indica. (XLSX 12 kb)
View article: Additional file 9: Table S6b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica
Additional file 9: Table S6b. of A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica Open
SSR type and microsatellites present in H. indica. (XLSX 187 kb)