45 Result(s)
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Laxmi Parida
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Latent human herpesvirus 6 is reactivated in CAR T cells
Cell therapies have yielded durable clinical benefits for patients with cancer, but the risks associated with the development of therapies from manipulated human cells are understudied. For example, we lack a ...
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Open AccessCorrection: A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
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Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome
Richter syndrome (RS) arising from chronic lymphocytic leukemia (CLL) exemplifies an aggressive malignancy that develops from an indolent neoplasm. To decipher the genetics underlying this transformation, we c...
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Open AccessStandardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a ...
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Molecular map of chronic lymphocytic leukemia and its impact on outcome
Recent advances in cancer characterization have consistently revealed marked heterogeneity, impeding the completion of integrated molecular and clinical maps for each malignancy. Here, we focus on chronic lymp...
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Distinct cellular dynamics associated with response to CAR-T therapy for refractory B cell lymphoma
Chimeric antigen receptor (CAR)-T cell therapy has revolutionized the treatment of hematologic malignancies. Approximately half of patients with refractory large B cell lymphomas achieve durable responses from...
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Open AccessAuthor Correction: Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis
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Open AccessIntegrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis
Acral melanoma, the most common melanoma subtype among non-White individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we perform integrative genomic and clin...
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Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers
Although single-gene perturbation screens have revealed a number of new targets, vulnerabilities specific to frequently altered drivers have not been uncovered. An important question is whether the compensator...
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Open AccessA common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones
All diseases containing genetic material undergo genetic evolution and give rise to heterogeneity including cancer and infection. Although these illnesses are biologically very different, the ability for phylo...
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Open AccessSARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment
SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic ...
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Challenges in benchmarking metagenomic profilers
Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classification of metagenomic data and estimation of taxonomic profiles, broadly referred t...
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Open AccessFunctional profiling of COVID-19 respiratory tract microbiomes
In response to the ongoing global pandemic, characterizing the molecular-level host interactions of the new coronavirus SARS-CoV-2 responsible for COVID-19 has been at the center of unprecedented scientific fo...
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Open AccessExplainable AI reveals changes in skin microbiome composition linked to phenotypic differences
Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and hu...
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Open AccessMonitoring the microbiome for food safety and quality using deep shotgun sequencing
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test this hypothesis, we sequenced the total RNA of 31 high ...
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Open AccessLies, Gosh Darn Lies, and not enough good statistics: why epidemic model parameter estimation fails
We sought to investigate whether epidemiological parameters that define epidemic models could be determined from the epidemic trajectory of infections, recovery, and hospitalizations prior to peak, and also to...
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Open AccessRe-purposing software for functional characterization of the microbiome
Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software. For analysis of the microbiome, workflows typically begin with taxonomic classifi...
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Author Correction: Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Open AccessFood authentication from shotgun sequencing reads with an application on high protein powders
Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (F...
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Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers
During cancer therapy, tumor heterogeneity can drive the evolution of multiple tumor subclones harboring unique resistance mechanisms in an individual patient1–3. Previous case reports and small case series have ...
