Author

S. Arya

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biochemistry· 2 Cancer Biology· 2 Ecology· 2 Biophysics· 1 Evolutionary Biology· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 6 Research Focus:cell type annotation· 4 Approach:statistical model· 4 Research Focus:differential expression· 3 Organism:human· 3 Research Focus:benchmarking· 2 Research Focus:chromatin & epigenetic regulation· 2 Approach:deep learning· 2

Frequent Co-Authors

N. Dai· 3 shared S. Qi· 3 shared S.-H. Chan· 3 shared Y. K. Gupta· 3 shared D. J. Stekel· 2 shared J.-U. Kreft· 2 shared L. Martinez-Sobrido· 2 shared R. A. Hromas· 2 shared

Activity by Year

2020-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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3 shared papersBiochemistry

N. Dai

Mutual co-authors in cluster

Author profile →

10 papers

Recent·Most cited

The brittle star genome illuminates the genetic basis of animal appendage regeneration

E. Parey, O. Ortega-Martinez, J. Delroisse, L. Piovani, A. Czarkwiani, D. Dylus, S. Arya, S. Dupont, M. Thorndyke, T. Larsson, K. Johannesson, K. M. Buckley, P. Martinez, P. Oliveri, F. Marletaz

This study presents a chromosome-scale genome assembly of the brittle star and identifies conserved gene expression patterns during regeneration across invertebrates and vertebrates.

bioRxiv · Oct 30, 2023Evolutionary Biology

IRF8-mutant B cell lymphoma evades immunity through a CD74-dependent deregulation of antigen processing and presentation in MHC CII complexes

Z. Qiu, J. Khalife, A.-P. Lin, P. Ethiraj, C. Jaafar, L. Chiou, G. Huelgas-Morales, S. Aslam, S. Arya, Y. Gupta, P. Dahia, R. Aguiar

This study shows that IRF8 mutations in DLBCL lymphomas impair antigen processing and presentation by reducing CD74 and HLA-DM, leading to immune evasion and increased tumor burden.

bioRxiv · Oct 14, 2023Cancer Biology

Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0

B. J. R. Cockx, T. Foster, R. J. Clegg, K. Alden, S. Arya, D. J. Stekel, B. F. Smets, J.-U. Kreft

The paper introduces iDynoMiCS 2.0, an individual-based modeling platform for microbial communities, showing that filamentous bacteria outcompete spherical bacteria regardless of growth strategy.

bioRxiv · Jun 27, 2023Ecology

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes

S. Arya, A. B. George, J. P. O'Dwyer

This paper introduces a mechanism-agnostic method to predict microbial community compositions and functions using sparse representations and compressive sensing, validated on both simulated and experimental data.

bioRxiv · Apr 12, 2023Ecology

RootSlice: a novel functional-structural model for root anatomical phenotypes

J. S. Sidhu, I. Ajmera, S. Arya, J. P. Lynch

RootSlice simulates root anatomical phenotypes to evaluate their impact on plant fitness in unfavorable soils.

bioRxiv · Jun 29, 2022Plant Biology

Identification of plasma proteins associated with oesophageal cancer chemotherapeutic treatment outcomes using SWATH-MS

N. Guo, G. Minas, S. A. Synowsky, M. R. Dunne, H. Ahmed, R. McShane, A. Bhardwaj, N. E. Donlon, C. Lorton, J. O'Sullivan, J. V. Reynolds, P. D. Caie, S. L. Shirran, A. G. Lynch, A. Stewart, S. Arya

This study identifies plasma proteins associated with response to chemotherapeutic treatment in oesophageal adenocarcinoma using SWATH-MS and ELISA.

bioRxiv · Apr 7, 2022Cancer Biology

RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro

S. Qi, J. Mota, S.-H. Chan, J. Villarreal, N. Dai, S. Arya, R. A. Hromas, M. K. Rao, I. R. Correa, Y. K. Gupta

This study investigates how the METTL3-METTL14 complex binds and methylates DNA and RNA, revealing distinct preferences for single-stranded DNA and structured RNA.

bioRxiv · Jan 8, 2022Biochemistry

A metal ion orients mRNA to ensure accurate 2'-O ribosyl methylation of the first nucleotide of the SARS-CoV-2 genome

T. Viswanathan, A. Misra, S.-H. Chan, S. Qi, N. Dai, S. Arya, L. Martinez-Sobrido, Y. K. Gupta

The paper reports structures of the SARS-CoV-2 nsp16/nsp10 enzyme complex before and after RNA product release, revealing conformational changes and the role of a metal ion in 2'-O methylation of the first nucleotide.

bioRxiv · Mar 12, 2021Biochemistry

Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids

S. Arya, A. Williams, S. Vazquez Reina, C. W. Knapp, J.-U. Kreft, J. L. Hobman, D. J. Stekel

The paper develops a mathematical model to predict minimal metal concentrations that co-select for antibiotic resistance plasmids, applying it to copper, zinc, mercury, lead, and silver.

bioRxiv · Sep 14, 2020Microbiology

Structural Basis of RNA Cap Modification by SARS-CoV-2 Coronavirus

T. Viswanathan, S. Arya, S.-H. Chan, S. Qi, N. Dai, R. A. Hromas, J.-G. Park, F. Oladunni, L. Martinez-Sobrido, Y. K. Gupta

The paper reports the high-resolution structure of SARS-CoV-2 nsp16/nsp10 complex during mRNA cap methylation, revealing conformational changes and a novel ligand-binding site for antiviral targeting.

bioRxiv · Apr 26, 2020Biophysics