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Research from our Life Sciences team

There is one paper published by Sequoia. The rest were published elsewhere by members of our team. They cover cancer genomics, population genetics, viral sequencing, genome assembly and machine learning.

ON THIS PAGEOur own paperCancer genomicsPopulation geneticsViral genomicsAssembly and toolingMachine learningPatents and books
Published by Sequoia

GenXflo: a browser based visual interface for authoring Nextflow DSL2 bioinformatics pipelines

Sequoia Applied Technologies · Joe Jerry · Joshua Jebaraj · Gopika S Nair · Mohammed Sinan · Ariya S S

This paper describes GenXFlo, our visual builder for Nextflow pipelines. It covers the browser based editor, the generated DSL2 and the way a pipeline is assembled and used.

About GenXFlo
The GenXFlo pipeline canvas

The papers below were published by members of our team outside Sequoia. They are here to show the scientific work people on the team have done. They are not Sequoia publications.

Where the background sits

Research areas in the publications

Research areas the team has published in, mapped to the services on this siteCancer genomicsPopulation geneticsViral genomicsAssembly andtoolingML formoleculesBioinformatics andGenomicsAI forLife SciencesDigitalPathologyClinical DataPlatformsPUBLISHED RESEARCH AREASWHAT WE BUILD HERE

The work

Cancer genomics and gene expression

Gene expression in cancer

Several of these papers deal with gene expression in lung, oral and neuroblastoma cancers, including work on master regulators and miRNAs.

  • Identification of lung cancer master genes triggered by smoking and their key pathways based on gene expression profiling
    S. S. Ariya, R. J. Akhila, J. Baby
    GENE REPORTS 21, 100812, 2020
  • Comprehensive gene expression analysis and identification of STAT-1 as master regulator in oral squamous cell carcinoma
    S. S. Ariya, R. J. Akhila, J. Baby
    INTERNATIONAL JOURNAL OF PSYCHOSOCIAL REHABILITATION 24, 399-417, 2020
  • Role of KIF2C and TEK as master regulators in lung cancer: insights from NGS data
    S. S. Ariya, P. Vijayababu
    IN SILICO PHARMACOLOGY
  • HES1 promoter activation dynamics reveal the plasticity, stemness and heterogeneity in neuroblastoma cancer stem cells
    P. A. Riya, B. Basu, S. Surya, and others including R. Sukumaran
    JOURNAL OF CELL SCIENCE 135(22), 2022
Population and statistical genetics

Population genetics and statistical analysis

The publications here include population genetics of stroke and its comorbidities, structural equation models and monogenic diabetes.

  • Ethnic and region specific genetic risk variants of stroke and its comorbid conditions can define the variations in the burden of stroke and its phenotypic traits
    R. Sukumaran, A. S. Nair, M. Banerjee
    ELIFE 13:RP94088, 2024
  • Shared genetic architecture of stroke and its comorbid conditions reveals latent phenotypes that differ among populations
    R. Sukumaran, A. S. Nair, M. Banerjee
    MEDRXIV PREPRINT, 2025 DOI
  • Monogenic diabetes: genetic insight and precision therapeutics in the management of MODY
    G. Venkatesan, K. V. Kumari, S. S. Ariya, P. Vijayababu
    EXON 2(1), 16-24, 2025
Viral and microbial genomics

Viral and microbial genomics

There are also papers on whole genome sequencing of viruses and bacteria, structural variation and viral diversity.

  • PTAP motif duplication in the p6 Gag protein confers a replication advantage on HIV-1 subtype C
    S. Sharma, P. S. Arunachalam, M. Menon, and others including J. Jebaraj
    2018, PMC6066301 DOI
  • Analysis of viral diversity for vaccine target discovery
    A. M. Khan, Y. Hu, O. Miotto, and others including R. Sukumaran
    BMC MEDICAL GENOMICS 10(SUPPL 4), 78-91, 2017
  • Direct whole genome deep sequencing of human respiratory syncytial virus A and B from Vietnamese children
    L. A. H. Do, A. Wilm, J. E. Bryant, and others including R. Sukumaran
    JOURNAL OF GENERAL VIROLOGY 96(12), 3470-83, 2015
  • Comprehensive identification of Fim mediated inversions in uropathogenic Escherichia coli with structural variation detection using relative entropy
    C. W. Russell, R. Sukumaran, L. T. Liow, and others
    MSPHERE 4(2), 2019
Genome assembly and analysis tooling

Genome assembly and analysis

The genome assembly work includes chromosome scale assembly, repeat finding in whole genomes and NGS reads, and large mutagenesis screens.

  • Chromosome scale genome assembly and annotation of coconut cultivar Chowghat Green Dwarf
    M. K. Rajesh, R. Budhwar, R. Shukla, and others including A. Dinesh
    SCIENTIFIC REPORTS 14, 28778, 2024 DOI
  • RFGR: repeat finder for complete and assembled whole genomes and NGS reads
    R. Sukumaran, K. Shahina, A. S. Nair
    BIOCHEMICAL GENETICS, 2024 DOI
  • A multifunctional mutagenesis screen for analysis of gene function in zebrafish
    H. N. B. Quach, S. Tao, A. Joshi, and others including R. Sukumaran
    G3: GENES, GENOMES, GENETICS 5(6), 1283-99, 2015
Machine learning for molecular properties

Machine learning for molecular properties

One paper looks at interpretable machine learning for molecular solubility prediction.

  • Deciphering molecular and solvent effects on aqueous and organic solubility through interpretable machine learning approaches
    B. Gopichand, Gopika S. Nair, B. G. Nair, N. Melethadathil
    ACS OMEGA 11(20), 29757-29771, 2026 DOI

Patents and books

Patent
Novel method for recovery of phosphorus and nitrogen from human urine
APPLICATION NO. 202241057724A · ARIYA S S
Patent
IoT based drug waste management device
APPLICATION NO. 427600-001, SUBMITTED · ARIYA S S
Book
Genomic Insight
SALIHA PUBLICATIONS, IN PRESS · ARIYA S S WITH P. VIJAYABABU
Book
Human Physiology and Nutrition
ISBN 9789394198081 · ARIYA S S WITH T. M. VIJAYALAKSHMI
Chapter
Tools for drug discovery, in silico
IN RECENT TRENDS IN APPLIED SCIENCES AND COMPUTER ENGINEERING, ISBN 978-81-950236-3-9 · B. JOSEPH AND ARIYA S S

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