Publications

Research Publications

Peer-reviewed publications demonstrating expertise in NGS analysis, CRISPR screens, machine learning, and multi-omics integration. All work conducted with pharma-grade rigor and reproducible methods.

πŸ“š Peer-Reviewed Publications

Szymon Myrta as bioinformatics co-author contributing computational analysis

2025

Transcription factor Zfx regulates tumor’s evasion to T cell killing in immunotherapy

iScience, 2025 | DOI: 10.1016/j.isci.2025.113842

Authors: Kaufmann U, Wang J, Callow M, Fortin J, Myrta S, Nickles D, et al.

Bioinformatics Contributions:

  • CRISPR screen analysis (~160,000 sgRNAs with crisprVerse)
  • RNA-seq differential expression (HTSeqGenie, edgeR, limma-voom)
  • ChIP-seq integration (public GEO data)
  • TCGA survival modeling (Cox proportional hazards)
  • Pathway enrichment (MSigDB Hallmark)

Key Finding: Identified ZFX as biomarker for immunotherapy response; regulates apoptosis pathway genes including CASP3

πŸ“„ Read Paper πŸ“Š Data: GEO GSE276964, GSE276965

2024

T cell-dependent bispecific therapy enhances innate immune activation and antibody-mediated killing

Cancer Immunology Research, 2024 | DOI: 10.1158/2326-6066.CIR-23-0800

Authors: Besla R, Penuel E, Rosario GD, Cosino E, Myrta S, Polson AG, et al.

Bioinformatics Contributions:

  • RNA-seq of sorted NK cells (Smart-Seq V4, HTSeqGenie)
  • Differential expression (edgeR, limma-voom)
  • Gene set enrichment (fgsea with MSigDB)
  • Cytokine data integration (Luminex multiplex)
  • Flow cytometry analysis support

Key Finding: TDB activates NK cells via IL2/IL10 axis; enhanced ADCC in vitro and in vivo

πŸ“„ Read Paper πŸ“Š Data: EGA EGAS00001006914

2023

ERBB signalling contributes to immune evasion in KRAS-driven lung adenocarcinoma

bioRxiv, 2023 (Preprint) | DOI: 10.1101/2023.07.24.550274

Authors: Laing S, Kruspig B, Shaw R, Officer-Jones L, Edwards S, McKinven D, Myrta S, et al.

Bioinformatics Contributions:

  • Bulk RNA-seq (multiple timepoints, Metacore GeneGO)
  • scRNA-seq analysis (10X Genomics, 40,000 cells, 22 clusters)
  • ImmGen databrowser annotation
  • PANTHER overrepresentation analysis
  • WES analysis (COSMIC signatures)

Key Finding: ERBB ligand upregulation (AREG, HBEGF) mediates immune escape; Afatinib restores immune infiltration

πŸ“„ Read Preprint

2021

Transcriptional subtypes resolve tumor heterogeneity and identify vulnerabilities to MEK inhibition in lung adenocarcinoma

Clinical Cancer Research, 2021 | DOI: 10.1158/1078-0432.CCR-20-1835

Authors: Daemen A, Cooper JE, Myrta S, Wongchenko MJ, Lin E, Long JE, Foreman O, Junttila MR, et al.

Bioinformatics Contributions:

  • Consensus NMF subtype discovery (>800 patients)
  • 113-gene PAM classifier development (87-91% accuracy)
  • Multi-cohort integration (TCGA + clinical trials)
  • Gene set enrichment (Camera + MSigDB Hallmark)
  • Drug response modeling (526 compounds, 89 cell lines)
  • Survival analysis (Cox models, Kaplan-Meier)
  • Preclinical validation (175 cell lines, 232 PDX, 108 GEMM)

Key Finding: Identified 3 subtypes (MUC, PRO, MES) with differential MEK inhibitor response; MES benefits most from cobimetinib

πŸ“„ Read Paper πŸ’» Code: GitHub

2020

Transcriptional heterogeneity in lung adenocarcinoma reveals distinct therapeutic vulnerabilities

Cancer Research (AACR Conference Abstract), 2020 | Abstract PO-101

Authors: Daemen A, Cooper JE, Myrta S, Wongchenko MJ, et al.

Note: Preliminary data presentation of LUAD subtyping project (published in Clinical Cancer Research 2021)

πŸ“„ View Abstract

2013

Inhibition of phosphodiesterase-4 promotes oligodendrocyte precursor cell differentiation and enhances CNS remyelination

EMBO Molecular Medicine, 2013 | DOI: 10.1002/emmm.201303123

Authors: Syed YA, Baer A, Hofer MP, GonzΓ‘lez GA, Rundle J, Myrta S, et al.

Bioinformatics Contributions:

  • Microarray analysis (Rat Exon 1.0ST, Affymetrix)
  • RMA normalization, limma differential expression
  • FDR correction (Storey & Tibshirani)
  • qRT-PCR validation analysis
  • Western blot quantification

Key Finding: PDE4 inhibition (rolipram) accelerates OPC differentiation via cAMP-Mapk-Creb1 signaling; therapeutic approach for remyelination

πŸ“„ Read Paper πŸ“Š Data: GEO GSE50042

πŸ“Š Research Metrics

6
Peer-Reviewed Publications

3
Top-Tier Journals
(Impact Factor >10)

>800
Patients Analyzed

5
Public Datasets
(GEO/EGA)

160K
sgRNAs Processed

113
Gene Classifier
(87-91% accuracy)

🎯 Expertise Demonstrated

Technical Skills Validated by Publications

βœ… RNA-seq Analysis
Bulk RNA-seq (HTSeqGenie, limma-voom, edgeR, DESeq2) demonstrated across 6 publications

βœ… Single-Cell RNA-seq
10X Genomics analysis with Seurat-equivalent tools, 22-cluster identification, ImmGen annotation

βœ… CRISPR Screen Analysis
Genome-wide screens with crisprVerse, TMM normalization, limma-voom, hit prioritization

βœ… Machine Learning
Unsupervised (consensus NMF) and supervised (PAM classifier with 87-91% accuracy) methods

βœ… Multi-Omics Integration
Combined RNA-seq, WES, ChIP-seq, clinical data across multiple publications

βœ… Survival Analysis
Cox proportional hazards models, Kaplan-Meier curves, clinical trial data (TCGA, OAK, POPLAR)

βœ… Pathway Enrichment
fgsea, Camera, MSigDB Hallmark/C2/C5/C7, PANTHER, IPA, Metacore GeneGO

βœ… Reproducible Research
Public data deposition (GEO: 3 datasets, EGA: 1 dataset), code sharing (GitHub)

πŸ”¬ Research Impact

Clinical & Biological Insights

πŸ’Š Drug Response Prediction
113-gene classifier for MEK inhibitor response in lung cancer with cross-cohort validation

🎯 Biomarker Discovery
ZFX identified as immunotherapy response biomarker through CRISPR screening

🧬 Mechanism Identification
ERBB signaling pathway as immune evasion mechanism in KRAS-driven tumors

πŸ’‰ Therapeutic Strategy
IL2/IL10 axis targeting for enhanced NK cell activation in bispecific antibody therapy

🧠 CNS Regeneration
PDE4 inhibition as therapeutic approach for myelin regeneration in MS

πŸ“Š Patient Stratification
Three molecular subtypes (MUC, PRO, MES) with distinct clinical outcomes

πŸ“– Complete Publication Record

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For complete citation metrics, co-author networks, and detailed publication history:

ORCID

ORCID: 0000-0003-1714-6105

Includes:

  • Citation counts and h-index
  • Co-author collaboration networks
  • Publication timeline
  • Research contributions
  • Peer review activity

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