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List of works by Zlatko Trajanoski

A new platform linking chromosomal and sequence information

scientific article published on 10 May 2007

A quantization method based on threshold optimization for microarray short time series

scientific article published in December 2005

A survey of tools for variant analysis of next-generation genome sequencing data

scientific article

Activin a plays a critical role in proliferation and differentiation of human adipose progenitors

scientific article

Addressing current challenges and future directions in immuno-oncology: expert perspectives from the 2017 NIBIT Foundation Think Tank, Siena, Italy

scientific article published on 18 December 2018

Adipose triglyceride lipase and hormone-sensitive lipase are involved in fat loss in JunB-deficient mice

scientific article

Adoptive T Cell Therapy: New Avenues Leading to Safe Targets and Powerful Allies

scientific article published on 09 October 2018

Analysis of DNA microarray data

scientific article

Arsenic trioxide induces apoptosis preferentially in B-CLL cells of patients with unfavourable prognostic factors including del17p13.

scientific article

Arxes: retrotransposed genes required for adipogenesis

scientific journal article

Bioinformatics for cancer immunology and immunotherapy

scientific article

Biomolecular Network Reconstruction Identifies T-Cell Homing Factors Associated With Survival in Colorectal Cancer

article by Bernhard Mlecnik et al published April 2010 in Gastroenterology

CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis

scientific article

Cardiopulmonary recovery after COVID-19 - an observational prospective multi-center trial

scientific article published on 10 December 2020

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy.

scientific article

Client-server environment for high-performance gene expression data analysis.

scientific article

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

scientific article

ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

scientific article published on 29 January 2004

Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories.

scientific article

Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis

scientific article

Computational genomics tools for dissecting tumour-immune cell interactions

scientific article

Cooperativity of stress-responsive transcription factors in core hypoxia-inducible factor binding regions

scientific article

Coordination of intratumoral immune reaction and human colorectal cancer recurrence

scientific article published on 3 March 2009

Correction to: Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

scientific article published on 29 July 2019

Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction

scientific article

Differential transcriptional modulation of biological processes in adipocyte triglyceride lipase and hormone-sensitive lipase-deficient mice

scientific article

Effector memory T cells, early metastasis, and survival in colorectal cancer

scientific article

Evolution of genomic instability in diethylnitrosamine-induced hepatocarcinogenesis in mice.

scientific article

GOLD.db: genomics of lipid-associated disorders database

scientific article

Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation

scientific article

Generic features of tertiary chromatin structure as detected in natural chromosomes

scientific article published in November 2004

GiSAO.db: a database for ageing research

scientific article

High STAT1 mRNA levels but not its tyrosine phosphorylation are associated with macrophage infiltration and bad prognosis in breast cancer

scientific article

Histopathologic-based prognostic factors of colorectal cancers are associated with the state of the local immune reaction

scientific article published on 18 January 2011

Hypochlorite modification of sphingomyelin generates chlorinated lipid species that induce apoptosis and proteome alterations in dopaminergic PC12 neurons in vitro.

scientific article

IDO1+ Paneth cells promote immune escape of colorectal cancer

scientific article published on 22 May 2020

Identification of differential and functionally active miRNAs in both anaplastic lymphoma kinase (ALK)+ and ALK- anaplastic large-cell lymphoma

scientific article

Identification of evolutionarily conserved genetic regulators of cellular aging

scientific article

Identification of microRNA-mRNA functional interactions in UVB-induced senescence of human diploid fibroblasts

scientific article

In situ cytotoxic and memory T cells predict outcome in patients with early-stage colorectal cancer

scientific article published on 26 October 2009

Information technology solutions for integration of biomolecular and clinical data in the identification of new cancer biomarkers and targets for therapy

scientific article

Integrating Biomolecular and Clinical Data for Cancer Research: Concepts and Challenges

Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability

scientific article

Intratumoral HPV16-specific T-cells constitute a type 1 oriented tumor microenvironment to improve survival in HPV16-driven oropharyngeal cancer

scientific article published on 10 October 2017

Java editor for biological pathways

scientific article

MARS: microarray analysis, retrieval, and storage system

scientific article

MASPECTRAS 2: An integration and analysis platform for proteomic data.

scientific article

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data

scientific article

MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data

scientific article

MEMOSys: Bioinformatics platform for genome-scale metabolic models

scientific article

Mathematical models for translational and clinical oncology

scientific article

Mitochondrial DNA drives abscopal responses to radiation that are inhibited by autophagy

scientific article published on 03 August 2020

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

scientific article published on 24 May 2019

Molecular processes during fat cell development revealed by gene expression profiling and functional annotation

scientific article

Mutations in ROGDI Cause Kohlschütter-Tönz Syndrome

scientific article

NeoFuse: predicting fusion neoantigens from RNA sequencing data

scientific article published on 01 April 2020

Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy

scientific article published on 28 November 2017

Next-generation computational tools for interrogating cancer immunity

scientific article published on 12 September 2019

Novel insights into adipogenesis from omics data

scientific article

Nr4a1 is required for fasting-induced down-regulation of Pparγ2 in white adipose tissue

scientific article

Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1/PD-1 cancer immune checkpoint blockade.

scientific article published on 18 April 2018

Organization of chromatin and histone modifications at a transcription site.

scientific article

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.

scientific article published in January 2017

PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways

scientific article

Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages

scientific article

QPCR: Application for real-time PCR data management and analysis

scientific article

Quantifying tumor-infiltrating immune cells from transcriptomics data

scientific article published on 14 March 2018

Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ.

scientific article published on 15 June 2010

SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data

scientific article

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases

scientific article

Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data

scientific article published on 14 April 2020

Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data

scientific article published on 02 July 2020

Serum Autoantibodies in Chronic Prostate Inflammation in Prostate Cancer Patients

scientific article published on 10 February 2016

Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer.

scientific article

TAMEE: data management and analysis for tissue microarrays

scientific article

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy

scientific article

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution.

scientific article published on 2 January 2018

Transcription factories

scientific article

Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation

scientific article

Tumour-infiltrating lymphocytes (TILs) and BRCA-like status in stage III breast cancer patients randomised to adjuvant intensified platinum-based chemotherapy versus conventional chemotherapy

scientific article published on 16 January 2020

Type, density, and location of immune cells within human colorectal tumors predict clinical outcome

scientific article

YPL.db2: the Yeast Protein Localization database, version 2.0.

scientific article published in February 2005

YPL.db: the Yeast Protein Localization database

scientific article

iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

scientific article

meRanTK: methylated RNA analysis ToolKit.

scientific article published on 4 November 2015

miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human aging

scientific article

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