About the project
Cancer drug development is now one of the world’s leading markets. Our research group has been working in the field of bioinformatics in biomedical applications for five years, supported by international research grants and by the National Research Development and Innovation Office (OTKA #124652 and OTKA #129664). Our work is focused on new therapeutic targets, predictive and prognostic factors in cancer, and our results are published several times a year in peer-reviewed (Q1-D1) international journals, making us one of the most prominent research groups in this field. We analyze our results using complex data analysis, data visualisation, Big Data and AI (machine learning) solutions, which further strengthen our position internationally. We are looking for Postdoc researchers, TDK- and PhD students for these tasks.
Research summary, objectives
Methods for early detection of cancer still face multiple limitations. Although a wide repertoire of therapeutic options is now available (chemo-radiotherapy, radiotherapy, immunotherapy and their combinations), the therapeutic response of patients is highly heterogeneous, and in many cases there is no available scientific data about the underlying causes to date. Recently, researchers have found links between many (cancer) diseases and bacteria and other molecules in the body. One of our goals is to investigate in depth the microbial profiles (taxonomy and metabolites) of stool, blood and urine of cancer patients and to elucidate the DNA/RNA and protein patterns of tumour cells circulating in the blood of patients, which is increasingly used in the diagnosis and monitoring of tumour patients due to the proliferation of “liquid biopsy” sampling. We plan to correlate the large amount of data generated with clinical parameters and therapeutic response of lung cancer patients, including their side effect profile and success rate.
The analytical part of the study will be complemented by molecular histology of patient tumour samples, using immunocytochemistry (IHC) and RNAscope© techniques to identify potential biomarkers in situ. The expression pattern of marker molecules will be analysed using qualitative (fluorescent double staining, IHC-RNAscope multiplexing) and quantitative methods (manual and software automated scoring and morphometry) and correlated with clinical parameters of patients, including overall and progression-free survival (OS and PFS).
The resulting data and correlations can help in screening and early diagnosis of the disease, as well as in increasing the effectiveness of the treatment used and reducing its side effects. Our results could contribute to improving the quality of life of cancer patients and may also have an impact on survival. In addition, biomarker studies could provide an opportunity to identify novel drug targets.
For TDK students
Place and time of work
Törökbálint County Hospital occasionally
Department of Anatomy, Histology and Embryology, Semmelweis University 1 day per week
Duties
- Retrieve clinical data of thousands of patients from the IT system, process according to research criteria and literature. Queries, database construction and management
- Processing large amounts of clinical and biomarker data, statistical calculations
- Search for correlations in the data set; organise and synthesise data
- Data visualisation
- Routine histology techniques on human and mouse tissue: organ isolation, fixation, embedding, sectionong, immunostaining. Microscopic image analysis
- Software-assisted image analysis, morphometry, development and use of scoring techniques for quantitative analysis of immunostainings
Team
- The team will consist of 7 members, expected to include two Postdocs, two PhD students, two TDK students and one laboratory assistant. The team members will communicate and coordinate with each other and with the doctors and nurses of the County Hospital in Törökbálint. The tasks will be mainly carried out by the two research leaders, and the results will be presented and reported to them
- Meetings 1×45 minutes per week online. Once a month, probably in person for a longer period
Requirements
- Ongoing undergraduate studies: 3 years in medicine, BSc degree elsewhere, or last semester of BSc (medical doctor, biologist, bioinformatician, computer engineer, health engineer, molecular bionics, programmer mathematician, bioengineer)
- Fluency in written and spoken English (detailed elaboration and interpretation of results in English)
- Basic knowledge of database use and management
- High level of independence, proactivity, professional curiosity
Advantages - Basic knowledge of SQL and at least one scripting language (R or Python)
- Experience in genomics/transcriptomics/proteomics data analysis
- Basic experience in routine histology techniques (sectioning, routine histology staining)
- Experience in immunohistochemistry and microscopy
- Experience in software image analysis, measurement and editing (ImageJ, Adobe Photoshop/Illustrator)
- Experience in genomics/transcriptomics/proteomics data analysis
Compensation
- Possibility to enrol in a PhD course in the future
- Authorship in peer-reviewed scientific publications (D1-Q1)
- Mastery of tissue and RNA/Protein in situ detection techniques (IHC, RNAscope, Multiplexing)
- Possibility to master high level data analysis and visualisation techniques
- Opportunity to gain insight into the development of biomedical and drug discovery centres at international level
For PhD students
Place and time of work
Törökbálint County Hospital 20 hours per week
Department of Anatomy, Histology and Embryology, Semmelweis University occasionally
Duties
- Retrieve clinical data of thousands of patients from the IT system, process according to
research criteria and literature. Queries, database construction and management - Processing large amounts of clinical and biomarker data, statistical calculations
- Search for correlations in the data set; organise and synthesise data
- Data visualisation
- Routine histology techniques on human and mouse tissue: organ isolation, fixation,
embedding, sectionong, immunostaining. Microscopic image analysis - Software-assisted image analysis, morphometry, development and use of scoring techniques
for quantitative analysis of immunostainings - Recommendation on what to measure and what can be extracted from the data
- Participation in writing proposals, scientific publications with leading researchers
Team
- The team will consist of 7 people, which is expected to include two Postdocs, two PhD students, two TDK students and one laboratory assistant. The team members will communicate and coordinate with each other and with the doctors and nurses of the Törökbálint County Hospital. The tasks will be mainly assigned by the two principal investigators, and the results will be presented and reported to them
- Meetings 1×45 minutes per week online. Once a month, probably in person for a longer period
Requirements
- MSc degree in the field (medical doctor, biologist, bioinformatician, computer engineer, health
care engineer, molecular bionics, programmer mathematician, bioengineer) - Fluency in written and spoken English (detailed elaboration and interpretation of results in English)
- Basic knowledge of database use and management
- Knowledge of mathematical and statistical tools and methodologies
- High level of independence, proactivity, professional curiosity
Advantages
- Experience in metagenomic (microbial) data analysis (DNA, RNA, proteins, chemical compounds from existing databases) (MetaPhlan, Humann, Megan)
- Experience in genomics/transcriptomics/proteomics data analysis
- SQL and at least a basic knowledge of a scripting language (R or Python)
- Data visualisation experience
- Basic experience in routine histology techniques (sectioning, routine histology staining)
- Experience in immunohistochemistry and microscopy
- Experience in software image analysis, measurement and editing (ImageJ, Adobe Photoshop/Illustrator)
Compensation
- Scholarship for PhD position and opportunity to obtain a PhD degree
- Possibility to receive a salary supplement after half a year of work with a PhD fellowship
- Authorship in peer-reviewed scientific publications (D1-Q1)
- Mastery of tissue and RNA/Protein in situ detection techniques (IHC, RNAscope, Multiplexing)
- Possibility to master high level data analysis and visualisation techniques
- Free choice of training courses, participation in international conferences
- Opportunity to gain insight into the development of biomedical and drug discovery centres at international level
For Postdocs
Place and time of work
Törökbálint County Hospital 40 hours a week (full time job)
Department of Anatomy, Histology and Embryology, Semmelweis University occasionally
Duties
- Retrieve clinical data of thousands of patients from the IT system, process according to research criteria and literature. Queries, database construction and management
- Finding correlations and patterns from large amount of data using data mining approaches. Access, retrieve and manage open access clinical and genetic/transcriptomic/proteomic databases (TCGA, Oncomine, NCBI, etc…)
- Processing large amounts of clinical and biomarker data, statistical calculations
- Search for correlations in the data set; organise and synthesise data
- Data visualisation
- Communicating and coordinating with departmental physicians, nurses and supervising PhD students and assistant in collecting, storing and processing patient samples
- Algorithm development and performance testing, proof of concept, weekly update
- Software image analysis, morphometry, development and use of scoring techniques for quantitative analysis of immunostaining
- Recommendation on what to measure and what can be extracted from the data
- Participation in writing proposals, scientific publications with leading researchers
Team
- The team will consist of 7 members, expected to include two Postdocs, two PhD students, two TDK students and one laboratory assistant. The team members will communicate and coordinate with each other and with the doctors and nurses of the County Hospital in Törökbálint. The tasks will be mainly carried out by the two research leaders, and the results will be presented and reported to them
- Meetings 2×45 minutes per week online. Once a month, probably in person for a longer period
Requirements
- MSc and PhD degrees in the field (medical doctor, biologist, bioinformatician, computer engineer, medical engineer, molecular bionics, programmer mathematician, bioengineer) or last year of PhD studies (thesis in preparation)
- Fluency in written and spoken English (detailed elaboration and interpretation of results in English)
- Experience in genomics/transcriptomics/proteomics data analysis
- Advanced knowledge of SQL and at least one scripting language (R or Python)
- Data visualisation experience
- Knowledge of mathematical, statistical tools, algorithms and data mining tools and methodologies
- High level of independence, proactivity, professional curiosity
Advantages - Experience in metagenomic (microbial) data analysis (DNA, RNA, proteins, chemical compounds from existing databases) (MetaPhlan, Humann, Megan)
- Experience in software image analysis, measurements and editing (ImageJ, Adobe Photoshop/Illustrator)
- Access, retrieval and management of open access clinical and genetic/transcriptomic/proteomic databases (TCGA, Oncomine, NCBI, etc…
Compensation
- Competitive salary by agreement
- Authorship in peer-reviewed scientific publications (D1-Q1)
- Free choice of training courses, participation in international conferences
- Opportunity to gain insight into the development of biomedical and drug discovery centres at international level
- Opportunities for professional development which could pave the way for the candidate’s future scientific career as a leading researcher
References:
https://scholar.google.com/citations?user=d2Kh52oAAAAJ&hl=en
https://scholar.google.com/citations?hl=en&user=CbC9oxIAAAAJ
Contact:
Dr. Lohinai Zoltán PhD,
Pulmonology, oncology specialist, principal investigator zoltan.lohinai@koranyi.hu; +36 30 437 8992
Dr. Dóra Dávid PhD,
assistant professor, principal investigator
dora.david@med.semmelweis-univ.hu +36 30 375 0652