{"id":14924,"date":"2022-11-28T10:34:28","date_gmt":"2022-11-28T09:34:28","guid":{"rendered":"https:\/\/semmelweis.hu\/phd\/?p=14924"},"modified":"2022-11-28T10:45:05","modified_gmt":"2022-11-28T09:45:05","slug":"data-analyst-phd-student-position-translational-lung-cancer-research","status":"publish","type":"post","link":"https:\/\/semmelweis.hu\/phd\/en\/2022\/11\/28\/data-analyst-phd-student-position-translational-lung-cancer-research\/","title":{"rendered":"Data Analyst PhD student position Translational Lung Cancer Research"},"content":{"rendered":"<p><strong>About the project<\/strong><br \/>\nCancer drug development is now one of the world&#8217;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.<\/p>\n<p>\n<strong>Research summary, objectives<\/strong><br \/>\nMethods 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 &#8222;liquid biopsy&#8221; 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.<\/p>\n<p>The analytical part of the study will be complemented by molecular histology of patient tumour samples, using immunocytochemistry (IHC) and RNAscope\u00a9 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).<\/p>\n<p>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.<\/p>\n<p style=\"text-align: center\"><strong>For TDK students<\/strong><\/p>\n<p>\n<strong>Place and time of work<\/strong><br \/>\nT\u00f6r\u00f6kb\u00e1lint County Hospital occasionally<br \/>\nDepartment of Anatomy, Histology and Embryology, Semmelweis University 1 day per week<\/p>\n<p><strong>Duties<\/strong><\/p>\n<ul>\n<li>\u00a0Retrieve clinical data of thousands of patients from the IT system, process according to research criteria and literature. Queries, database construction and management<\/li>\n<li>\u00a0Processing large amounts of clinical and biomarker data, statistical calculations<\/li>\n<li>\u00a0Search for correlations in the data set; organise and synthesise data<\/li>\n<li>\u00a0Data visualisation<\/li>\n<li>\u00a0Routine histology techniques on human and mouse tissue: organ isolation, fixation, embedding, sectionong, immunostaining. Microscopic image analysis<\/li>\n<li>\u00a0Software-assisted image analysis, morphometry, development and use of scoring techniques for quantitative analysis of immunostainings<\/li>\n<\/ul>\n<p>\n<strong>Team<\/strong><\/p>\n<ul>\n<li>\u00a0The 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 T\u00f6r\u00f6kb\u00e1lint. The tasks will be mainly carried out by the two research leaders, and the results will be presented and reported to them<\/li>\n<li>\u00a0Meetings 1\u00d745 minutes per week online. Once a month, probably in person for a longer period<\/li>\n<\/ul>\n<p>\n<strong>Requirements<\/strong><\/p>\n<ul>\n<li>\u00a0Ongoing 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)<\/li>\n<li>\u00a0Fluency in written and spoken English (detailed elaboration and interpretation of results in English)<\/li>\n<li>\u00a0Basic knowledge of database use and management<\/li>\n<li>\u00a0High level of independence, proactivity, professional curiosity<br \/>\nAdvantages<\/li>\n<li>\u00a0Basic knowledge of SQL and at least one scripting language (R or Python)<\/li>\n<li>\u00a0Experience in genomics\/transcriptomics\/proteomics data analysis<\/li>\n<li>\u00a0Basic experience in routine histology techniques (sectioning, routine histology staining)<\/li>\n<li>\u00a0Experience in immunohistochemistry and microscopy<\/li>\n<li>\u00a0Experience in software image analysis, measurement and editing (ImageJ, Adobe Photoshop\/Illustrator)<\/li>\n<li>\u00a0Experience in genomics\/transcriptomics\/proteomics data analysis<\/li>\n<\/ul>\n<p>\n<strong>Compensation<\/strong><\/p>\n<ul>\n<li>\u00a0Possibility to enrol in a PhD course in the future<\/li>\n<li>\u00a0Authorship in peer-reviewed scientific publications (D1-Q1)<\/li>\n<li>\u00a0Mastery of tissue and RNA\/Protein in situ detection techniques (IHC, RNAscope, Multiplexing)<\/li>\n<li>\u00a0Possibility to master high level data analysis and visualisation techniques<\/li>\n<li>\u00a0Opportunity to gain insight into the development of biomedical and drug discovery centres at international level<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p style=\"text-align: center\">\n<strong>For PhD students<\/strong><\/p>\n<p>\n<strong>Place and time of work<\/strong><br \/>\nT\u00f6r\u00f6kb\u00e1lint County Hospital 20 hours per week<br \/>\nDepartment of Anatomy, Histology and Embryology, Semmelweis University occasionally<\/p>\n<p>\n<strong>Duties<\/strong><\/p>\n<ul>\n<li>\u00a0Retrieve clinical data of thousands of patients from the IT system, process according to<br \/>\nresearch criteria and literature. Queries, database construction and management<\/li>\n<li>\u00a0Processing large amounts of clinical and biomarker data, statistical calculations<\/li>\n<li>\u00a0Search for correlations in the data set; organise and synthesise data<\/li>\n<li>\u00a0Data visualisation<\/li>\n<li>\u00a0Routine histology techniques on human and mouse tissue: organ isolation, fixation,<br \/>\nembedding, sectionong, immunostaining. Microscopic image analysis<\/li>\n<li>\u00a0Software-assisted image analysis, morphometry, development and use of scoring techniques<br \/>\nfor quantitative analysis of immunostainings<\/li>\n<li>\u00a0Recommendation on what to measure and what can be extracted from the data<\/li>\n<li>\u00a0Participation in writing proposals, scientific publications with leading researchers<\/li>\n<\/ul>\n<p><strong>Team<\/strong><\/p>\n<ul>\n<li>\u00a0The 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 T\u00f6r\u00f6kb\u00e1lint County Hospital. The tasks will be mainly assigned by the two principal investigators, and the results will be presented and reported to them<\/li>\n<li>\u00a0Meetings 1\u00d745 minutes per week online. Once a month, probably in person for a longer period<\/li>\n<\/ul>\n<p><strong>Requirements<\/strong><\/p>\n<ul>\n<li>\u00a0MSc degree in the field (medical doctor, biologist, bioinformatician, computer engineer, health<br \/>\ncare engineer, molecular bionics, programmer mathematician, bioengineer)<\/li>\n<li>\u00a0Fluency in written and spoken English (detailed elaboration and interpretation of results in English)<\/li>\n<li>\u00a0Basic knowledge of database use and management<\/li>\n<li>\u00a0Knowledge of mathematical and statistical tools and methodologies<\/li>\n<li>\u00a0High level of independence, proactivity, professional curiosity<\/li>\n<\/ul>\n<p>\n<strong>Advantages<\/strong><\/p>\n<ul>\n<li>\u00a0Experience in metagenomic (microbial) data analysis (DNA, RNA, proteins, chemical compounds from existing databases) (MetaPhlan, Humann, Megan)<\/li>\n<li>\u00a0Experience in genomics\/transcriptomics\/proteomics data analysis<\/li>\n<li>\u00a0SQL and at least a basic knowledge of a scripting language (R or Python)<\/li>\n<li>\u00a0Data visualisation experience<\/li>\n<li>\u00a0Basic experience in routine histology techniques (sectioning, routine histology staining)<\/li>\n<li>\u00a0Experience in immunohistochemistry and microscopy<\/li>\n<li>\u00a0Experience in software image analysis, measurement and editing (ImageJ, Adobe Photoshop\/Illustrator)<\/li>\n<\/ul>\n<p>\n<strong>Compensation<\/strong><\/p>\n<ul>\n<li>\u00a0Scholarship for PhD position and opportunity to obtain a PhD degree<\/li>\n<li>\u00a0Possibility to receive a salary supplement after half a year of work with a PhD fellowship<\/li>\n<li>\u00a0Authorship in peer-reviewed scientific publications (D1-Q1)<\/li>\n<li>\u00a0Mastery of tissue and RNA\/Protein in situ detection techniques (IHC, RNAscope, Multiplexing)<\/li>\n<li>\u00a0Possibility to master high level data analysis and visualisation techniques<\/li>\n<li>\u00a0Free choice of training courses, participation in international conferences<\/li>\n<li>\u00a0Opportunity to gain insight into the development of biomedical and drug discovery centres at international level<\/li>\n<\/ul>\n<p style=\"text-align: center\">\n<strong>For Postdocs<\/strong><\/p>\n<p>\n<strong>Place and time of work<\/strong><br \/>\nT\u00f6r\u00f6kb\u00e1lint County Hospital 40 hours a week (full time job)<br \/>\nDepartment of Anatomy, Histology and Embryology, Semmelweis University occasionally<\/p>\n<p>\n<strong>Duties<\/strong><\/p>\n<ul>\n<li>\u00a0Retrieve clinical data of thousands of patients from the IT system, process according to research criteria and literature. Queries, database construction and management<\/li>\n<li>\u00a0Finding 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&#8230;)<\/li>\n<li>\u00a0Processing large amounts of clinical and biomarker data, statistical calculations<\/li>\n<li>\u00a0Search for correlations in the data set; organise and synthesise data<\/li>\n<li>\u00a0Data visualisation<\/li>\n<li>\u00a0Communicating and coordinating with departmental physicians, nurses and supervising PhD students and assistant in collecting, storing and processing patient samples<\/li>\n<li>Algorithm development and performance testing, proof of concept, weekly update<\/li>\n<li>Software image analysis, morphometry, development and use of scoring techniques for quantitative analysis of immunostaining<\/li>\n<li>\u00a0Recommendation on what to measure and what can be extracted from the data<\/li>\n<li>\u00a0Participation in writing proposals, scientific publications with leading researchers<\/li>\n<\/ul>\n<p>\n<strong>Team<\/strong><\/p>\n<ul>\n<li>\u00a0The 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 T\u00f6r\u00f6kb\u00e1lint. The tasks will be mainly carried out by the two research leaders, and the results will be presented and reported to them<\/li>\n<li>\u00a0Meetings 2\u00d745 minutes per week online. Once a month, probably in person for a longer period<\/li>\n<\/ul>\n<p>\n<strong>Requirements<\/strong><\/p>\n<ul>\n<li>\u00a0MSc 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)<\/li>\n<li>\u00a0Fluency in written and spoken English (detailed elaboration and interpretation of results in English)<\/li>\n<li>\u00a0Experience in genomics\/transcriptomics\/proteomics data analysis<\/li>\n<li>\u00a0Advanced knowledge of SQL and at least one scripting language (R or Python)<\/li>\n<li>\u00a0Data visualisation experience<\/li>\n<li>\u00a0Knowledge of mathematical, statistical tools, algorithms and data mining tools and methodologies<\/li>\n<li>\u00a0High level of independence, proactivity, professional curiosity<br \/>\nAdvantages<\/li>\n<li>\u00a0Experience in metagenomic (microbial) data analysis (DNA, RNA, proteins, chemical compounds from existing databases) (MetaPhlan, Humann, Megan)<\/li>\n<li>\u00a0Experience in software image analysis, measurements and editing (ImageJ, Adobe Photoshop\/Illustrator)<\/li>\n<li>\u00a0Access, retrieval and management of open access clinical and genetic\/transcriptomic\/proteomic databases (TCGA, Oncomine, NCBI, etc&#8230;<\/li>\n<\/ul>\n<p><strong>Compensation<\/strong><\/p>\n<ul>\n<li>\u00a0Competitive salary by agreement<\/li>\n<li>\u00a0Authorship in peer-reviewed scientific publications (D1-Q1)<\/li>\n<li>\u00a0Free choice of training courses, participation in international conferences<\/li>\n<li>\u00a0Opportunity to gain insight into the development of biomedical and drug discovery centres at international level<\/li>\n<li>\u00a0Opportunities for professional development which could pave the way for the candidate&#8217;s future scientific career as a leading researcher<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p>\n<strong>References:<\/strong><br \/>\n<a href=\"https:\/\/scholar.google.com\/citations?user=d2Kh52oAAAAJ&amp;hl=en\">https:\/\/scholar.google.com\/citations?user=d2Kh52oAAAAJ&amp;hl=en<\/a><br \/>\n<a href=\"https:\/\/scholar.google.com\/citations?hl=en&amp;user=CbC9oxIAAAAJ\">https:\/\/scholar.google.com\/citations?hl=en&amp;user=CbC9oxIAAAAJ<\/a><\/p>\n<p><strong>Contact: <\/strong><\/p>\n<p><strong>Dr. Lohinai Zolt\u00e1n PhD,<\/strong> <br \/>\nPulmonology, oncology specialist, principal investigator <a href=\"mailto:zoltan.lohinai@koranyi.hu\">zoltan.lohinai@koranyi.hu<\/a>; +36 30 437 8992<\/p>\n<p><strong>Dr. D\u00f3ra D\u00e1vid PhD,<\/strong> <br \/>\nassistant professor, principal investigator <br \/>\n<a href=\"mailto:dora.david@med.semmelweis-univ.hu\">dora.david@med.semmelweis-univ.hu<\/a> +36 30 375 0652<\/p>\n","protected":false},"excerpt":{"rendered":"<p>About the project Cancer drug development is now one of the world&#8217;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 &hellip;<\/p>\n","protected":false},"author":101719,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[27],"tags":[],"class_list":["post-14924","post","type-post","status-publish","format-standard","hentry","category-jobs"],"acf":[],"_links":{"self":[{"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/posts\/14924","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/users\/101719"}],"replies":[{"embeddable":true,"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/comments?post=14924"}],"version-history":[{"count":3,"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/posts\/14924\/revisions"}],"predecessor-version":[{"id":14931,"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/posts\/14924\/revisions\/14931"}],"wp:attachment":[{"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/media?parent=14924"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/categories?post=14924"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/semmelweis.hu\/phd\/wp-json\/wp\/v2\/tags?post=14924"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}