Vivek Das, PhD, M.Sc.
København, Region Hovedstaden, Danmark
10 t følgere
500+ forbindelser
Om
Experienced researcher with a demonstrated history of working in both non-profit…
Artikler af Vivek
Aktivitet
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🌟 Celebrating Success in Obesity Research! 🌟 I am incredibly proud to see my former PhD student, Malte Suppli, MD PhD, receiving the Early Career…
🌟 Celebrating Success in Obesity Research! 🌟 I am incredibly proud to see my former PhD student, Malte Suppli, MD PhD, receiving the Early Career…
Vivek Das, PhD, M.Sc. synes godt om dette
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🎉 Milestone moment — MedSAM is now the most cited paper among my 100+ publications! Huge thanks to Jun Ma and our amazing collaborators for making…
🎉 Milestone moment — MedSAM is now the most cited paper among my 100+ publications! Huge thanks to Jun Ma and our amazing collaborators for making…
Vivek Das, PhD, M.Sc. synes godt om dette
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🚀 Excited to share our latest preprint: "Single Cell Foundation Models Evaluation (scFME) for In-Silico Perturbation" Now live on bioRxiv:…
🚀 Excited to share our latest preprint: "Single Cell Foundation Models Evaluation (scFME) for In-Silico Perturbation" Now live on bioRxiv:…
Vivek Das, PhD, M.Sc. synes godt om dette
Erfaring
Uddannelse
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European School of Molecular Medicine
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Topic of thesis: Leveraging transcriptomic analysis to identify transcription factors orchestrating cancer progression
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Experienced in Bioinformatics tools ,databases and Bio programming. Proficient in Bioinfomatics tools and databases as well as developed a Bioinformatics Tool applicable for comparative genomics.
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Aktiviteter og foreninger:Debate, Quiz, Dancing, Sports, Drama
Worked as a trainee in Sridhar Bhatt's Lab and Biochemistry department of Calcutta Medical College learning different techniques of Plant Tissue Culture and Hybridization and Assay Procedures. This helped me take insights into the clinical work where I have worked with patients sample to get results for the assay procedures and also worked in Histopathology as well. It was a welcome experience for me in both PTC techniques in Bhatt Sir's Lab in Bangalore,Karnataka and in the Calcutta Medical…
Worked as a trainee in Sridhar Bhatt's Lab and Biochemistry department of Calcutta Medical College learning different techniques of Plant Tissue Culture and Hybridization and Assay Procedures. This helped me take insights into the clinical work where I have worked with patients sample to get results for the assay procedures and also worked in Histopathology as well. It was a welcome experience for me in both PTC techniques in Bhatt Sir's Lab in Bangalore,Karnataka and in the Calcutta Medical College Biochemistry Department.
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Licenser og certificeringer
Erfaring med frivilligt arbejde
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Secretary
Indian Association of Northern Italy
– 2 år 6 måneder
Kunst og kultur
Udgivelser
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A crosstalk between Mathematics, Computer Science and Biology holds the key to future human health
Se udgivelseCurrent human health in era of modern medicine and drug discovery entails crunching of Big Data that needs careful integration of interdisciplinary knowledge from Biology, Computer Science, Mathematics and Statistics in lieu of bringing new insights in the field of medicine and therapeutics. Thus, the need for efficient computing infrastructure, robust analytical methods, efficient algorithms, and quality software/tools, is increasingly important to make guided interpretations backed by data…
Current human health in era of modern medicine and drug discovery entails crunching of Big Data that needs careful integration of interdisciplinary knowledge from Biology, Computer Science, Mathematics and Statistics in lieu of bringing new insights in the field of medicine and therapeutics. Thus, the need for efficient computing infrastructure, robust analytical methods, efficient algorithms, and quality software/tools, is increasingly important to make guided interpretations backed by data and knowledge. In this presentation, Dr. Vivek Das intends to present cross-talks of such interdisciplinary fields, current state and indicates where to focus future attention to make knowledgeable and data-driven discoveries in modern medicine.
These slides are from the current talk I gave at A.K. Chowdhury School of IT, University of Calcutta. Sharing for the larger community if one finds it useful.
It is a part of an invited talk jointly organized by Association for Computing Machinery (ACM) Kolkata Professional Chapter & A.K. Chowdhury School of IT, University of Calcutta.
Disclaimer: the content of this talk are the author’s personal views and does not represent author’s employer in any capacity. -
State of the field in multi-omics research: From computational needs to data mining and sharing
Frontiers in Genetics
Se udgivelseMulti-omics, variously called integrated omics, pan-omics, and trans-omics, aims to combine two or more omics data sets to aid in data analysis, visualization and interpretation to determine the mechanism of a biological process. Multi-omics efforts have taken center stage in biomedical research leading to the development of new insights into biological events and processes. However, the mushrooming of a myriad of tools, datasets, and approaches tends to inundate the literature and overwhelm…
Multi-omics, variously called integrated omics, pan-omics, and trans-omics, aims to combine two or more omics data sets to aid in data analysis, visualization and interpretation to determine the mechanism of a biological process. Multi-omics efforts have taken center stage in biomedical research leading to the development of new insights into biological events and processes. However, the mushrooming of a myriad of tools, datasets, and approaches tends to inundate the literature and overwhelm researchers new to the field. The aims of this review are to provide an overview of the current state of the field, inform on available reliable resources, discuss the application of statistics and machine/deep learning in multi-omics analyses, discuss findable, accessible, interoperable, reusable (FAIR) research, and point to best practices in benchmarking. Thus, we provide guidance to interested users of the domain by addressing challenges of the underlying biology, giving an overview of the available toolset, addressing common pitfalls, and acknowledging current methods’ limitations. We conclude with practical advice and recommendations on software engineering and reproducibility practices to share a comprehensive awareness with new researchers in multi-omics for end-to-end workflow.
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A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer
Genome Medicine
Se udgivelseThrough an integrated approach, our work demonstrates that both FI and OSE are possible origins for human HGSOC, whose derived subtypes are both molecularly and clinically distinct. These results will help define a new roadmap towards rational, subtype-specific therapeutic inroads and improved patients’ care.
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Mapping Cell Types in Single Cell: A walk through the Past, Present Practices and Future Challenges
Zenodo
Se udgivelseBioTuring Single-cell Webinar slide deck
The webinar was held on August, 28th, 2020.
"Key highlights:
1. The purpose of “Cell Type” and Annotation in single cell omics.
2. The process in place: state-of-the-art methods currently available in the field.
3. The outcome, remaining challenges and future scopes of the Cell Type Annotation."
DISCLAIMER: The content of the webinar is author’s personal views and doesn’t represent NNRCSI in any capacity. -
Learning Biology at a High-Dimensional Scale
YouTube Genewiz channel
Se udgivelseInvited talk as a part of Genewiz 2020 Educational webinars.
Topic:
"High-dimensional data generated via high-throughput technologies has been the current wave of the biomedical research community, having the potential to address complex biomedical issues and open avenues for possible therapies. However, the use of these methods has led to the generation of enormous data sets, presenting a variety of challenges for applied users. Therefore, highlighting the need for efficient computing…Invited talk as a part of Genewiz 2020 Educational webinars.
Topic:
"High-dimensional data generated via high-throughput technologies has been the current wave of the biomedical research community, having the potential to address complex biomedical issues and open avenues for possible therapies. However, the use of these methods has led to the generation of enormous data sets, presenting a variety of challenges for applied users. Therefore, highlighting the need for efficient computing infrastructure, robust analytical methods, efficient algorithms, and quality software/tools that are well bench-marked, is increasingly important to make guided interpretations backed by data science. In this presentation, Vivek Das, M.Sc., Ph.D., presents current avenues from the data science front and indicates where to focus future attention to make knowledgeable, data-driven discoveries.
Disclaimer: The content of this webinar is the author’s personal views and does not represent NNRCSI in any capacity." -
A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high grade serous ovarian cancer
bioRxiv Preprint Server for Biology
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LEVERAGING TRANSCRIPTOMIC ANALYSIS TO IDENTIFY TRANSCRIPTION FACTORS ORCHESTRATING CANCER PROGRESSION - Milano : Università degli studi di Milano. DIPARTIMENTO DI ONCOLOGIA ED EMATO-ONCOLOGIA
Doctoral Thesis , Università degli Studi di Milano
Se udgivelseNext generation sequencing (NGS) technology is currently employed to explore the molecular profiles associated to different biological contexts. The application of this technology provides at same time a high-resolution and global view of the genome and epigenome phenomena, enabling us to study the molecular events underlying many human diseases, including cancer. Our lab tries to exploit the utility of high throughput sequencing technologies generating genomic, transcriptomic and epigenomic…
Next generation sequencing (NGS) technology is currently employed to explore the molecular profiles associated to different biological contexts. The application of this technology provides at same time a high-resolution and global view of the genome and epigenome phenomena, enabling us to study the molecular events underlying many human diseases, including cancer. Our lab tries to exploit the utility of high throughput sequencing technologies generating genomic, transcriptomic and epigenomic data from patient's cohort to study the underlying molecular mechanisms that characterize the specific diseases and map the key regulators that can be critical targets for relevant therapeutic measures. I take the advantage of this technology to mainly understand two aggressive cancers: Ovarian Cancer (OC) and Glioblastoma multiforme (GBM). OC is a leading cause of cancer-related death for which no significant therapeutic progress has been made in the last decades. Also, in this case, despite multimodal treatment its prognosis remains extremely poor. This is due to the fact that the molecular mechanisms underlying OC tumorigenesis and progression are still poorly understood (Vaughan et al., 2011). GBM is the most common and aggressive primary brain malignancy with very poor prognosis (Frattini et al., 2013). The median survival rate is of 12-15 months (Singh et al., 2012) with 5-year survival that is less than 5% despite the multimodal treatment which include surgery, radiotherapy and chemotherapy. To this end, I will be integrating various genomic and transcriptomic analysis to define the key regulatory actors that characterize the disease progression paving. This integrated analysis has been devised in form of a computational workflow that gives way for a discovery pipeline for physiopathologically meaningful epigenetic targets that can lead to therapies.
Udmærkelser og priser
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FEBS Travel grant award at ENABLE 2017 symposium for poster presentation.
FEBS
Recipient of Travel grant award for the poster abstract presented at ENABLE 2017 symposium in Barcelona
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AIRC-FIRC Fellowship
AIRC - Associazione Italiana per la Ricerca sul Cancro
Recipient of the 3 year AIRC-FIRC cancer research fellowship to carry independent research in the field of cancer biology.
Sprog
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English
Modersmåls- eller tosprogsfærdighed
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Hindi
Modersmåls- eller tosprogsfærdighed
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Bengali
Modersmåls- eller tosprogsfærdighed
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Italian
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Thrilled to highlight a wonderful club I am in: the Atheroma Club! A club of enthusiastic cardiovascular researchers, pushing the frontiers of…
Thrilled to highlight a wonderful club I am in: the Atheroma Club! A club of enthusiastic cardiovascular researchers, pushing the frontiers of…
Vivek Das, PhD, M.Sc. synes godt om dette
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🧬 Large Perturbation Models: Training AI to predict biological responses across contexts Most virtual cell models learn correlations from…
🧬 Large Perturbation Models: Training AI to predict biological responses across contexts Most virtual cell models learn correlations from…
Vivek Das, PhD, M.Sc. synes godt om dette
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SyzOnc is proud to announce our collaboration with Eli Lilly and Company through their new AI-enabled drug discovery portal, Tune Lab. This…
SyzOnc is proud to announce our collaboration with Eli Lilly and Company through their new AI-enabled drug discovery portal, Tune Lab. This…
Vivek Das, PhD, M.Sc. synes godt om dette