Predictive Computational Engineering (PCE) Workshop

16 August 2024 | University of Buffalo

Hosted by: Dr. Danial Faghihi and Pratyush Singh, PhD

In this workshop, I learnt about and engaged with hands-on exercises in research area of computational prediction for solving modern engineering problems. Application range of patient-specific cancer treatment to the design of buildings’ superinsulation were discussed.

• Highlights:
  Acquired knowledge on developing computational models that predict the progression of brain cancer, emphasizing patient-specific data to tailor treatment strategies, including the simulation of tumor growth and response to therapies.

• Explored the application of predictive computational tools in modeling complex biological systems, with a particular focus on understanding the molecular and cellular dynamics involved in brain cancer progression.

• Learned about the integration of multi-scale computational models with biological data to enhance the accuracy of predictions in brain cancer treatment, facilitating personalized medicine approaches.

• Engaged in hands-on exercises focused on optimizing therapeutic interventions for brain cancer using computational simulations, aiming to improve treatment efficacy and minimize adverse effects.

• Gained proficiency in computational biology techniques that support the identification of biomarkers and therapeutic targets in brain cancer, advancing the potential for precision oncology.

• Discussed the broader implications of predictive computational engineering in biomedicine, particularly how these techniques can be leveraged to address challenges in brain cancer diagnosis, prognosis, and treatment planning.

Science Dialogue Series: Webinar on 'Target of Rapamycin Signalling: A Key Signalling Pathway for Starch Accumulation in Red Algae'

10 August 2024 | American Society for Microbiology

Speaker: Dr. Imran Pancha | Moderator: Dr Gopal Jee

Learning Outcomes:

• Gained insights into the fundamental role of the Target of Rapamycin (TOR) signaling pathway in regulating cellular growth and metabolism, particularly in the context of nutrient availability and energy status in red algae.

• Explored the mechanisms by which TOR signaling influences starch accumulation in red algae, highlighting the pathway’s impact on metabolic processes that govern carbohydrate biosynthesis.

• Learned about the regulatory functions of TOR in algal metabolism, including how it modulates various biosynthetic pathways and impacts the overall energy balance within the cell.

• Discussed potential biotechnological applications of manipulating TOR signalling in red algae for enhanced starch production, which could have implications for biofuel production and other industrial processes.

• Analyzed how TOR signaling in red algae compares with its function in other organisms, such as plants and animals, providing a broader understanding of its evolutionary conservation and divergence.

• Examined the influence of environmental factors, such as light, temperature, and nutrient availability, on TOR signaling and its downstream effects on starch accumulation in red algae.

• Identified key areas for future research, including the exploration of TOR pathway components in red algae and their potential as targets for genetic and metabolic engineering to optimize starch production.

ASM-MicroGen One-Week Bioinformatics Workshop 

August 19 - August 22, 2024 | American Society for Microbiology

Instructor: Mr Mohammed Alfaki

MircroGen, the initiative behind organising the program, was established by the ASM's Young Ambassador to Sudan, Sara Albagir Abdalla.

This workshop covered key bioinformatics topics for microbiology, including genome sequencing, transcriptomics, proteomics, pathogen detection, and epidemiology. Through this workshop, I explored WGS for microbial identification, RNA-Seq for gene expression analysis, protein identification & interaction networks, and rapid pathogen detection. This initiative also addressed antibiotic resistance, drug discovery, and structural bioinformatics, including protein structure prediction and molecular docking. Additional sessions were based on functional genomics, microbial community analysis, phylogenetics, and data integration in systems biology models.

During the hands-on sessions, we also practiced the analysis of the hypothetical proteins from the first step to the manuscript writing as an application for bioinformatics research in microbiology.

Diabetes Virtual Camp Research Intern 2024

July to August 2024 | American Diabetes Association | 15 sessions

Selected as one of 160 undergraduates worldwide to participate in the Diabetes Virtual Summer Camp 2024, a collaborative initiative between leading academic institutions and the American Diabetes Association. This intensive two-week program provided an immersive experience into the latest advancements in diabetes research, treatment strategies, and interdisciplinary approaches within the biomedical sciences. 

The sessions are led by 11 Experts, who are renowned diabetes researchers and clinicians from reputable universities and will include a Q&A period at the end of each session.

Key Experiences and Learnings:

1) Comprehensive Understanding of Diabetes Pathophysiology:

• • Engaged in detailed discussions on the etiology and progression of various forms of diabetes, including Type 1 and Type 2, with a strong emphasis on the mechanisms of insulin resistance and beta-cell dysfunction.

  • Explored the 'Thrifty Gene Hypothesis' under the guidance of Dr. Jason Kim, understanding its implications in modern-day metabolic disorders, particularly within the Indian demographic context, and its historical roots tracing back to events like the Bengal Famine of the 1940s.

2) Advancements in Therapeutic Interventions:

• • Studied novel treatment modalities such as the development of Palmitic Acid Hydroxy Stearic Acids (PAHSAs), elucidated by Dr. Barbara Kahn, highlighting their role in activating GPR120 and GPR40 receptors to enhance insulin sensitivity and maintain glucose homeostasis.

  • Gained insights into pancreatic beta-cell regeneration techniques from Dr. Laura Alonso, focusing on strategies to restore endogenous insulin production through stimulating beta-cell proliferation and addressing autoimmunity challenges.

3) Molecular and Genetic Research Techniques:

• • Studied the role of mRNA modifications, particularly the functions of METTL3 and METTL14 methyltransferases, as presented by Dr. Rohit Kulkarni, and their distinct impacts on insulin secretion and beta-cell viability in both Type 1 and Type 2 diabetes contexts.

  • Analyzed the intersection of metabolic stress responses and cellular adaptation mechanisms in diabetic conditions through sessions led by Dr. Alan Saltiel, enhancing my understanding of intracellular signaling pathways and metabolic regulation.

4) Translational and Clinical Research Exposure:

• • Explored the journey from bench to bedside with Dr. Raghu Mirmira, examining the process of drug development from initial zebrafish model screenings to advancing towards human clinical trials, emphasizing the importance of translational research in therapeutic advancements.

  • Reviewed critical findings from prominent clinical trials and observational studies, including TODAY, SEARCH, and RISE, through Dr. Leslie Soyka's session, focusing on the unique challenges and management strategies for Type 2 diabetes in youth.

Interdisciplinary Research and Future Directions:

1) Engaged in discussions on the link between diabetes and oncogenesis, reinforcing my current research pursuits in exploring the metabolic crosstalk between diabetes and cancer progression, particularly in breast cancer studies.

2) Identified potential collaborative research opportunities and future career pathways within biomedical sciences through interactions with experts like Dr. Robert Gabbay and Dr. Maren Laughlin, understanding the role of institutions like the NIH in supporting emerging scientists.

Skills and Competencies Developed:

1) Enhanced proficiency in interpreting complex biomedical research data and integrating multidisciplinary approaches to address health challenges.

2) Improved ability to formulate research hypotheses related to metabolic diseases and design experimental frameworks for investigating disease mechanisms.

3) Strengthened communication skills through active participation in interactive Q&A sessions, fostering collaborative discussions and networking with professionals and peers in the field.

This program has significantly enriched my scientific acumen and provided a robust foundation for my ongoing research into the interrelation between diabetes and cancer metabolism. The knowledge and experience gained will be instrumental in advancing my academic pursuits and contributing to innovative research that aims to develop integrated therapeutic strategies for complex diseases.

Interpreting Genomic Variation: Overcoming Challenges in Diverse Populations

29 July 2024 | Wellcome Connecting Science Learning and Training | 3 weeks (5 hours/week)

Educators: Professor Katta Girisha, Julia Foreman, Zané Lombard, Amanda Krause

The course was designed to empower learners with essential skills, tools and concepts required for genomic variant classification and interpretation, particularly in diverse populations and resource-limited settings. This course provided opportunities for hands-on skill development, applying guidelines for variant classification and interpretation, and analysing real-world challenging case studies.

Week 1: Basic Concepts: Fundamentals of Variant Interpretation, Disease-associated Varients, Predictions and Annotations

Week 2: Advanced Concepts: Impact of Variation on Proteins, Interpreting Genomic Variants, and Variant Investigation in Clinical Practice
Week 3: Applying Concepts to Diverse Populations: Dealing with Uncertainty, Initiatives to Improve Interpretation, and Beyond Variant Interpretation

Syllabus:
1) Use of genome browser tools, such as DECIPHER to classify and interpret genomic variants in their biological and clinical contexts

2) Applying guidelines for variant classification and interpretation and dealing with uncertainty 

3) Real-world case studies illustrating challenges in variant classification and interpretation 

4) Variant classification and interpretation in underserved and diverse populations and resource-limited settings

5) Exploring different types of genetic variation

6) Recognising the role of multidisciplinary teams for variant classification and interpretation

Learning Outcomes:

1) Used tools for genomic variant classification and interpretation in different contexts 

2) Interpreted and applied international guidelines for variant classification and interpretation and dealing with uncertainty

3) Understood how changes in the understanding of biological implications of variants affect their classification and interpretation 

4) Assessed the implications of clinical context in dealing with variants of unknown significance

5) Recognised the challenges in variant classification and interpretation in diverse populations and resource-limited settings

Revolutionising Immunotechnology: Decade of Advancements & Proteomics and Target Discovery for Cancer Immunotherapy

27 July 2024 | OmicsLogic

Speaker: Ankit Halder, Dr. Deeptarup Biswas, Abhilash Barpanda

OmicsLogic is a program that embeds data-driven concepts into biological projects, spanning the student learning journey from observer to participant in research. The webinar started with an introduction to the basics of immunology, covering key topics like innate immunity, antibody functions, and lymphocyte development. Further, the immune system's components, including T-cell and B-cell responses, autoimmune diseases, and allergies were discussed. Transitioning to omics, the webinar focussed on biomarker discovery, drug target identification, and hands-on omics data analysis. The major session was on the synergy between immunology and omics in disease therapy, focusing on immuno-oncology, CAR T therapies, and innovative immunotherapies.

Three topics were discussed in this webinar:

1) Harnessing the Synergy of Immunology and Omics: The Nexus of Innovation by Ankit Halder, Research Scholar, IIT Bombay

2) Role of Proteomics in Biomarker Identification and Therapeutic Advances by Dr. Deeptarup Biswas, Post-Doctoral Researcher, Harvard Medical School

3) Proteomics and Target Discovery for Cancer Immunotherapy by Abhilash Barpanda, PhD, University of California San Francisco (UCSF)

Topics Covered:

• Advancements of Immunotherapy in recent times

• Role of immunotherapies in combating deadly diseases

• Integration of Omics Technologies with immunology

• Role of Proteomics in Biomarker Identification & Therapeutic Advances

• Proteomics & Target Discovery for Cancer Immunotherapy

• Novel therapies like CAR-T Cell, Antibody Engineering

Crash Course: Python Scripting for Molecular Docking

18 July 2024 | Rutgers Institute for Quantitative Biomedicine, Protein Data Bank, MolSSI | 4 hours

Instructors: Paul A. Craig | Jessica A. Nash | Levi Naden

This comprehensive workshop focused on using Python scripting to understand ligand binding to enzymes. Over the course of four hours (10 PM to 2 AM IST), we engaged in extensive script work and utilised various Python libraries to customise notebooks for individual research and teaching purposes.

The following are the four sessions conducted in this live class: 

• Enzyme Commission Class with Ligands

• Manipulating Molecules with RDKit

• Docking Preparation

• Docking with AutoDock Vina.

Upon completion of this workshop, I am now proficient in: 

- Performing advanced searches of the RCSB Protein Data Bank using the rcsbsearchapi package. 

- Modifying chemical structures with the rdkit library. 

- Docking ligands with enzymes to yield visual and quantitative energy results. 

As a biotechnology student with research interests in precision medicine and drug discovery in oncology, this workshop has helped me enhance my computational skills, enabling me to conduct effective molecular docking studies. These skills are critical for understanding molecular interactions, optimizing drug candidates, and advancing personalised medicine approaches.

Summer Scholar: XIX International Summer School-Conference on 'Molecular Biology, Biotechnology, and Biomedicine'

08 July 2024 - 20 July 2024 | Odesa Mechnikov National University, Ukraine

Faculties: Dr. Roberto Kolter, Prof. Zofia Szweykowska, Dr. Olena Rzhepishevska, Dr. Peter C. Kahn, Dr. Oleksandr Zinenko, Dr. Jose Dominguez, Dr. Alona Voronkina, Dr. Olena Moshynets, Dr. Iryna Bohovych and Dr. Kai Blin 

University Info: Odesa I. I. Mechnykov National University, often referred to as Odesa National University, located in Odesa, Ukraine, is one of the country's major universities, named after the scientist Élie Metchnikoff, a Nobel prizewinner in 1908.

Selected as the only Indian for this two-week intensive summer school, this program provided an in-depth exploration of cutting-edge topics in the fields of molecular biology, biotechnology, and biomedicine through a series of lectures and hands-on sessions.

Highlights:

1) Bacterial Evolution: Dr. Roberto Kolter from Harvard Medical School discussed the mode and tempo of bacterial evolution, providing a fascinating perspective on microbial life.

2) Plant Response to Environmental Cues: Prof. Zofia Szweykowska shared her expertise on RNA metabolism in shaping plant responses, focusing on barley and nitrogen excess.

3) Metabolomics and Erasmus+ Program: Dr. Olena Rzhepishevska from Umea University delivered comprehensive lectures on study design, multivariate analysis in metabolomics, and opportunities within the Erasmus+ program.

4) Water Molecule Significance: Dr. Peter C. Kahn from Rutgers University explained the importance of understanding water molecules in biochemical processes.

5) Biomonitoring and Immunological Diagnosis: Dr. Oleksandr Zinenko and Dr. Jose Dominguez presented innovative approaches in biomonitoring and diagnosing non-tuberculous mycobacteria infections.

6) Pharmaceutics and Biomimetics: Dr. Alona Voronkina and Dr. Olena Moshynets discussed how pharmaceutics can benefit from sponges, highlighting the potential of extreme biomimetics.

7) Mitochondrial Homeostasis and Genome Mining: Dr. Iryna Bohovych and Dr. Kai Blin shared their insights into mitochondrial homeostasis and genome mining using advanced biotechnological tools.

Fruther, I atended sessions on advanced topics such as metagenomics, CRISPR-based gene editing strategies, and the production of novel antibodies using phage display technology. This summer school provided an enhanced understanding of microbial and viral communities, molecular mechanisms of plant-fungi interactions, and the engineering of virus-like particles for vaccines and delivery vehicles.

Bioinformatics for Biologists: Analysing and Interpreting Genomics Datasets

15 July 2024 | Wellcome Connecting Science Learning and Training | 3 weeks (6 hours/week)

Educators: Andries van Tonder, Ruth Nanjala, Fatma Guerfali

The course covered Next Generation Sequencing (NGS)  and its significance in genomics, the installation of widely-used bioinformatics tools, the use of different file formats, and Linux commands for sequence quality control, mapping, and variant calling. The analysis was also performed using the workflow management system Nextflow, and applied to viralrecon, an existing bioinformatics pipeline. Downstream analysis included RStudio data visualization of variants obtained from genomic data sample.

Week 1: Introduction to sequence quality control, mapping and variant calling

Week 2: Workflow Management and Analysis
Week 3: Downstream analysis with R

Syllabus:
1) Brief introduction to sequencing technologies and an overview of current sequencing outputs

2) Sequence quality control to ensure data accuracy and reliability

3) Bioinformatics workflows utilising tools such as Nextflow using nf-core pipelines

4) Mapping sequencing data to a reference genome for alignment and variant calling

5) Working with pipeline outputs in R to perform downstream analysis and visualisation

Learning Outcomes:

1) Used software managers to install and run reproducible bioinformatics tools

2) Handled and analysed sequence datasets through hands-on exercises

3) Analysed quality control metrics for sequencing data

4) Modified existing workflows to suit specific task requirements and optimise analysis processes

5) Interrogated and interpreted the results obtained from running bioinformatics pipelines

6) Performed downstream analyses of pipeline outputs using R, enabling data visualisation and further exploration

cBioPortal Introductory Workshop

04 July 2024 | Netherlands X-omics Initiative & Netherlands Cancer Institute

Speakers: Mariska Bierkens, Iris Huitink

cBioPortal is an open-source web platform used for the interactive exploration of multidimensional cancer (gen)omics data sets. The platform provides a user-friendly interface for exploring various types of cancer multi-omics data (such as DNA sequencing, gene expression, protein and phosphoprotein, DNA methylation and clinical data). 

Users can create custom queries to retrieve and visualise data from multiple studies, perform survival analysis, group comparisons, and generate customised reports. The platform is widely used by cancer researchers and has been adopted by many large-scale cancer genomics projects, including The Cancer Genome Atlas (TCGA), the International Cancer Genome Consortium (ICGC) and the American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange (AACR GENIE).

Summary: During the workshop, I was given an overview of the functionality of cBioPortal by exploring public study data and I learned how to navigate the portal and use its features to extract valuable insights from the available data.

Interdisciplinary Training of the NCT Heidelberg - Personalized Therapy for Patients with Head and Neck Tumors

26 June 2024 | National Center for Tumor Diseases (NCT) Heidelberg & Deutsches Krebsforschungszentrum (DKFZ) | German

Speakers: Dr. Julius Moratin, Dr. Gerhard Dyckhoff, Dr. Thomas Held, Dr. Sebastian Dieter

Learning Outcomes:

• Acquired comprehensive knowledge on the principles and practices of personalized therapy tailored for patients with head and neck tumors.

• Gained insights into the interdisciplinary approaches in treating head and neck tumors, including collaboration among oral and maxillofacial surgery, otolaryngology, and medical oncology departments.

• Learned to integrate genomic and molecular data into clinical decision-making processes to optimize treatment plans for individual patients.

• Participated in case-based discussions and analyses, enhancing practical skills in diagnosing and managing complex cases of head and neck tumors.

• Emphasized the importance of evidence-based practice in the development and implementation of personalized therapeutic strategies.

• Understood the integration of multimodal therapies, including surgery, radiotherapy, and chemotherapy, in the comprehensive treatment of head and neck cancers.

• Discussed the regulatory and ethical considerations in personalized cancer therapy, ensuring compliance with medical standards and patient safety.

General Best Practice Guidelines for Immunization (WB4458R)

25 June 2024 | Centers for Disease Control and Prevention | 0.35 CEU

Faculty/Credentials: Lynn Bahta, Andrew Kroge, Sarah S. Long

Learning Outcomes:
After the completion of this course, I am able to:

• Describe the minimum intervals between doses for vaccines routinely used.

• Describe methods for preventing and managing adverse reactions. 

• Describe recommended practices for administration of vaccines.

• Describe proper storage and handling procedures for immunobiologics. 

• Identify evidence-based interventions shown to improve vaccination rates among children. 

• Locate current immunization resources to increase knowledge of team’s role in program implementation for improved team performance. 

• Implement disease detection and prevention health care services (e.g., smoking cessation, weight reduction, diabetes screening, blood pressure screening, immunization services) to prevent health problems and maintain health.

Sustainable Aquaculture for Low Trophic Species

22 June 2024 | UiT The Arctic University of Norway | 6-10 hours/week for 12 weeks

Course Builders: Adrianna Kochanska, Ronan Gombau, Ben Opara, Katrin Hulda Gunnarsdottir, Mark Stenersen

Motivation: 

• Climate change and increased pressures on freshwater and land resources have affected our capacity to produce food for the growing population. As a result, food security has become one of the most pressing challenges we are currently facing. 

• Food coming from marine aquaculture is known to have some of the lowest carbon footprints among animal products. Moreover, producing marine food at a lower trophic level delivers additional environmental benefits through ecosystem services, which are fundamental to creating a sustainable food system.

• This course has been highly beneficial for me in aligning my organisation's vision with SDG goals.

Summary:

• Understood the essential principles and practices of low trophic aquaculture. The course provided a holistic view of the most recent developments in low trophic aquaculture, focusing on selected species groups, including molluscs, echinoderms, macroalgae and freshwater fish. 

• Throughout the course, various topics, including the biology of the four species groups, the design and operation of the cultivation practices, and their environmental impact, were covered. 

• Furthermore, I also analysed the economic and social aspects of aquaculture and the policies and regulations that govern the industry. The interdisciplinary approach has improved my idea of the subject matter and provided me with the knowledge and skills essential to contribute to a sustainable industry.

Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites

19 June 2024 | Association for Molecular Pathology | 1 ASCP CMLE Credit Hours

Speaker: Dr Esther Babady from Memorial Sloan Kettering Cancer Center

Learning Outcomes:

• Reviewed the current benefits and challenges to using multiplex PCR panels for the detection of microbial pathogens from gastrointestinal, central nervous system, lower respiratory tract, and joint specimens.

• Discussed future directions and novel approaches to detect pathogens in alternate specimen types, and outlined challenges associated with the implementation of these multiplex PCR panels.

Workshop | Data Insights: Bridging Nature with Data Science

18 June - 19 June 2024 | Azim Premji University

Instructors: Dr. Achyut Kumar Banerjee, Dr. Tanujit Chakraborty, Dr. Amiya Ranjan Bhowmick, Dr. Abhishek Mukherjee

I recently had the opportunity to attend this two-day workshop titled conducted by Azim Premji University, Bhopal, from June 18 to June 19, 2024. The workshop focused on some of the most pressing environmental problems and assessed the applications of data science in addressing these issues. 

Interdisciplinary research in the natural sciences has made significant strides in recent years, thanks to modern data science methods. However, natural science students and researchers, particularly those with limited technical expertise, still encounter both theoretical and practical obstacles amidst this data revolution.

Highlights of the workshop:

Day 1: Quantitative Methods for Environment and Natural Resources (June 18, 2024)

1. Dr. Achyut Kumar Banerjee from Azim Premji University, Bhopal, provided an introduction to data science and delivered a detailed lecture on artificial intelligence and environmental challenges. 

2. Dr. Tanujit Chakraborty from Sorbonne University, UAE, discussed machine learning (ML) methods to address environmental problems such as the exploitation of natural resources, pollution, and invasive species. The session covered foundations in data science, including regression problems, classification problems, and introductory Bayesian methods. 3. Dr. Amiya Ranjan Bhowmick from the Institute of Chemical Technology, Mumbai, guided a hands-on session based on case studies using R. This session covered the basics of plotting, fitting statistical models for generalized linear and non-linear models, producing maps, and performing spatial analysis in R. 

Day 2: Environment Across Space and Time (June 19, 2024)

1. Introduction to spatial data and geographic information systems was covered by Dr. Achyut Banerjee, discussing the need for data-driven tools and technologies. 

2. Dr. Abhishek Mukherjee from the Indian Statistical Institute, Kolkata, provided a comprehensive understanding of spatial analysis and data processing using 𝐐𝐆𝐈𝐒. The hands-on session covered topics such as vector and raster data, species distribution modeling across space and time, enhancing methodologies for GIS analyses.

Apart from this agenda, there was also a session on MaxEnt, a software application used for modeling species niches and distributions through maximum entropy modeling.

These hands-on activities on the working principles of data science in natural sciences have significantly improved my proficiency in R and QGIS. As an undergraduate in biotechnology, this experience will be invaluable in applying data-driven approaches to biological research and environmental conservation projects.

Webinar: Introduction to Gene Therapy Manufacturing

14 June 2024 | National Institute for Bioprocessing Research and Training, Dublin

Instructor: John Milne

Overview: The webinar covered about the rapidly developing landscape, interest and recent approvals in gene therapy. As recombinant adeno-associated viruses (rAAV’s) are widely used as the viral vector system to deliver therapeutic genes to cells, the webinar focussed on this delivery system. Key to the use of rAAVs is an efficient production and purification system that will produce viral vector in sufficient quantity and of requisite quality for clinical applications. The webinar provided an introduction to the current methods employed in the manufacturing of rAAV’s to address the growing demand for this class of therapy.

The Fundamentals of Cancer Genomics

13 June 2024 | The Royal College of Radiologists | 6 RCR CPD Credits in total

A unique aspect of this course is that the content not only addressed heritable genetic risk factors for cancer but also emphasised the translational application of somatic and/or genomic results in diagnostics and prognostication, as well as in directing treatment.

Learning Outcomes: Upon completion, I can do the following:

Module 1 – Fundamentals of Cancer Genomics

1) Describe how genomic information is stored

2) Outline different types of chromosomal and genetic variants

3) Explain patterns of genomic evolution of cancer

4) Outline basis mutation signature profiling 

5) Define tumour mutation burden 

6) Distinguish between somatic variants and variants of germline-origin

Module 2 – Variant Interpretation

1) Describe consequences of misattribution of pathogenicity to germline genetic variants

2) Differentiate between clinically actionable and non-actionable germline variants

3) Explain the lines of evidence applied for variant classification

4) Correctly interpret variant reports and appraise evidence applied for variant classification

5) Distinguish between low, moderate and highly penetrant variants of germline origin 

6) Classify somatic variants in terms of actionability and define mosaicism

Module 3 – Molecular Phenotyping for Cancer Care– Technologies and Practical Considerations

1) Justify use of different sample types for genetic testing in different clinical scenarios 

2) Outline steps involved in sanger and next generation sequencing

3) Describe uses and limitations of liquid biopsies in cancer care 

4) Differentiate between MMR deficiency, microsatellite instability, hypermutation and PDL1 expression

5) Describe the relevance of MMR deficiency, microsatellite instability, hypermutation and PDL1 expression in immunotherapy response

Module 4 – NHS England Genomic medicine service and National Genomic Test Directory

1) Describe reconfiguration of NHS lab services

2) Navigate the NHS genomic directory

Polygenic Scores for Cancer Prevention

12 June 2024 | International Agency for Research on Cancer (IARC)

Speaker: Dr Nilanjan Chatterjee, Johns Hopkins University | Dr Linda Kachuri, Stanford University School of Medicine

Summary:

1) Polygenic Scores for Stratified Cancer Prevention

• Genome-wide association studies of increasing sample size and diverse ancestry are now leading to polygenic scores with significant potential for risk stratification across cancers. 

• This presentation provided a brief overview of emerging opportunities and discuss some limitations of the use of polygenic scores for developing risk-stratified approaches to cancer prevention. 

• Dr Chatterjee described results from a recent study on the validation of a breast cancer risk prediction model that integrates polygenic scores with other established risk factors and provided an assessment of the potential clinical utility of the model for breast cancer prevention.

2) Genetic Determinants for Prostate-Specific Antigen Levels Improve Cancer Screening Utility

• Prostate-specific antigen (PSA) screening for prostate cancer is widely used, but it remains controversial because of issues with sensitivity and specificity. 

• PSA level is highly heritable, and therefore one avenue for improving its diagnostic accuracy is to account for variation in PSA level that is due to genetics and does not reflect prostate cancer.

• Dr Kachuri presented findings from the largest genome-wide association study of PSA levels and demonstrated how using a polygenic score to correct PSA values can improve the clinical utility by reducing overdiagnosis and unnecessary testing and increasing detection of aggressive disease.

Advanced Image Navigation Techniques for Percutaneous Ablation

12 June 2024 | Cardiovascular and Interventional Radiological Society of Europe (CIRSE) | 1.5 European CME credits (ECMEC)

Instructors: Prof. Dimitrios Filippiadis, Prof. Luigi Solbiati, Prof. Rosario Francesco Grasso, Dr. Marie Beermann, Prof. Thierry de Baere, Dr. Marco van Strijen, Prof. Reto Bale

Modules:

• Stereotaxy, Robotics and Image Fusion in IO

• Electromagnetic Navigation

• Stereotactic Microwave Ablation of Liver Lesions

• Robotic Interventions

Learning Outcomes:
1) The theoretical foundations and clinical applications of stereotaxy, robotics, and image fusion in interventional oncology (IO): Explored the principles of stereotactic targeting, robotic arm manipulation, and image guidance for precise needle placement during ablation.

2) The emerging role of electromagnetic navigation in percutaneous ablation: Addressed the technical aspects and potential advantages of electromagnetic tracking for real-time needle guidance and ablation monitoring. 

3) Current practices and best practices for stereotactic microwave ablation (MWA) of liver lesions: Clear understanding of patient selection criteria, treatment planning considerations, and technical aspects of MWA using image guidance. 

4) The evolving landscape of robotic interventions in percutaneous ablation: Talked about the current capabilities and limitations of robotic platforms for ablation procedures, along with potential future directions in this field.

By attending this webinar, I am equipped with the knowledge to critically evaluate the role of advanced image navigation techniques in percutaneous ablation and their potential impact on treatment efficacy and patient outcomes.

Challenges and Opportunities for Primary Cancer Prevention

12 June 2024 | International Agency for Research on Cancer (IARC) & European Society for Medical Oncology (ESMO)

Speaker: Prof David Hunter, University of Oxford | Prof Bernard W. Stewart, University of New South Wales

Summary:

1) Cancer Modifiable Risk Factors: Opportunities and Challenges for Cancer Prevention

• The World Health Organization estimates that 30–50% of all cancer cases are preventable. There is strong scientific evidence about the role of a number of modifiable risk factors and protective factors in the incidence of and mortality from some of the most common cancer types around the world, such as lung cancer, colorectal cancer, breast cancer, and cervical cancer. 

• Discussed questions like, "What is the current status of that evidence, and how far have we progressed?"

2) Cancer Prevention Perspectives Beyond Reduced Carcinogen Exposure

• Decreased risk of lung cancer after smoking cessation epitomizes primary cancer prevention. Comparable responses to alcohol consumption, exposure to ultraviolet radiation, and human papillomavirus (HPV) infection remain crucial.

• Reduced cancer incidence may also be targeted for risk factors not involving recognized carcinogens. More broadly, health impacts due to inequalities offer the prospect of reducing a spectrum of diseases. However, even the immediate goal of avoiding exposure to carcinogens may fail because of beliefs and expectations.

Webinar: Breast Cancer Diagnostics Today: Is a Sensitive Liquid Biopsy the Missing Piece?

11 June 2024 | European Molecular Biology Laboratory (EMBL) & Merck Life Science | 

Instructors: Prof. Nicola Fusco, Chief of the Pathology Division at the European Institute of Oncology in Milan

Breast cancer's diversity can pose challenges to effective diagnosis and personalised treatment. This webinar, featuring leading expert Professor Nicola Fusco, explored the applications of liquid biopsy - a minimally invasive approach analysing tumour DNA circulating in the blood. 

Recognised for his expertise in molecular pathology, liquid biopsy, digital pathology and the application of artificial intelligence in diagnostic pathology, Prof. Fusco's clinical efforts primarily focus on histopathological diagnostics and the predictive pathology of solid tumours, with a special interest in breast cancer.

Professor Fusco shared his insights into how liquid biopsy can: 

• Enhance breast cancer diagnostics 

• Inform personalised treatment strategies 

• Complement and potentially improve traditional biopsy methods

Learning Outcomes:

• Studied how the integration of liquid biopsy can complement current limitations in the diagnostics of breast cancer

• Understood why sensitivity is crucial for accurate detection of tumor-derived mutations in liquid biopsies

• Gained insights on how monitoring specific mutations (ESR1, PIK3CA, PTEN) can inform personalised treatment decisions for advanced breast cancer patients.

The CRISPR Revolution: A Course for Educators and CRISPR Enthusiasts

09 June 2024 | European Molecular Biology Laboratory (EMBL) & Merck Life Science

Instructors: Dr Neil Humphreys, Dr Evangelia Petsalaki, Dr Melanie Krause

Hosted by EMBL's Science Education and Public Engagement team in partnership with Merck Group, this comprehensive 6-week course, running from May 1 to June 9, 2024, was specifically designed for science educators, researchers, and students interested in genome editing and CRISPR technology.

Highlights

1. Dr Neil Humphreys, Head of the Gene Editing and Virus Facility at EMBL, Rome, provided in-depth knowledge on the evolution of gene editing and practical applications of CRISPR technology in creating genetically modified mice. His insights on CRISPR-Cas9 technology and its applications in transgenic mouse generation and cell line engineering were invaluable.

2. Dr Evangelia Petsalaki from EMBL-EBI, UK offered a clear understanding of CRISPR technology for studying drug evasion mechanisms in melanoma cells. Dr. Petsalaki's research group has been studying human cell signalling in both healthy and disease conditions.

3. Dr Melanie Krause from EMBL, Heidelberg shared her pioneering work in imaging and genomic biology. Dr. Krause also talked about how she has been visualising proteins with a pooled tagging approach, which was informative.

In addition to exploring CRISPR-based research across EMBL, the course included hands-on learning with EMBL resources. The bioethics resource on genome editing was designed to address key ethical issues surrounding genome editing. It encouraged reflection and discussion among learners on the implication of CRISPR technology in the field of biotechnology. 

This course has been immensely beneficial as I prepare to work on CRISPR-Cas9 mediated gene therapy for glioblastoma in the upcoming years.

The State of CRISPR and Gene Editing Summit 2024

05 June 2024 | Genetic Engineering and Biotechnology News

Following the approval of the first CRISPR-based cell therapy in December 2023, the CRISPR community is looking ahead to the next wave of commercial successes, fueled by continued innovation in the development of new gene editing and delivery tools and technologies. Equally exciting advances are occurring in livestock editing, xenotransplantation, and many other specialties.

Highlights:

• An opening keynote from David Liu, PhD (Broad Institute) on the state of programmable genome editing, including new research on large-fragment gene editing. 

• A keynote conversation with Laura Sepp-Lorenzino, PhD (CSO Intellia) as her company advances a pair of landmark in vivo therapies in the clinic.

• Talks on two cutting-edge areas of CRISPR-related biology—a new mechanism of anti-phage immunity from Sam Sternberg, PhD (Columbia) and the world of anti-CRISPRs with Joe Bondy-Denomy, PhD (UCSF). 

• The state of livestock gene editing—a panel discussion with Elena Rice, PhD (CSO, Genus plc) and Alison Van Eenennaam, PhD (UC Davis). 

• A chat with the co-founders of Tome Biosciences, Omar Abudayyeh, PhD and Jonathan Gootenberg, PhD (Harvard Medical School) on programmable genome engineering and more. 

• A fireside chat with two leading genome engineers and co-founders of the non-profit Arc Institute—Patrick Hsu, PhD and Silvana Konermann, PhD. 

Introduction to Breast Cancer

05 June 2024 | Yale University

Instructor: Anees B. Chagpar, MD, MSc, MPH, MA, MBA, FRCS(C), FACS 

Learning Outcomes:

• Learnt about what breast cancer is, the epidemiology of this disease and the risks associated with it. In these lectures, I also understood the genetic mutations that predispose people to developing breast cancer.

• Briefly reviewed the fundamentals of cancer and its types (in-situ/invasive, lobular/ductal, grade/stage). Learned aboot the hallmarks of cancer.

• Gained insights into how biopsies are done for diagnosis and on what basis the stage of cancer progression is done.

• Learned about radiation therapy – who needs it, when, what are the different types, and how do we minimize side effects. Also checked who needs chemotherapy, hormonal therapy and what targeted therapy is. Also studied various drugs used in treating breast cancer.

LifeArc Life Sciences: Biology Research Job Simulation on Forage

03 June 2024 | LifeArc Life Sciences | Forage

Summary: 

• Completed a job simulation involving optimizing experimental conditions for Lifearc's Biology Research team.

• Analyzed the differentiation protocol for optimization needs. 

• Reviewed and compared experimental results. 

• Populated presentation slides with data and conclusions.

Drug and Chemical Information - Exploring New Drug Research

27 May 2024 | Medical Library Association | 2 MLA CE Credits

Through hands-on exercises, I practiced advanced PubMed search techniques using the MeSH vocabulary to find the latest research about drugs and chemicals, including clinical trials. I also practiced their new skills in authentic problem-based scenarios focused on assisting library users with their clinical and research information needs.

Learning Outcomes:

• Evaluated how drugs, chemicals, and related topics are indexed in MeSH in order to hone a PubMed search strategy

• Used advanced PubMed search strategies in order to locate the most relevant literature

• Located clinical trials in PubMed and ClinicalTrials.gov about a specific drug therapy

Evolving Perspectives on HR-Positive Metastatic Breast Cancer: Current Understanding and New Insights

27 May 2024 | WebMD | 0.5 CPD Credits

The goal of this activity is for learners to be better able to recognize the latest developments in novel and emerging therapies for hormone receptor (HR)-positive metastatic breast cancer (MBC) and their implications for practice.

Upon completion of this activity, I:

• Am aware of the latest clinical trial data of novel and emerging therapies for patients with HR-positive MBC 

• Have greater competence related to tailoring treatment for patients with HR-positive MBC

• Demonstrate greater confidence in my ability to integrate novel therapies for HR-positive MBC into clinical practice in future.

Fundamentals of Publishing

27 May 2024 | Elsevier

Summary: Discussed the fundamentals of publishing, research metrics, ethics, open science, and how to find the right journal for your research. The course contains 7 topics with 40+ modules.

Introduction to Precision Medicine

27 May 2024 | National Library of Medicine & Medical Library Association | 2.0 MLA CE Credits

Instructor: Michael Balkenhol, Engagement Coordinator, NAPC

Summary: This class is designed to introduce learners to the concept of precision medicine, the NIH All of Us Research Program (All of Us), and how All of Us contributes to advancing precision medicine. Precision medicine considers three aspects of life: biology, environment, and lifestyle specific to family health history and genetic makeup. This course will focus more on topics related to the third aspect, such as genetics testing and how it relates to precision medicine in the context of All of Us Research Program.

Pharmaceutical Systems Strengthening 101 Course

26 May 2024 | USAID & Global Health eLearning Center

The purpose of the pharmaceutical systems strengthening (PSS) course is to teach participants the basic principles of PSS, including how addressing pharmaceutical system problems advance universal health coverage; combat antimicrobial resistance, HIV and AIDS, malaria, TB, and other public health threats; and promote maternal and child health.

Upon completing the course, I can:

• Identify what a country pharmaceutical system is, how it relates to the supply chain system, and how it impacts the broader health system (in terms of service quality, coverage equity, and financial protection/resource optimization) as well as improved health outcomes.

• Demonstrate how USAID’s pharmaceutical systems strengthening approach can lead to more sustainable improvements in medicines access and appropriate use to achieve expected health outcomes.

• Explain how the problem can be better understood by looking at the underlying factors contributing to the problem, and how those factors may be linked to one or more pharmaceutical system and/or health system function.

• Compare alternative strategies for interventions to counter problems of the pharmaceutical systems in similar contexts, taking into account the local situation, political and regulatory considerations, feasibility of implementation, and the resources available.

• Identify methods and tools for evaluating pharmaceutical systems to ensure that the expected outcomes have been achieved.

• Identify specific pharmaceutical system weaknesses in USAID-supported countries that have an impact on USAID’s health goals.

• Identify the effect of antimicrobial resistance (AMR) on the health system and demonstrate base knowledge of strategies against AMR.

Navigating Alzheimer’s Disease Diagnosis and Biomarkers: Making an IMPACT Through a Medical Simulation Challenge

25 May 2024 | Medscape | 1.25 AMA PRA Category 1 Credit(s)

Instructors: Sharon Cohen, MD, FRCPC; Oskar Hansson, MD, PhD; Charlotte Teunissen, PhD; Alok S. Patel, MD

Goal: The goal of this activity is for learners to be better able to understand recent advances in biomarkers and gain experience on how they can utilize cognitive assessment tools and advanced diagnostics for early diagnosis of Alzheimer’s disease (AD).

Upon completion of this activity, I am be able to: 

• Explain the importance of cerebrospinal fluid, imaging and blood-based biomarkers to aid the diagnosis and staging of AD

• Assess individuals with cognitive complaints for mild cognitive impairment and dementia

• Choose an appropriate biomarker to aid in the diagnosis of early AD and diagnose early AD 

• Confidently explain potential applications of blood-based biomarkers in the diagnosis and staging of AD

Generative AI in Medicine: Transforming Competence, Learning and Practice

24 May 2024 | Royal College of Physicians and Surgeons of Canada | 0.5 Royal College MOC Credits

Main Speaker: Brian Hodges, MD, PhD, FRCPC, (Chair)

Summary: The course described the emerging innovations and competencies and outlined the uses of technologies like ChatGPT to propel learning and assessment and writing for research.

Specialized Module on Human Health and Climate Change

24 May 2024 | The United Nations Institute for Training and Research (UNITAR)

The course is structured around 3 modules: 

1) Climate Change and Human Health 

2) Adaptation: Building Health Systems’ Resilience to Climate Change 

3) The Mutual Benefits of Climate Change Mitigation and Health Policies

After completing this specialised module, I can:

• Explain how weather, climate variability and climate change affect human health. 

• Describe the health benefits of mitigation and adaptation policies and measures in health and related sectors. 

• Identify a variety of tools to assess and integrate health within climate change policies and strategies, and integrate climate change within health policies and strategies. 

• Provide examples of how countries are responding to the health challenges posed by climate change, including taking advantage of the opportunities.

The Intersection of Medicine and AI

24 May 2024 | Royal College of Physicians and Surgeons of Canada | 0.5 Royal College MOC Credits

Main Speaker: Richard K. Reznick, MD, FRCSC, FACS, FRCSEd (hon), FRCSI (hon), FRCS (hon) (Chair)

Summary: A discussion with experts on how artificial intelligence and emerging technologies are transforming medicine and the lifelong careers of specialists, and their roles in supporting the health care system now and in the near future.

Training: Immature Platelets and Clinical Insight in Thrombocytopenia

23 May 2024 | Sysmex

The training covered the following content: 

• Immature platelets and their measurement

• Diagnosis and monitoring of thrombocytopenia

• Management of thrombocytopenia

Analytical Techniques of Biotechnology

22 May 2024 | European Open University (Academy Europe) | Professional Certificate Program

Instructor: Mark Thomasson

Summary: This course dealt with various techniques, their principles, experimental details, including general laboratory techniques, separation techniques based on hydrodynamic properties, centrifugation (sub-cellular fractionation and more),  chromatographic, electrophoretic  techniques, HPLC,  purification methods, ELISA, among others. Application in biomedical research and some clinical diagnostic methods (RIA, ELISA, PET), moleular diagnostics, PCR, microscopic techniques and clinical biochemistry were also focussed in the course.

Introduction to Bacteriophage Therapy Masterclass

22 May 2024 | Maryland University of Integrative Health | 1.5 CEU

Presenter: Dr. Sarica Cernohous

Learning Outcomes:

• Can identify the two 2 types of bacteriophage (lytic and lysogenic) and explain how they replicate

• Recalled a brief history of the therapy’s development in Europe and Russia

• Can articulate how bacteriophage compares to antibiotic therapy xplain how bacteriophage are harvested and refined

• Outline the challenges and benefits of bacteriophage therapy and how it is applied in the food system.

ICH Good Clinical Practice E6 (R2)

21 May 2024 | The Global Health Network

Good clinical practice provides a framework of principles which aim to ensure the safety of research participants and the integrity and validity of data. This short course aims to provide the researcher with the basic principles of GCP and how these principles can be applied practically in the research setting. The course is aimed at all those involved in clinical research.

Updates in Clinical Medicine, Hong Kong

02 May 2024 | Royal College of Physicians of Edinburg | 2 Category 1 (External) CPD Credits

Summary: 

• During this International Medical Update (IMU), I learnt about the progress and novel treatment for Chronic Hepatitis B infections with a focus on novel agents, explore how the gut microbiome affects multi-facets of human life and clinical applications of the human microbiome, including its role for biomarker development and precision therapeutics for diseases. 

• The final presentation provided insights into the accomplishments and ongoing efforts in provision of peritoneal dialysis service in Hong Kong and its potential for application to other countries.

Workshop: Integrated Diagnostics in Haemato-Oncology

01 May 2024 | Sysmex (From the XXXVth International Symposium on Technical Innovations in Laboratory Haematology)

Speaker: Dr Timothy Farren | Head of Immunophenotyping & Lead Scientist for Specialist Integrated Haematological Malignancy Diagnostics Service

Summary:

• The speaker portrayed several real-life case studies focusing on the clinical presentation, digital morphology and the subsequent investigations leading to a definitive diagnosis. This provided us an insight into how important correct diagnosis is, and also the need to educate ourselves whilst breaking down silo barriers.

Aspire Leaders Program 2024

January 2024 - April 2024 | Aspire Institute (Funded by Harvard University) | 30 hours

Summary:

I have successfully completed the 2024 Aspire Leaders Program at Aspire Institute, an initiative fully funded by Harvard University. This program is dedicated to empowering young leaders to utilize their talent to foster thriving communities. Over 30 hours of intensive coursework in the first cohort (from January to April), I have had the privilege of connecting with passionate peers from around the globe, discussing innovative project proposals across sustainability, public health, technology, entrepreneurship, and more.

The Aspire Leaders Program consisted of 3 modules:

• Personal and Professional Development: Equipped with professional resources co-created by Harvard Business School. 

• Immersive Learning: Engaged in both asynchronous and synchronous learning with a global cohort of peers and mentors. 

• Aspire Horizons Course: Participated in a six-session leadership development course and masterclasses led by esteemed educators such as Tarun Khanna and Karim Lakhani.

I am eager to apply the insights gained from this program to bring my own project proposal in public health and biotechnology to life. I am incredibly grateful for the opportunity provided by Aspire Institute to expand my network and engage with a vibrant community of future leaders.

Webinar: Facing the Challenges of Anti-dsDNA Antibody Testing

14 November 2023 | Bio-Rad Laboratories

Speaker: Melissa R. Snyder, PhD, DABCC | Co-Director, Antibody Immunology Laboratory, Mayo Clinic

Learning Outcomes:

• Reviewed various dsDNA antibody methods, challenges associated with limited standardization, and approaches for troubleshooting discrepant results and other questions associated with dsDNA antibody testing.

• Learned methods/platforms available for anti-dsDNA antibody testing and analysed the challenges that limit standardization of testing for anti-dsDNA antibodies 

• Can describe how to investigate discrepancies relative to anti-dsDNA antibody testing

Cell Biology Course Fall '23

October 2023 - Febraury 2024 | Scienspur | Student Trainee

Instructors: Dr. Abhijit Majumder, Joseph Thottachery, Parijat Sil, Farah Haque, Veena Tikiyani, Anup Parchure, Rajan Thakur, Sanjeev Sharma, Bhaswati Bhattacharya, Maya Anjur, Neha Varshney, Venkat Rao, Mrigya Babuta, Gunjan Singh

Special Seminar Guests: Alok Javali, Sukanya Madhwal, Swedha Madhwal, Gayatri Ramachandran, Dr. Guruharsha Bhat, Dr. Arun Kondadi

Career Guidance Session Speakers: Maya Anjur, Parijat, Shiva Prasad

Through a rigorous application process and an interview, I was one among the top 100 applicants to be selected for the Cell Biology Course Fall '23 offered by Scienspur, an initiative funded by Harvard University's The Lakshmi Mittal and Family South Asia Institute, Harvard University. I successfully completed the course by attending 3 classes of 60-90 min duration every week from October to January. Distinguished instructors from prominent institutes across the US, Europe, and India held classes, covering topics such as membrane organisation, cell signalling, microscopy, cytoskeleton, metabolism, quantitative cell biology, cancer biology, among others.

Beyond the classroom, I gained invaluable experiences:

• Developed a conceptual and research-oriented understanding of topics.

• Received career advice and mentoring from renowned researchers.

• Networked with scientists in academia and life science industry through career counselling sessions and guest lectures.

The quality of the lectures and the diversity of participants made this course a profoundly positive learning experience. Engaging discussions fuelled my passion for the subject, and I am eager to apply these newfound skills in my future endeavours.

Python for Data Science, AI & Development

31 July 2023 | IBM

Learning Outcomes:

• Learned how to use expressions in mathematical operations, store values in variables, and different ways to manipulate strings.

• Explored various data structures in Python.

• Gained insights into fundamentals, starting from conditions and branching. Learned how to implement loops to iterate over sequences, create functions to perform a specific task, perform exception handling to catch errors, and how classes are needed to create objects.

• Uncovered Python libraries that will aid in data manipulation and mathematical operations and explored ways to collect data by the use of APIs and web scraping.

Stanford Introduction to Food and Health

02 April 2023 | Stanford University

Learning Outcomes:

• Examined the social and cultural shifts that have contributed to our modern epidemics of overweight and obesity.

• Explored the ways in which highly processed foods differ from whole food and the implications of food processing on our health, and studied the change in sugar consumption trend in recent decades.

• Focused on sustainable solutions to the challenge of choosing healthier foods more frequently.

Case Studies in Personalized Medicine

30 March 2023 | Vanderbilt University

Learning Outcomes:

• Reviewed fundamentals of genetics, statistical concepts and skills important to clinical data analysis (odds ratios, relative risk, P values, multiple testing, sensitivity, specificity, ROCs)

• Studied the contemporary techniques and technologies used to study genetic variation, including genome-wide association and sequencing

• Looked at a case of familial hypercholesterolemia and investigated how genomic medicine can be used to move from a rare disease to a common medication, using genomics to find new drug targets, and a discussion of the side effects of statin therapy.

• Focussed on case studies with a look at some cases that illustrate how personalized medicine informs treatment decisions related to specific diseases/conditions, such as cystic fibrosis, Marfan syndrome, heart failure, neuropsychiatric diseases, and diabetes. 3 cases/lessons focus specifically on how genomic medicine informs testing for and treatment of cancer.

• Explored some critical considerations for implementing and operationalizing personalized medicine in a system of care, particularly in the area of informatics.

Nanotechnology: A Maker’s Course

31 March 2023 | Duke University

Learning Outcomes:

• Learned the basics of nano-fabrication and nanocharacterization techniques as well as specific applications of nanotechnology in commercial products.

• Able to explain sample preparation and imaging techniques used in scanning electron microscopy and how energy-dispersive x-ray spectroscopy can be paired with scanning electron microscopy to gain elemental information about samples.

• Understood the basic function of the equipment as well as how samples are prepared and imaged using techniques like transmission electron microscopy and cryo-transmission electron microscopy.

• Observed the demonstrations of micro-computed tomography, X-ray photoelectron spectroscopy, and optical spectroscopy.

• Analysed how and why a vacuum environment is required in nanofabrication, compared the operation of three types of vacuum pumps, and looked at vacuum deposition of thin films using three different methods: sputter evaporation, e-beam evaporation and thermal evaporation.

• Compared atomic layer deposition, chemical vapor deposition, and plasma-enhanced chemical vapor deposition.

• Investigated 5 different methods used in nanotechnology for patterning. Understood the basic processes of photolithography, e-beam lithography, ion beam lithography, hot embossing, and self-assembly.

• Studied wet and dry etching processes (these processes are used to selectively remove material in nanofabrication).

Writing in the Sciences

31 March 2023 | Stanford University

Learning Outcomes:

• Practiced effective writing using practical examples and exercises. Topics include: principles of good writing, tricks for writing faster and with less anxiety, the format of a scientific manuscript, peer review, grant writing, ethical issues in scientific publication, and writing for general audiences.

Introduction to Statistics & Data Analysis in Public Health

16 February 2023 | Imperial College London

Learning Outcomes:

• Defined research questions from some news stories eighteenth century London and statistics in public health by the United Nations.

• Statistical analysis: types of variables, common distributions and sampling.

• Learned to import the data set and run essential descriptive analyses to get to know the variables in R and RStudio.

• Applied hypothesis testing in R and interpreted the result. This involves the calculation of a p value and confidence interval, fundamental concepts in statistical analysis.

Introduction to the Biology of Cancer (Honors)

05 February 2023 | The Johns Hopkins University

Learning Outcomes:

• Had a high-level introduction to the basics of cancer biology as well as incidence and common types of cancer.

• Learned genetics of cancer, variation and mutation, two-hit hypothesis, and genomic instability.

• Identified 10 cellular hallmarks of cancer in order to distinguish a normal cell from a cancerous cell.

• Looked into TNM staging, the metastatic process, and an ecological paradigm.

• Examined imaging as a tool for diagnosis, staging, and treatment of cancer.

• Checked the variety of treatment options available to doctors and patients as well as the features of clinical trials and how they are used to improve the treatment arsenal.

Internship: Computer Aided Drug Design (CADD)

November 2022 | Washington University in St. Louis

Instructors: Dr. Vikram Dalal | Ms. Jasmine Kaur

Attended a 1-month international remote internship-cum-training on 'Computer-Aided Drug Design (CADD)' from instructors Dr. Vikram Dalal, a Post-Doctoral Fellow at Washington University in St. Louis and Ms. Jasmine Kaur.

Weekly Summary

Week 1: Target selection - Finalized target protein to understand the process of drug discovery

Week 2: Structure/ Homology Modeling - Finalized the structure to be used either by database retrieval or homology modelling

Week 3: Docking and Virtual Screening - Finalized the chemical library and performed docking

Week 4: Molecular Dynamics and Simulations - Captured the molecular changes in action

Learning Outcomes:

• Learned about structure-based drug designing via insight into molecular modelling, virtual screening, pharmacophore modelling, and ADMET analysis.

• Used cross-platform molecular graphic tools and softwares such as PyMOL, AutoDock Vina, GROMACS, Clustal Omega and Swiss ADME.

• Visualized a few human proteins using such tools that are enhanced by plugins, including macromolecular analysis, homology modeling, protein–ligand docking, pharmacophore modeling, VS, and MD simulations.

• Currently skilled in structural bioinformatics, molecular docking, and molecular dynamics simulations, all of which are involved in the drug discovery and design process.

Introduction to Genomic Technologies

08 November 2022 | The Johns Hopkins University

Learning Outcomes:

1: Overview - Brushed up the basic concepts of Central Dogma

2: Measurement Technology - Learned about polymerase chain reaction, next generation sequencing, and applications of sequencing

3: Computing Technology - Gained insights into the foundations of computer science, algorithms, memory and data structures, efficiency, software engineering, and computational biology software

4: Data Science Technology - Covered reproducibility, analysis, statistics, question types, the central dogma of inference, analysis code, testing, prediction, variation, experimental design, confounding, power, sample size, correlation, causation, and degrees of freedom.

Algae Biotechnology

07 November 2022 | University of California

Learning Outcomes:

• This 6-module course is part of a series of courses produced by the Algae Technology Educational Consortium and UC San Diego.

• Covered how synthetic biology, genetic engineering, and metabolic engineering are used in algae biotechnology, and also examine the current state of algae biotechnology research and tools.

• Explores some of the common bio-products we can make from algae, and looked at some real-world algae companies that are using algae biotechnology to create products consumers can buy today.

Specialization Course: Drug Development Product Management

06 November 2022 | University of California

Learning Outcomes from all 3 courses:

1: Drug Discovery

• Learned the major aspects of the drug discovery process, starting with target selection, to compound screening to designing lead candidates.

• Increased understanding of the various drug discovery tools and methods that are used for finding, identifying and designing a new drug.

2: Drug Development

• Explored the different stages of clinical development as well as the regulatory including but not limited to, an Investigational New Drug Application (IND), New Drug Application (NDA), and product labeling.

• Learnt how to incorporate study design methods for consideration in the design of clinical protocols to assess safety, tolerability, and efficacy in multiple therapeutic areas.

3: Drug Commercialization

• Covered pharmacoeconomic, marketing strategy, intellectual property strategy, portfolio management, managed markets and strategic alliances. It also had a lecture case study from startup to success.

• Also discussed post-marketing clinical trials or Phase 4 trials.

6 steps for sustainable implementation of national action plans on antimicrobial resistance

25 October 2022 | World Health Organisation

Learning Outcomes:

• Recognized the need for stepwise implementation based on the local context, available data and a participatory approach to identification and implementation of priority activities

• Identified existing funding, funding gaps and map potential funders for resource mobilization efforts

• Aware of a range of WHO tools to support implementation of prioritized activities and the importance of monitoring and evaluating progress in NAP implementation.

Industrial Biotechnology

05 October 2022 | University of Manchester

Learning Outcomes:

1: Enzymes, Enzyme Discovery and Engineering - Learned about enzyme catalysts and their roles in chemicals manufacture, drug discovery, therapeutics, and bioprocessing. Explored their significance in synthetic biology for biofuels, bulk chemicals, and novel therapeutics.

2: Methods in Systems and Synthetic Biology - Gained insight into synthetic biology, turning biology into an engineering discipline. Studied the design-build-test cycle for novel biosystems, and its application in microbial production of high-value chemicals and drugs. Discussed responsible research and innovation in this field.

3: Biochemical and Bioprocess Engineering - Understood the design of processes for manufacturing bio-based chemicals, biopharmaceuticals, and biofuels. Learned about the integration of life sciences and synthetic biology discoveries into scalable production processes, focusing on key engineering concepts and problem-solving approaches.

4: Pharmaceuticals and Fine Chemicals - Studied the production of pharmaceuticals and fine chemicals using biocatalysis. Examined biocatalytic transformations with isolated enzymes or whole cells, focusing on sustainability metrics, enzyme stability, and key attributes for successful scale-up.
5: Case Studies: Bioenergy and Biomaterials - Explored biofuel production and the challenges of increasing bioenergy contribution sustainably in the UK. Studied the development of novel biomaterials for industrial and medical applications, including trends and future directions in biomaterials research and biomanufacturing technologies.

6: Case Studies: Glycoscience and Biotherapeutics - Learned about glycoscience and its impact on the bioeconomy through key challenges and glycan-based solutions in pharmaceuticals, personalized medicine, and food security. Studied the production of biopharmaceuticals, focusing on safe and effective production methods using various expression systems.

The Science of Stem Cells

01 October 2022 | American Museum of Natural History

Learning Outcomes:

1: Introduction to Stem Cells - Overview of stem cells, history of stem cell research, and potential therapies

2: How Do Stem Cells Work? Differentiation of stem cells into specific cell types, stem cell-assisted technologies like mitochondrial replacement therapy, and ethical considerations of cloning.

3: Using Stem Cells to Study Disease - Utilising cultured cells to model diseases and search for potential cures, with a focus on Alzheimer's and diabetes research.

4: Stem Cells to Treat Disease - Potential of adult stem cells to treat diseases such as age-related macular degeneration, and tools for evaluating stem cell treatments.

5: The Bioethics of Stem Cell Research and Therapy - Discussion on the ethical, legal, and policy challenges of human embryonic stem cells and the future of reproductive technology.

ASM-MicroGen One-Week Bioinformatics Workshop 

August 19 - August 22, 2024 | American Society for Microbiology

Instructor: Mr Mohammed Alfaki

MircroGen, the initiative behind organising the program, was established by the ASM's Young Ambassador to Sudan, Sara Albagir Abdalla.

This workshop covered key bioinformatics topics for microbiology, including genome sequencing, transcriptomics, proteomics, pathogen detection, and epidemiology. Through this workshop, I explored WGS for microbial identification, RNA-Seq for gene expression analysis, protein identification & interaction networks, and rapid pathogen detection. This initiative also addressed antibiotic resistance, drug discovery, and structural bioinformatics, including protein structure prediction and molecular docking. Additional sessions were based on functional genomics, microbial community analysis, phylogenetics, and data integration in systems biology models.

During the hands-on sessions, we also practiced the analysis of the hypothetical proteins from the first step to the manuscript writing as an application for bioinformatics research in microbiology.