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DTSTART;TZID=UTC:20230227T160000
DTEND;TZID=UTC:20230227T170000
DTSTAMP:20260406T020333
CREATED:20230220T221755Z
LAST-MODIFIED:20230220T221946Z
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SUMMARY:Seminar by Dr. Rati Sharma on "Systems Biology In Action: A dive into signaling pathways and behavioral dynamics"
DESCRIPTION:Speaker: Dr. Rati Sharma \nTitle: Systems Biology In Action: A dive into signaling pathways and behavioral dynamics \nAbstract: \n“Systems Biology” refers to the study of biological systems through modeling\, experiments and computational tools. In particular\, the workings and implications of genetic networks\, behavior and signal-response can be studied through the tools and techniques adapted from the field of systems biology. This field\, therefore\, has an important role to play in the understanding of biological entities\, be it at the level of the cell\, tissue or organism. In this talk\, I will discuss our work in the area of systems biology along four major themes\, namely\, (i) theoretical and computational modeling of signaling pathways using concepts from chemical kinetics and non-equilibrium statistical mechanics; (ii) signal response studies in the nematode (roundworm) C. elegans; (iii) development of microfluidics devices and (iv) development of machine learning tools for the study of biological systems. \nIn the first part of my talk\, I will discuss one example of a cellular pathway\, viz. the immune response pathway\, where noise or fluctuations plays an important role. Through the analysis of this system and upon comparing the theoretically predicted average virus levels to those of COVID-19 patients\, we hypothesize that the long lived viral dynamics are due to the long range correlations in the temporal fluctuations of the virion [1\, 2]. Next\, I will discuss the sensation and behavioral aspects of the model organism C. elegans in response to a heat shock and chemical stimuli [3]. Third\, I will talk about the development of microfluidics devices that can aid in performing controlled experiments with these model organisms [4]. And finally\, given the need for automation in labor intensive behavioral studies in C. elegans\, I will also discuss our efforts in this direction and talk about the recently developed Deep-Worm-Tracker from our lab [5]. I will\, therefore\, provide an overview of the kind of important biological questions that can be addressed through a combination of modeling\, computational and experimental studies. \nReferences: \n\nPersistent correlation in cellular noise determines longevity of viral infections. Abhilasha Batra\, Shoubhik Banerjee and Rati Sharma*\, J. Phys. Chem. Lett. 13\, 7252 (2022). https://doi.org/10.1021/acs.jpclett.2c01875\nA near analytic solution of a stochastic immune response model considering variability in virus and T-cell dynamics. Abhilasha Batra and Rati Sharma*\, J. Chem. Phys. 154\, 195104 (2021). https://doi.org/10.1063/5.0047442\nLessons learned from two decades of modeling the heat shock response. Ayush Ranawade\, Rati Sharma and Erel Levine\, Biomolecules 12\, 1645 (2022).https://doi.org/10.3390/biom12111645\nMicrofluidics based bioimaging with cost-efficient fabrication of multi-level micron sized trenches. A Anand\, Abhilasha Batra\, Santanu Talukder and Rati Sharma*\, Submitted.\nDeep-Worm-Tracker: Deep Learning Methods for Accurate Detection and Tracking for Behavioral Studies in C. elegans.Shoubhik Chandan Banerjee\, Khursheed Ahmad Khan and Rati Sharma*\, Under review. (bioRxiv preprint: https://doi.org/10.1101/2022.08.18.504475)\n\nAbout the Speaker:  \nDr. Rati Sharma is an Assistant Professor in the Dept. of Chemistry at Indian Institute of Science Education and Research (IISER) Bhopal. She graduated in Chemistry from Stella Maris College\, Madras University in 2007. Following this\, she joined the Integrated PhD program of the Division of Chemical Sciences at Indian Institute of Science\, Bangalore\, where she completed her MS and PhD in 2013 under the guidance of Prof. Binny J. Cherayil. Her PhD thesis primarily focussed on questions in theoretical biophysics and polymer physics. She then pursued postdoctoral research at the Dept. of Biophysics\, Johns Hopkins University\, USA from 2013-2016 and at the Dept. of Physics\, Harvard University\, USA from 2016 to 2018. Her postdoctoral research training encompassed a variety of topics in systems biology. She moved back to India in 2019 where she has steadily established her group. She has received research grants from both DST-SERB and DBT since she joined IISER Bhopal. Her current research interests focus on computational and experimental biophysics\, ranging from topics such as stress response dynamics in C. elegans and modeling of signaling pathways to machine learning applications in biological research\, to name a few. \n 
URL:https://be.iisc.ac.in/event/seminar-by-dr-rati-sharma-on-systems-biology-in-action-a-dive-into-signaling-pathways-and-behavioral-dynamics/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20230223T143000
DTEND;TZID=UTC:20230223T153000
DTSTAMP:20260406T020333
CREATED:20230219T223953Z
LAST-MODIFIED:20230219T223953Z
UID:4393535-1677162600-1677166200@be.iisc.ac.in
SUMMARY:Seminar by Dr. Lorena Escudero Sanchez on "AI applications in radiological image analysis for cancer research
DESCRIPTION:Speaker: Dr. Lorena Escudero Sanchez\, University of Cambridge \nTitle: AI applications in radiological image analysis for cancer research \nAbstract: \nImaging is one of the main pillars of clinical protocols for cancer care that provides essential non-invasive biomarkers for detection\, diagnosis and response assessment. The development of Artificial Intelligence (AI) tools have proven potential to transform the analysis of radiological images\, by significantly reducing processing time\, by increasing the reproducibility of measurements and by improving the sensitivity of tumour detection compared to the standard visual interpretation\, leading to cancer early detection. In this talk I will highlight some of the work done in our Radiogenomics and Quantitative Image Analysis group\, covering methods for automated tumour segmentation\, in particular in ovarian cancer\, a highly complex\, heterogeneous and metastatic cancer. I will also present studies on Radiomic features\, quantitative measurements extracted directly from images such as CT or MR\, and examples of Machine Learning models based on these variables to predict response to chemotherapy treatment. Finally\, we will briefly see some examples of clinical applications of such image analysis methods. \nAbout the Speaker: \nDr Lorena Escudero Sánchez is a particle physicist\, with a PhD in neutrino physics\, who has worked in large international collaborations for the neutrino oscillation experiments T2K (Japan)\, MicroBooNE and DUNE (US). She now works on AI applications to radiological image analysis for cancer research\, at the Department of Radiology of the University of Cambridge and CRUK Cambridge Centre. She is also part of the Repository team of the National Cancer Imaging Translational Award (NCITA) consortium across different UK institutions. As a Senior Research Associate at the Department of Radiology in Cambridge\, she leads the Radiogenomics and Quantitative Image Analysis group. She is also a Turing Fellow of The Alan Turing Institute\, the UK national centre for AI and Data Science\, a Borysiewicz Interdisciplinary Fellow of the University of Cambridge\, and a Rokos Postdoctoral Research Associate at Queens’ College Cambridge.
URL:https://be.iisc.ac.in/event/seminar-by-dr-lorena-escudero-sanchez-on-ai-applications-in-radiological-image-analysis-for-cancer-research/
LOCATION:M Tech Classroom\, BSSE Annex
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20230222T110000
DTEND;TZID=UTC:20230222T120000
DTSTAMP:20260406T020333
CREATED:20230215T010952Z
LAST-MODIFIED:20230215T010952Z
UID:4393512-1677063600-1677067200@be.iisc.ac.in
SUMMARY:Seminar by Dr. Mirunalini Thirugnanasambandam on Image-based biomechanics
DESCRIPTION:Title of Talk: Image-based biomechanics in the era of personalized medicine \nSpeaker Name: Mirunalini Thirugnanasambandam \nSpeaker Affiliation: Eindhoven University of Technology\, Netherlands \nAbstract of Talk \nIn the age of digital twins\, when clinical management is moving towards a more personalized approach\, it is often desired to evaluate patient-specific geometry and mechanical behavior. While ex-vivo tests can estimate individualized tissue properties\, they are usually not a viable solution due to either tissue unavailability\, or due to the tests being destructive. In my talk\, I will shed light on novel methods for evaluation of patient-specific vascular biomechanics using an innovative combination of in-vivo imaging modalities (ultrasound and MRI)\, and image-based biomechanical modeling. In particular\, aortic wall motion takes the central stage since it inherently contains information on local mechanical behavior of the aorta. I will also demonstrate the value of building multi-scale circulation loops representing (patho-) physiological conditions – illustrating that they not only serve to validate new techniques\, but also possess the ability to shed light on disease mechanisms which may otherwise go unnoticed. Finally\, a futuristic outlook on ways to improve the translational potential of these sophisticated models will be discussed. \nBrief Bio of Speaker \nDr. Mirunalini Thirugnanasambandam obtained her undergraduate degree in Mechanical Engineering from College of Engineering Guindy\, Anna University\, Chennai. She did her Masters’ degree in Mechanical Engineering at McGill University\, Canada\, where she worked on signal processing techniques in non-linear systems. Her curiosity about non-linear systems in nature led her to pursue a PhD in cardiovascular biomechanics at University of Texas at San Antonio\, USA\, with Prof. Ender Finol\, while doing a research exchange at Ecole des Mines\, St Etienne\, France\, with Prof. Stephane Avril. She began her postdoctoral research at University of Bern\, Switzerland\, where she worked with Prof Dominik Obrist\, and later began her current postdoctoral position at Eindhoven University of Technology\, Netherlands with Dr. Richard Lopata. Her research focuses on both experimental and computational sides of cardiovascular mechanics\, with special emphasis on abdominal aortic aneurysms and coronary microvascular obstruction. She has developed and validated computationally inexpensive novel methods to estimate vascular biomechanics from medical images.
URL:https://be.iisc.ac.in/event/seminar-by-dr-mirunalini-thirugnanasambandam-on-image-based-biomechanics/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20230221T110000
DTEND;TZID=UTC:20230221T120000
DTSTAMP:20260406T020333
CREATED:20230220T015219Z
LAST-MODIFIED:20230220T015219Z
UID:4393550-1676977200-1676980800@be.iisc.ac.in
SUMMARY:Special talk by Mr. Sarath Kolli on "Automation of therapeutics design in the era of Artificial Intelligence"
DESCRIPTION:Speaker: Mr. Sarath Kolli\, CEO of Boltzmann Labs \nTitle: Automation of therapeutics design in the era of Artificial Intelligence \nAbstract:  \nAutomation of the therapeutic design process through the integration of AI has drastically improved the efficiency and effectiveness of pharmaceutical research. With the power to assess large amounts of data within a short timeframe\, AI algorithms can detect patterns\, recognize target proteins and design potential treatments – all of which can be achieved much faster than human scientists can manage. This has resulted in the creation of groundbreaking drugs which have revolutionized the way that diseases are tackled. The speed of AI algorithms is one of the major benefits that has been gained from automating therapeutic design. \nAI algorithms are capable of rapidly processing massive data sets and accurately pinpointing target proteins and designing potential medications. This allows scientists to save time and money. Furthermore\, these AI tools can be used to refine the production process of these pharmaceuticals\, making them more efficient. Additionally\, AI algorithms can assess vast amounts of data and make predictive conclusions with a higher degree of accuracy compared to manual methods. This has significantly raised the success rate of clinical trials\, which has been a long-standing difficulty in the pharmaceutical sector. \nThe emergence of AI in the pharmaceutical industry has meant a shift in the way treatments are discovered. By using AI algorithms to analyze data from various sources\, such as genomics\, proteomics\, and pharmacology\, new targets for drugs have been identified\, which has resulted in new treatments for previously incurable diseases. As AI technology advances\, even more\, breakthroughs can be expected in the future\, providing much-needed hope to those in need.
URL:https://be.iisc.ac.in/event/special-talk-by-mr-sarath-kolli-on-automation-of-therapeutics-design-in-the-era-of-artificial-intelligence/
LOCATION:CES Classroom\, CES Classroom\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20230220T160000
DTEND;TZID=UTC:20230220T170000
DTSTAMP:20260406T020333
CREATED:20230219T224107Z
LAST-MODIFIED:20230219T224107Z
UID:4393537-1676908800-1676912400@be.iisc.ac.in
SUMMARY:Seminar by Prof. Herbert Levine on "Cell – ECM interactions and their relevance for cancer progression
DESCRIPTION:Speaker: Prof. Herbert Levine (Satish Dhawan Visiting Chair Professor\, IISc) \nTitle: Cell – ECM interactions and their relevance for cancer progression \nAbstract: \nDuring metastasis\, tumor cells must traverse fibrous extracellular matrix (ECM) en route to the circulation. Conversely\, immune cells must traverse the same medium en route to attacking a tumor. Thus\, the study of the reciprocal feedbacks between cell motility and ECM is a crucial aspect of understanding cancer progression and its possible interdiction. This understanding is made more difficult by the highly nonlinear mechanics of ECM and by the multiple modes of cell motion in complex media. This talk will focus on recent progress as well as open issues in this rapidly advancing research topic. \nAbout the Speaker:  \nHerbert Levine is a University Distinguished Professor of Physics and Bioengineering at Northeastern University. He is also the co-director of a National Science Foundation Physics Frontier Center devoted to theoretical biological physics. He earned his Ph.D. and an M.A. in physics from Princeton University and a B.S. in physics from Massachusetts Institute of Technology. For several decades\, he has been an acknowledged leader in applying methods from physical science to diverse living systems – self-organization of bacterial colonies\, directed motion of eukaryotic cells\, biophysical modeling of cancer progression and metastasis\, and tumor-immune interactions. He spent 25 years on the faculty of UCSD before moving to Rice University in 2012. He has served as an Associate Editor of Biophysical Journal and as the Editor-in-Chief of Physical Biology. He is a Fellow of American Physical Society (APS)\, and an elected member of the American Academy of Arts and Sciences (AAAS) & National Academy of Sciences (NAS).
URL:https://be.iisc.ac.in/event/seminar-by-prof-herbert-levine-on-cell-ecm-interactions-and-their-relevance-for-cancer-progression/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20230215T120000
DTEND;TZID=UTC:20230215T130000
DTSTAMP:20260406T020333
CREATED:20230214T000318Z
LAST-MODIFIED:20230214T000318Z
UID:4393510-1676462400-1676466000@be.iisc.ac.in
SUMMARY:LUMICKS (Amsterdam\, The Netherlands) \, "Tractor beams and single molecules: How to visualize and manipulate single biomolecules in real-time
DESCRIPTION:Title: Tractor beams and single molecules: How to visualize and manipulate single biomolecules in real-time \nAbstract: \nImagine you could directly see the location and dynamics of individual proteins binding to a piece of single DNA. What if you could assemble your biological complex step by step and see it in action in real-time? What if you could manipulate the structure of your biomolecule and quickly change buffer conditions to test your experimental hypotheses? By using “molecular tractor beams”\, the C-trap makes that a reality. \nEssential biological processes performed by proteins interacting with DNA or cytoskeletal protofilaments are key to cell metabolism and life. In order to understand the molecular basis of life\, as well as the pathological conditions that develop when processes go wrong\, it is critical to get detailed insights into these processes at the molecular level. Not only at the highest resolution\, but also in real time. \nDuring this seminar\, we will take you through an exciting journey of different research topics in which dynamic single molecule studies revealed remarkable insights. In each study\, the C-Trap system was used; our easy-to-use platform that combines optical tweezers with fluorescence microscopy. We will explain how the ability to control\, visualize and manipulate single molecules in real time\, changes the way we answer tough scientific questions in the field of DNA processing\, single-protein dynamics\, liquid-liquid phase separation (LLPS) and beyond.
URL:https://be.iisc.ac.in/event/lumicks-amsterdam-the-netherlands-tractor-beams-and-single-molecules-how-to-visualize-and-manipulate-single-biomolecules-in-real-time/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20230214T100000
DTEND;TZID=UTC:20230214T110000
DTSTAMP:20260406T020333
CREATED:20230213T000405Z
LAST-MODIFIED:20230213T000405Z
UID:4393506-1676368800-1676372400@be.iisc.ac.in
SUMMARY:Guest Lecture by Areejit Samal on Elucidating and leveraging the design principles towards realistic Boolean models of gene regulatory networks
DESCRIPTION:Title: Elucidating and leveraging the design principles towards realistic Boolean models of gene regulatory networks \nSpeaker: Areejit Samal (The Institute of Mathematical Sciences (IMSc)\, Chennai) \nVenue: MRDG Conference Room \nAbstract: \nBoolean networks is a widely-used mathematical framework to model gene regulatory networks. Such Boolean models consist of a set of nodes\, directed edges between the nodes\, and Boolean functions representing the regulatory logic at each node in the network. \nIn the first part of my talk\, I will discuss several biologically-meaningful types of BFs\, and present our systematic study of their preponderance in a compilation of 2687 regulatory rules extracted from published Boolean models of diverse biological systems [1]. A surprising observation in the empirical dataset is that most Boolean functions have an odd ‘bias’. Thereafter\, we are able to explain this observation along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset\, in terms of two complexity measures: Boolean complexity and average sensitivity. In particular\, we show that the RoFs minimize Boolean complexity and the NCFs minimize the average sensitivity in addition to minimizing the Boolean complexity\, and this highlights the importance of minimum complexity in the regulatory logic of biological networks [1]. \nIn the second part of my talk\, I will present our systematic framework leveraging biologically-meaningful regulatory logic and relative stability of cell fates or attractors for model selection of Boolean developmental gene regulatory networks [2]. In particular\, I show the usefulness of mean first passage time (MFPT) as a measure to capture cell state transitions within the Boolean framework and construction of cellular lineage trees. Thereafter\, I will show an application of these tools towards in-depth analysis and subsequent improvement of existing Boolean models of Arabidopsis root development [2]. \n\nA. Subbaroyan\, O.C. Martin & A. Samal\, Minimum complexity drives regulatory logic in Boolean models of living systems\, PNAS Nexus\, 1(1): pgac017 (2022).\nA. Subbaroyan\, P. Sil\, O.C. Martin & A. Samal\, Leveraging Developmental Landscapes for Model Selection in Boolean Gene Regulatory Networks\, bioRxiv 2023.01.08.523151.\n\nAbout the Speaker: \nAreejit Samal is a faculty member in the computational biology group of The Institute of Mathematical Sciences\, Chennai since April 2014. He obtained his Bachelors\, Masters and PhD from University of Delhi. Subsequently\, he did Postdoctoral research at the Max Planck Institute for Mathematics in the Sciences Leipzig\, CNRS/LPTMS Orsay\, Institute for Systems Biology Seattle\, and ICTP Trieste. He has been a recipient of FEBS Short term Research Fellowship\, Ramanujan Fellowship\, Simons Associateship of ICTP and a Max Planck Partner Group. His research interests span the broad area of complex systems / networks\, in particular\, its applications to biological systems.
URL:https://be.iisc.ac.in/event/guest-lecture-by-areejit-samal-on-elucidating-and-leveraging-the-design-principles-towards-realistic-boolean-models-of-gene-regulatory-networks/
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20230213T160000
DTEND;TZID=UTC:20230213T170000
DTSTAMP:20260406T020333
CREATED:20230212T233801Z
LAST-MODIFIED:20230212T233801Z
UID:4393504-1676304000-1676307600@be.iisc.ac.in
SUMMARY:Seminar by Prof. Herbert Levine on The Tumor-Immune Interaction: Pieces of a Multiscale Story
DESCRIPTION:Title: The Tumor-Immune Interaction: Pieces of a Multiscale Story \nAbstract: \nOne of the most important advances in cancer research over recent years has been the renewed excitement regarding using the immune system to attack malignant cells. Understanding and managing the battle between adaptive immunity and the tumor is a complex multiscale problem\, involving the molecular biophysics of immune recognition\, the cellular processes of direct checkpoint-dependent evasion\, and the ecological dynamics of the microenvironmental milieu. This talk will highlight some of our recent attempts to analyze pieces of this problem and to begin to assemble these pieces into a coherent picture. \nAbout the speaker: \nHerbert Levine is a University Distinguished Professor of Physics and Bioengineering at Northeastern University. He is also the co-director of a National Science Foundation Physics Frontier Center devoted to theoretical biological physics. He earned his Ph.D. and an M.A. in physics from Princeton University and a B.S. in physics from Massachusetts Institute of Technology. For several decades\, he has been an acknowledged leader in applying methods from physical science to diverse living systems – self-organization of bacterial colonies\, directed motion of eukaryotic cells\, biophysical modeling of cancer progression and metastasis\, and tumor-immune interactions. He spent 25 years on the faculty of UCSD before moving to Rice University in 2012. He has served as an Associate Editor of Biophysical Journal and as the Editor-in-Chief of Physical Biology. He is a Fellow of American Physical Society (APS)\, and an elected member of the American Academy of Arts and Sciences (AAAS) & National Academy of Sciences (NAS).
URL:https://be.iisc.ac.in/event/seminar-by-prof-herbert-levine-on-the-tumor-immune-interaction-pieces-of-a-multiscale-story/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20230102T160000
DTEND;TZID=UTC:20230102T170000
DTSTAMP:20260406T020333
CREATED:20221229T013402Z
LAST-MODIFIED:20221229T013402Z
UID:4392999-1672675200-1672678800@be.iisc.ac.in
SUMMARY:Seminar by Dr. Tarini Shankar Ghosh on The gut microbiome and biological aging
DESCRIPTION:Speaker: Dr. Tarini Shankar Ghosh (Indraprastha Institute of Information Technology\, IIIT-Delhi) \nTitle: The gut microbiome and biological aging \nAbstract: \n“The gut harbours one of the largest microbial communities found in human body\, with more than 1.3 trillion microbial cells encoding a functional capacity estimated to be more than 150 times the coding capacity of our own. Alterations in the gut microbiome have been associated with many aspects of human physiology\, some of the medically and economically significant multifactorial non-communicable diseases as well as with the treatment responses of individuals to different therapeutic interventions. \nAge is one such aspect of host physiology having one of the strongest associations with the composition of the gut microbiome. Aging is associated with a progressive decline in multiple bodily functions and an onset of low-grade inflammation (referred to as ‘Inflammaging’). But even in healthy people\, the gut microbiome alters with age. Are age-associated gut microbiome alterations a cause or a mere consequence of a declining state of human health? Or do these alterations indicate a transition to an even more vicious cycle of deterioration in host physiology? Can these alterations in a host be ‘reset’ using microbiome-targeted therapeutics to delay the transition to an unhealthy aging trajectory? In this talk\, I will some of the recent genomic and metagenomic studies (including some of my previous works) that have attempted to answer the above questions. I will also briefly describe specific examples\, where in we observed the gut microbiome to be a key transducer of the beneficial signals of diet on health of older people. Finally\, my talk will provide implications for future\, including the prospects of devising microbiome-targeted diagnostic/therapeutic strategies specifically customized for societies like India for improving human health.” \nAbout the Speaker: \nTarini Shankar Ghosh is an Assistant Professor of Computational Biology at the Indraprastha Institute of Information Technology Delhi (IIIT-Delhi). He received his B.Tech from Indian Institute of Technology (IIT) Kharagpur\, his M.Tech from IIT Kanpur and his Ph.D from the University of Hyderabad. After completing his PhD\, he first moved to the Genome Institute of Singapore (as a post-doctoral researcher) and then to his current institute APC Microbiome Ireland at Cork. His core research focus is to understand gut microbial ecology using an in-silico approach. He uses a combination of metagenome informatics\, machine learning and statistical approaches to identify the generic microbial markers of health\, their variation across various population-strata\, their alterations in different disease conditions and finally the formulation of personalized diet/symbiotic-based microbiome restoration strategies for improving human health. He has published more than 50 research papers in notable journals including Nature Medicine\, Nature Reviews Gastroenterology and Hepatology\, Nature Aging\, Nature Ecology and Evolution\, Gut (British Medical Journals)\, Gastroenterology (American Gastroenterological Association) and Cell hosts and microbes. He has 8 US/EU based patents pertaining to metagenomic data analysis algorithms and design of microbial consortia targeted to ameliorate frailty and colorectal cancer. Dr. Ghosh was also selected for the Pathway Investigator Award by the Science Foundation of Ireland and the Irish Research Council for the year 2022. He has also been a recipient of the Yakult Young Investigator Award in the year 2014 and the Torrent Pharmaceuticals – ISHR Young Investigator Award in the year 2017.
URL:https://be.iisc.ac.in/event/seminar-by-dr-tarini-shankar-ghosh-on-the-gut-microbiome-and-biological-aging/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20221229T080000
DTEND;TZID=UTC:20221229T170000
DTSTAMP:20260406T020333
CREATED:20221229T041455Z
LAST-MODIFIED:20221229T042037Z
UID:4393016-1672300800-1672333200@be.iisc.ac.in
SUMMARY:9th Annual Symposium\, BSSE 2023 (19th-21st Jan 2023)
DESCRIPTION:
URL:https://be.iisc.ac.in/event/9th-annual-symposium-bsse-2023-19th-21st-jan-2023/
CATEGORIES:Announcement,BSSE Symposium
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20221214T160000
DTEND;TZID=UTC:20221214T170000
DTSTAMP:20260406T020333
CREATED:20221212T033147Z
LAST-MODIFIED:20221212T033147Z
UID:4392761-1671033600-1671037200@be.iisc.ac.in
SUMMARY:Seminar (Talk-2) by Dr. Shyni Varghese on Ex vivo 3D tumor models to study cancer cell invasion and T cell recruitment
DESCRIPTION:Title: Ex vivo 3D tumor models to study cancer cell invasion and T cell recruitment \nAbstract:  \n“Advancement in three-dimensional (3D) cell cultures and microfabrication has led to the development of physiologically relevant ex vivo models to understand the interdependency between cells and their microenvironment as well as various cellular functions involved in development and pathogenesis. In this talk\, I will discuss about our efforts on understanding the role of physical properties of the matrix in disease progression such as cancer metastasis. Metastatic dissemination of cancer cells is a key contributor to >90% of cancer-related mortality. Though metastasis involves multiple steps\, the ability of cancer cells to invade and traverse through dense 3D structures (i.e.\, extracellular matrix such as collagen network) is a crucial manifestation of cancer malignancy. In order to understand cancer cell invasion and migration\, we have developed a single cell resolution quantitative assay to estimate the three-dimensional (3D) traction stresses generated by the cancer cells during their migration. We also examined the effect of material properties on protease independent vs. dependent mode of migration of cancer cells. Such quantitative analysis would lead to identification of new pathways that might be targeted to develop therapies to treat cancer metastasis. I will also talk about the application of tumor-on-chip platform involving heterotypic cells to study tumor associated microenvironment on cell recruitment.” \nAbout the Speaker: \nShyni Varghese\, Ph.D.\, is a Professor of Biomedical Engineering\, Mechanical Engineering & Materials Science\, and Orthopaedics Surgery at Duke University. She is the inaugural MEDx Investigator at Duke University. Prior to moving to Duke\, she was a Professor of Bioengineering at University of California\, San Diego. Dr. Varghese’s research covers a broad range of topics including stem cells\, biomaterials\, biologically inspired systems\, tissue chips\, and regenerative medicine. Her research activities have resulted in over 100 publications and over a dozen patent disclosures. Examples of ongoing research activities in her laboratory involve developing functional biomaterials such as self-healing hydrogels and biomineralized matrices; technologies to improve cell-based therapies including stem-cell differentiation\, cell transplantation\, activating endogenous stem cells\, and engineered functional tissue grafts; and organ-on-a-chip technologies. She is a fellow of AIMBE and Royal Society of Chemistry. She is currently serving as an Associate Editor of Biomaterials Science (an RSC journal).
URL:https://be.iisc.ac.in/event/seminar-talk-2-by-dr-shyni-varghese-on-ex-vivo-3d-tumor-models-to-study-cancer-cell-invasion-and-t-cell-recruitment/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20221212T160000
DTEND;TZID=UTC:20221212T170000
DTSTAMP:20260406T020333
CREATED:20221207T000240Z
LAST-MODIFIED:20221207T000240Z
UID:4392759-1670860800-1670864400@be.iisc.ac.in
SUMMARY:Seminar by Dr. Shyni Varghese on Engineering the interface: From smart materials to devices to cell transplantation
DESCRIPTION:Title: Engineering the interface: From smart materials to devices to cell transplantation \nAbstract:  \n“In this talk\, I will discuss our efforts in engineering the bio-material interface to achieve unique biological functions and medical applications. First\, I will talk about design of hydrogel matrices to control stem cell fate in vitro and in vivo and use of such engineered matrices to understand the molecular mechanism underlying stem cell differentiation (Ayala et al.\, Biomaterials\, 2011; Shih et al.\, PNAS 2014; Zeng et al.\, Adv. Mater. 2020). I will next talk about developing biomaterial interfaces to support xenogeneic transplantation of cells\, where the transplanted cells act as a “drug store” for biomolecules (Kumar et al.\, Adv. Funct. Mater.\, 2021). Finally\, I will talk about how interfacial engineering can be exploited to creating materials with “living” functions such as self-healing along with their applications in cartilage tissue repair and soft robotics (Phadke et al.\, PNAS\, 2012; Kumar et al.\, Adv. Int. Syst. 2021; Gilpin et al.\, Adv. Healthc. Mater. 2021).” \nAbout the Speaker: \nShyni Varghese\, Ph.D.\, is a Professor of Biomedical Engineering\, Mechanical Engineering & Materials Science\, and Orthopaedics Surgery at Duke University. She is the inaugural MEDx Investigator at Duke University. Prior to moving to Duke\, she was a Professor of Bioengineering at University of California\, San Diego. Dr. Varghese’s research covers a broad range of topics including stem cells\, biomaterials\, biologically inspired systems\, tissue chips\, and regenerative medicine. Her research activities have resulted in over 100 publications and over a dozen patent disclosures. Examples of ongoing research activities in her laboratory involve developing functional biomaterials such as self-healing hydrogels and biomineralized matrices; technologies to improve cell-based therapies including stem-cell differentiation\, cell transplantation\, activating endogenous stem cells\, and engineered functional tissue grafts; and organ-on-a-chip technologies. She is a fellow of AIMBE and Royal Society of Chemistry. She is currently serving as an Associate Editor of Biomaterials Science (an RSC journal).
URL:https://be.iisc.ac.in/event/seminar-by-dr-shyni-varghese-on-engineering-the-interface-from-smart-materials-to-devices-to-cell-transplantation/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20221205T160000
DTEND;TZID=UTC:20221205T170000
DTSTAMP:20260406T020333
CREATED:20221128T234235Z
LAST-MODIFIED:20221128T234404Z
UID:4392744-1670256000-1670259600@be.iisc.ac.in
SUMMARY:Seminar by Dr. Parag Katira on Mechanics of Cancer
DESCRIPTION:Title: Mechanics of Cancer \nAbstract:  \nCancer is a disease rooted in genetic mutations and epigenetic regulation of cell biology. There is extensive heterogeneity in the biological drivers of this disease across cancer types\, across patients with one type of cancer\, and even within tumors within a single patient\, making early cancer diagnosis\, accurate prognosis and treatment challenging. We take the view that all the varying biological factors influencing cancer ultimately lead to similar mechanical outcomes that define the disease – uncontrolled cell proliferation and tumor growth within the host tissue environment\, cell migration and invasion of neighboring tissues\, and formation of secondary neoplasms within the invaded tissues. Can the mechanics of these physical processes then shed light on key elements of cancer occurrence and progression? Can these mechanistic insights provide avenues for better prognosis and treatments of cancer? This talk will describe our efforts to understand the role of mechanics in cancer progression\, some interesting physical paradoxes that cancer progression presents and what biological insights if any can be gained from such understanding. \nAbout the Speaker: \nDr. Parag Katira is an Associate Professor in Mechanical Engineering and Associate Director of the Computational Sciences Research Center at San Diego State University. He is also the program coordinator for the Bioengineering Graduate Program at San Diego State University. Prior to his current position\, he was a Research Scientist at Columbia University in New York from 2013-2015 and a Postdoctoral Fellow at the University of Texas at Austin from 2009-2013. He completed his PhD. in Materials Science and Engineering from the University of Florida in 2009. His current research focuses on modeling active matter systems such as assemblies of driven cytoskeletal filaments\, cellular collectives on 2D and in 3D environments\, and tissue dynamics during processes such as wound-healing and cancer. His research is funded by grants from the US National Science Foundation\, Department of Defence Army Research Office and the National Institutes of Health. He was awarded the 2021 Outstanding Leadership in Engineering Award by the San Diego County Engineering Council for his efforts on transforming engineering education and training at San Diego State University.
URL:https://be.iisc.ac.in/event/seminar-by-dr-parag-katira-on-mechanics-of-cancer/
LOCATION:M Tech Classroom\, BSSE Annex
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20221205T110000
DTEND;TZID=UTC:20221205T120000
DTSTAMP:20260406T020333
CREATED:20221128T233152Z
LAST-MODIFIED:20221128T233152Z
UID:4392740-1670238000-1670241600@be.iisc.ac.in
SUMMARY:Seminar by Dr. Vinaya Simha on Lipodystrophy and Insulin Resistance
DESCRIPTION:Speaker Name and Affiliation: Dr. Vinaya Simha\, Mayo Clinic (currently Satish Dhawan visiting professor at IISc) \nSeminar Title: Lipodystrophy and Insulin Resistance: Lessons learned and to be learned \nAbstract: Lipodystrophy syndromes are a diverse group of congenital and acquired disorders characterized by selective fat loss and features of marked insulin resistance including early-onset diabetes\, hyperlipidemia and hepatic steatosis. Much progress has been made recently in understanding the molecular basis of fat loss and metabolic complications. It has also thrown light on the pathogenesis of insulin resistance in obesity and metabolic syndrome and the importance of adipocyte endocrine function. Recent studies focusing on muscle mitochondrial dysfunction in lipodystrophy may help to further elucidate mechanisms of insulin resistance contributing to diabetes and dyslipidemia. \nBrief Bio of Speaker: Prof. Simha is an Associate Professor of Medicine at the Mayo Clinic College of Medicine and Science and a Consultant in Endocrinology in the Department of Internal Medicine at Mayo Clinic\, Rochester\, Minnesota. He has won numerous awards\, the latest of which is the 2018 Laureate Award from the Mayo Clinic. He has been an active clinical practitioner and researcher\, specializing in diabetes and other endocrine disorders and their complications. He has been and is currently an investigator on several NIH grants and the lead investigator/director on clinical trials supported by the pharmaceutical industry.
URL:https://be.iisc.ac.in/event/seminar-by-dr-vinaya-simha-on-lipodystrophy-and-insulin-resistance/
LOCATION:CES Seminar Hall\, CES Seminar Hall\, 3rd Floor\, Biological Science Building
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20221202T150000
DTEND;TZID=UTC:20221202T160000
DTSTAMP:20260406T020333
CREATED:20221125T055815Z
LAST-MODIFIED:20221125T060318Z
UID:4392711-1669993200-1669996800@be.iisc.ac.in
SUMMARY:Guest Lecture by Dr. Andrew Holle on "Tight squeeze: Engineering confinement for mechanobiology research"
DESCRIPTION:Abstract:  \nSelf-induced cellular confinement has been shown to play a role in a wide variety of biological processes\, including cancer invasion and metastasis\, immune cell navigation\, and mechanosensitive gene expression and localization. However\, the ability of adult stem cells to enter tight confinements has been less studied\, despite the fact that stem cells are capable of finely tuned mechano-transduction\, must migrate from their home niche to their regenerative niche\, and have been shown to integrate past stimuli in a form of ‘mechanical memory’. Here\, we characterize the interstitial spaces in cleared tissue\, providing a physiological basis for the design of biomimetic microchannel devices. Next\, we show that adipose-derived stem cells (ASCs) and bone marrow stem cells (hMSCs) are capable of entering and permeating PDMS-based microchannels as narrow as 3 µm. Patterns of microchannel permeation as a function of width are similar to those found in cancer cells\, despite the fact that these stem cells are more well-spread and exhibit higher cell diameters. Both narrow and wide confinements were shown to induce an upregulation of the osteogenic differentiation marker CBFA1. Interestingly\, narrow confinements led to enhanced CBFA1 nuclear localization compared to wide channels\, suggesting that the level of confinement imposed upon a stem cell via its extracellular environment ultimately plays a role in differentiation. In conjunction with these changes in fate\, stem cells exposed to confinement also showed significant changes in epigenetic state as measured by H3K9Ac localization. Future work will ultimately discern if the migratory journey a stem cell undergoes during development and regeneration\, and the confinement it experiences along the way\, drive tissue-specific stem cell differentiation \nAbout the Speaker: \nDr. Andrew Holle is currently an Assistant Professor at the Department of Biomedical Engineering\, National University of Singapore (NUS) and the Principal Investigator at the Mechanobiology Institute\, NUS. He received Ph.D. at the University of California\, San Diego\, where he worked in Prof. Adam Engler’s Stem Cell Biology and Bioengineering group. He identified the mechanosensitive role of the focal adhesion protein vinculin in substrate stiffness-induced stem cell differentiation. Looking to explore the commonalities between stem cells and cancer mechanobiology\, he then joined Prof. Joachim Spatz’s Cellular Biophysics group at the Max Planck Institute for Medical Research (Stuttgart\, Germany). He used photolithography and microfluidics to build microchannel assays better to characterize cancer cell invasion and migration in confinement. His current work at the Mechanobiology Institute and in the NUS Biomedical Engineering department is focused on the role of confinement in mechanobiology\, with an emphasis on novel strategies for controlling stem cell differentiation.
URL:https://be.iisc.ac.in/event/guest-lecture-dr-andrew-holle-tight-squeeze-engineering-confinement-for-mechanobiology-research/
LOCATION:M Tech Classroom\, BSSE Annex
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Asia/Kolkata:20220926T143000
DTEND;TZID=Asia/Kolkata:20220926T153000
DTSTAMP:20260406T020333
CREATED:20220924T000728Z
LAST-MODIFIED:20220924T001126Z
UID:4392413-1664202600-1664206200@be.iisc.ac.in
SUMMARY:Guest Lecture by Dr. Jason T. George  on "Stochastic modeling of the tumor-immune interaction"
DESCRIPTION:Abstract: “Harnessing the adaptive immune system to recognize and eliminate cancer cells has ushered in T cell-based immunotherapies\, which have revolutionized cancer treatment by inducing durable remission for many patients. Due to the immense complexity of T cell immunotherapy\, nearly all attempts to improve these approaches and to expand their applications have been driven empirically. To predict treatment failure and optimize current therapies\, we must understand the dynamic interplay between an adaptive immune system and an evolving cancer population. My talk will describe stochastic modeling that our group has been actively developing\, which include random energy models of the T cell receptor-antigen interface developed to characterize immune recognition potential against tumor antigens\, and dynamical models of the interaction between an evolving cancer population and an adaptive immune system. \nAbout the speaker: Jason T. George is an assistant professor in the Department of Biomedical Engineering at Texas A&M University. His research interests lie at the intersection of engineering and applied mathematics\, where he focuses on developing dual theoretical and data-driven mathematical models to characterize cancer development and evasion with the goal of improving treatment outcomes. Prior to joining A&M\, Dr. George was a postdoctoral fellow in the Center for Theoretical Biological Physics at Rice University. He was a student in the Medical Scientist Training Program where he earned his M.D. at Baylor College of Medicine and Ph.D. in the Department of Bioengineering at Rice University under the mentorship of Herbert Levine. Prior to this\, Dr. George completed his undergraduate training at Texas A&M University\, where he earned a B.S. in Biomedical Engineering and a B.A. in Mathematics. Dr. George is the recipient of the CPRIT First-Time Tenure-Track Faculty Recruitment Award. His graduate thesis work was funded by a Ruth L. Kirschstein Fellowship through the NIH National Cancer Institute.
URL:https://be.iisc.ac.in/event/guest-lecture-by-dr-jason-t-george-on-stochastic-modeling-of-the-tumor-immune-interaction/
LOCATION:M Tech Classroom\, BSSE Annex
CATEGORIES:Seminar
ORGANIZER;CN="BSSE%20Seminar%20Team":MAILTO:seminars.bsse@iisc.ac.in
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20220328T163000
DTEND;TZID=UTC:20220328T173000
DTSTAMP:20260406T020333
CREATED:20220327T221341Z
LAST-MODIFIED:20220327T221516Z
UID:4392186-1648485000-1648488600@be.iisc.ac.in
SUMMARY:Seminar: Microenvironment regulation of metastasis
DESCRIPTION:The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend a departmental seminar. \n  \nSpeaker: Dr. Kandice Tanner\, National Cancer Institute\, NIH
URL:https://be.iisc.ac.in/event/seminar-microenvironment-regulation-of-metastasis/
LOCATION:Online
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20220307T160000
DTEND;TZID=UTC:20220307T170000
DTSTAMP:20260406T020333
CREATED:20220305T231405Z
LAST-MODIFIED:20220305T231405Z
UID:4392176-1646668800-1646672400@be.iisc.ac.in
SUMMARY:Discoveries in natural light sensing and probing cellular dynamics: an interdisciplinary approach and a need for engineering in biology
DESCRIPTION:The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend a departmental seminar.Speaker: Dr. Akash Gulyani\, Department of Biochemistry\, School of Life Sciences\, University of Hyderabad
URL:https://be.iisc.ac.in/event/discoveries-in-natural-light-sensing-and-probing-cellular-dynamics-an-interdisciplinary-approach-and-a-need-for-engineering-in-biology/
LOCATION:Online
CATEGORIES:Seminar
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20220223T160000
DTEND;TZID=UTC:20220223T180000
DTSTAMP:20260406T020333
CREATED:20220221T043429Z
LAST-MODIFIED:20220221T043439Z
UID:4392095-1645632000-1645639200@be.iisc.ac.in
SUMMARY:Mechanobiology of Liver Cirrhosis: The Role of Hepatocytes in Fibrosis Progression
DESCRIPTION:The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend an Annual Work Presentation. \nStudent: Anwesha Barua  (BSSE) \nAdvisors: Prof. G.K. Ananthasuresh (ME) and Prof. Saumitra Das (MCB)
URL:https://be.iisc.ac.in/event/mechanobiology-of-liver-cirrhosis-the-role-of-hepatocytes-in-fibrosis-progression/
LOCATION:Online
CATEGORIES:Announcement
END:VEVENT
END:VCALENDAR