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X-WR-CALDESC:Events for Department of Bioengineering
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DTSTART:20230101T000000
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BEGIN:VEVENT
DTSTART;TZID=UTC:20230213T160000
DTEND;TZID=UTC:20230213T170000
DTSTAMP:20260412T182522
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:20230214T100000
DTEND;TZID=UTC:20230214T110000
DTSTAMP:20260412T182522
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:20230215T120000
DTEND;TZID=UTC:20230215T130000
DTSTAMP:20260412T182522
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:20230220T160000
DTEND;TZID=UTC:20230220T170000
DTSTAMP:20260412T182522
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:20230221T110000
DTEND;TZID=UTC:20230221T120000
DTSTAMP:20260412T182522
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:20230222T110000
DTEND;TZID=UTC:20230222T120000
DTSTAMP:20260412T182522
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:20230223T143000
DTEND;TZID=UTC:20230223T153000
DTSTAMP:20260412T182522
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:20230227T160000
DTEND;TZID=UTC:20230227T170000
DTSTAMP:20260412T182522
CREATED:20230220T221755Z
LAST-MODIFIED:20230220T221946Z
UID:4393589-1677513600-1677517200@be.iisc.ac.in
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
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