====Abhishek Upadhyay (Abhi) ==== {{:members:upadhyay:abhiclock.jpg?215 |}} **[[Education & Research experiences]]**\\ Postdoctoral fellow (Developmental Chronobiology) @ Friedrich Miescher Institute (FMI), Basel, SWITZERLAND\\ \\ **Ph.D (Chronobiology, Molecular Systems Biology)** 2016-20 \\ **cumulative thesis**: **"Molecular switches facilitate rhythms in the circadian clock of //Neurospora crassa//"** in supervision @ Charite & Humboldt University of Berlin (HU) & co-supervision @ Heidelberg University, GERMANY\\ \\ Predoctoral fellow (Evolutionary Biology) @ University of Witwatersrand (Wits), Johannesburg, SOUTH AFRICA\\ \\ **M.Phil (Marine Biology, Proteomics, Climate Change)** 2013-15 @ The University of Hong Kong (HKU), HONG KONG\\ \\ Premasters fellow @Indian Institute of Science (IISc), INDIA\\ \\ **B.Eng (Biotechnology Engineering)** 2008-12 , INDIA\\ \\ //__**"Timing matters !"**__// \\ \\ \\ ===== THEORETICAL CHRONOBIOLOGY GROUP MEETINGS DIRECTORY ===== [ Seminar of the __**Hanspeter Herzel Group**__ ([[https://scholar.google.com/citations?hl=en&user=4uT7ljsAAAAJ|Hanspeter_Scholar]] and [[https://itb.biologie.hu-berlin.de/wiki/groups/herzel/start|Hanspeter_Web]]). We met every __**Tuesday at 14:45**__ in the Haus4 seminar room(s) of the ITB unless stated otherwise. Seminar list was compiled by Abhi ([[https://medium.com/@abhiup01/how-a-switch-between-doing-science-and-playing-soccer-with-phd-supervisor-motivates-my-research-803a0bf5b1c6|Abhi_Medium]]) since 05.12.2017 until 30.07.2020]\\ \\ {{:members:upadhyay:1.jpg?300 |}} {{:members:upadhyay:group_pic2.jpg?300|}} {{:members:upadhyay:herzel_group_virtual_pic_2020.jpg?300|}} {{ :members:upadhyay:seasonal_rhythm_from_my_lab_window_berlin-1.jpg?300|}} {{ :members:upadhyay:brunnergrouppic1.jpg?300|}} \\ \\ \\ \\ **28.07.2020 **\\ **Summer vacation**\\ \\ **14.07.2020 **\\ **Christoph**\\ Compensation Mechanisms in the Mammalian Circadian Clock \\ \\ **07.07.2020 **\\ **Stephanie**\\ East-West Asymmetry in Recovery from Jetlag \\ \\ **30.06.2020 **\\ **Rebekka**\\ Circadian Rhythms: Data Analysis and Mathematical Modelling \\ \\ **23.06.2020 **\\ **All**\\ SRBR2020 debriefing \\ \\ **16.06.2020 **\\ **Maria**\\ Human chronobiology in Sydney \\ \\ **09.06.2020 **\\ **Bharath**\\ Modeling the cockroach circadian clock \\ \\ **01.06.2020 - 03.06.2020 **\\ **SRBR 2020**\\ https://srbr.societyconference.com/v2/ \\ \\ **26.05.2020**\\ **Hanspeter**\\ Q&A session on basics of statistics-II \\ \\ **19.05.2020**\\ **Hanspeter**\\ Q&A session on basics of statistics-I \\ \\ **12.05.2020**\\ **Hanspeter**\\ The dynamic origin of genomic isochores \\ \\ **05.05.2020**\\ **Anna**\\ Peripheral circadian oscillators couple via exchange of paracrine signaling molecules, including TGF-β \\ \\ **28.04.2020**\\ **Nora**\\ Inferring signaling pathways activation from circadian time series using PROGENy \\ \\ **21.04.2020**\\ **Inge**\\ Nonlinear dynamics in models of the circadian clock \\ \\ **14.04.2020**\\ **Abhi**\\ Multiple random phosphorylations provide long delays and switches in //Neurospora// clock \\ \\ **07.04.2020**\\ **Marta**\\ Progress report on anna's manuscript: mechanisms of intercellular coupling among peripheral circadian oscillators \\ \\ **31.03.2020**\\ **Everyone**\\ Updates to Hanspeter\\ \\ \\ **Following COVID-19 guidelines we switched to "online virtual meetings (via ITB zulip jitsi and/or Zoom)" while working from home offices since 16.03.2020**\\ \\ \\ **10.03.2020**\\ **Ecegül**\\ Amplitudes and phases of clock genes in mammalian tissues \\ **Hanspeter**\\ Chronobiology and network theory \\ \\ **25.02.2020**\\ **Hanspeter**\\ Brainstorming: Control of circadian phases \\ \\ **11.02.2020**\\ **Hanspeter**\\ Strange nonchaotic attractors \\ \\ **04.02.2020**\\ **Abhi**\\ **1)** Introduction to kinetic proofreading (KPR)\\ **2)** CK1a role in //Neurospora// clock \\ \\ **28.01.2020**\\ **Christoph**\\ Ending the message: Alternative Polyadenylation in U-2 OS \\ \\ **21.01.2020**\\ **Abhi**\\ Perspectives on multisite phosphorylation \\ \\ **14.01.2020**\\ **Bharath**\\ Exact Confidence Intervals for Circadian Parameters \\ \\ **07.01.2020**\\ **Nora**\\ inferring signaling pathways activity from time-series gene expression data \\ \\ **17.12.2019**\\ discussion regarding GCC meeting March, 2020 \\ \\ **10.12.2019**\\ **Christoph**\\ New manuscript under prep: clocks in the wild- entrainment and seasonality related \\ \\ **03.12.2019**\\ **Andreas (Dresden)**\\ The mathematics of brain tumour invasion and progression \\ \\ **19.11.2019**\\ **No meeting**\\ Raghavendra's talk at ITB seminar \\ \\ **12.11.2019**\\ **Hanspeter**\\ brainstormings \\ \\ **05.11.2019**\\ **Gregor (Heidelberg)**\\ Spatially resolved Wavelet Analysis of SCN slices \\ \\ **29.10.2019**\\ **Hanspeter, Christoph & Bharath**\\ PRCs, jet-lag, seasonality: data and models \\ \\ **22.10.2019**\\ **Leylanur**\\ Tissue-specific regulation of clock-controlled genes- Learning from MyoD1 in muscle\\ **Abhi**\\ impressions from LASC-2019 Uruguay meeting \\ \\ **15.10.2019**\\ **Anna**\\ Potential mechanism of intercellular coupling between peripheral circadian oscillators \\ \\ **24.09.2019**\\ **Nikhil**\\ Heritable gene expression variability governs clonal heterogeneity in circadian period \\ \\ **17.09.2019**\\ **Anne**\\ Statistical Analysis of Circadian Rhythms in Mice Liver under Different Diets \\ \\ **03.09.2019**\\ **Hanspeter**\\ impressions from EBRS, Lyon https://www.ebrs2019.com/ \\ \\ **13.08.2019**\\ **Sara (Zurich)**\\ The Forebrain Synaptic Transcriptome Is Organized by Clocks, but Its Proteome Is Organized by Sleep \\ \\ **30.07.2019**\\ **Literature seminar**\\ everyone \\ \\ **23.07.2019**\\ **Gordon and interesting papers/reviews**\\ Gordon Chronobiology 2019 conference impressions \\ \\ **02.07.2019**\\ **Muge**\\ Update on master thesis: Time Series Analysis of Circadian Rhythms in Single Cells– Effect of Cell Cycle \\ \\ **18.06.2019**\\ **Peter (Newzealand)**\\ Origin of genetic coding and deep phylogeny of aaRS coding enzymes. \\ \\ **28.05.2019**\\ **Hanspeter**\\ Lecture: Simulating stochastic oscillations \\ \\ **21.05.2019**\\ **Bharath**\\ Analysing circadian datasets at ultradian timescales. \\ \\ **07.05.2019**\\ **Christof's lab**\\ Discussion about experimental data and modelling. \\ \\ **30.04.2019**\\ **Patrick's PhD defense**\\ Systems level generation of mammalian circadian rhythms and its connection to liver metabolism. \\ \\ **25.04.2019**\\ **Patrick's rehearsal**\\ rehearsal on 14:00. \\ \\ **23.04.2019**\\ **Claudia (Münster)**\\ The analysis of resource allocation in the genetic material as a tool to link molecular evolution to ecosystems biology. \\ \\ **16.04.2019**\\ **Marta**\\ Discussion/presentation about the next projects. \\ \\ **09.04.2019**\\ **Abhi**\\ Discussion/presentation about the next projects. \\ \\ **19.03.2019**\\ **Brainstorming with Hanspeter**\\ How to write research papers, project thesis. \\ \\ **05.03.2019**\\ **Müge**\\ The phase shifting effects of Cisplatin on Single Cell Traces \\ \\ **12.02.2019**\\ ** Dieter **\\ topic of his interest \\ \\ **05.02.2019**\\ **Brainstorming with Hanspeter**\\ Scientific career : goldmine or minefield \\ \\ **29.01.2019**\\ **Marta**\\ Ojalvo model: spontaneous synchronization \\ \\ **22.01.2019**\\ **Discussion: Hanspeter, Marta and Abhi**\\ Some interesting fundamental biochemical oscillators \\ \\ **15.01.2019**\\ **Erich (Muenster)**\\ Brainstorming with Bornberg-Bauer - everybody could present his/her project briefly \\ \\ **08.01.2019**\\ **Jan**\\ Bachelors Thesis (Uwe Ohler Group @MDC Berlin): Revealing the regulatory effect of RNA-binding proteins on transcript abundances in single cell studies \\ \\ **Happy New Year 2019** \\ \\ **27.11.2018**\\ **Janita**\\ Masters rotation: Nonsinusoidal transcription rhythms in the mouse liver \\ \\ **20.11.2018**\\ **Discussion: Hanspeter & Christoph**\\ Some interesting fundamental biochemical oscillators\\ \\ **07.11.2018**\\ **Dorothee (Bielefeld)**\\ Everyone's brief presentation of their project's state of the art\\ \\ **30.10.2018**\\ **All**\\ Literature seminar\\ \\ **23.10.2018**\\ **Hanspeter**\\ Lecture: Understanding diffusion, super diffusion and sub diffusion using the Kubo formula\\ \\ **16.10.2018**\\ **Hanspeter**\\ Lecture: Time series analysis: ARIMA models\\ \\ **09.10.2018**\\ **Pablo (Kassel)**\\ Multi-scale electrical activity in Cockroach circadian clock\\ \\ **08.10.2018**\\ **Kwangwon (USA)**\\ Fitness in a microbe: how the circadian clock is shaped by the environment\\ \\ **18.09.2018**\\ **Hanspeter**\\ Lecture: Floquet multipliers and intermittency\\ \\ **11.09.2018**\\ **Isao (Japan)**\\ Single cell analysis of Arabidopsis circadian clock and its mathematical modeling\\ \\ **04.09.2018**\\ **Hanspeter**\\ Lecture: Fractal basin boundaries\\ \\ **31.07.2018 to 28.08.2018**\\ **Summer Holidays Intermission**\\ Group meetings would resume from 04.09.2018 \\ \\ **17.07.2018**\\ **Elmir**\\ Master thesis report: Modelling of gene regulatory network in mammalian circadian clock\\ \\ **10.07.2018**\\ **Hanspeter and others**\\ Literature seminar\\ \\ **03.07.2018**\\ **Bharath, Patrick, Marta, Abhi and Hanspeter**\\ Impressions from the SRBR Florida, EMBL Heidelberg, Solvay Brussels\\ \\ **26.06.2018**\\ **Hanspeter**\\ Impressions from the SRBR Florida conference\\ \\ **19.06.2018**\\ **Pietro**\\ Bachelors thesis project: A mathematical model of cannabinoids' kinetics in dairy cow's milk \\ \\ **12.06.2018**\\ **Christoph**\\ Dissociation of Bmal1 and Per1 rhythms (results from the work being done in Japan) \\ \\ **29.05.2018**\\ **Hanspeter**\\ Lecture: How to write a thesis? \\ \\ **22.05.2018**\\ **Anton**\\ Masters thesis project: Emerging properties of systems of oscillators in regard to SCN desynchronization \\ \\ **09.05.2018**\\ **Wolfram**\\ Master Thesis (@EBI Cambridge, UK) defense: Gene un-prediction: Developing a new method to identify spurious protein sequences \\ \\ **24.04.2018**\\ **Tanmay**\\ Emergence of memory and learning in intra-cellular signaling networks:where reverberations meet Arnold tongue \\ \\ **17.04.2018**\\ **General discussions**\\ Papers, meetings feedbacks, next! \\ \\ **03.04.2018**\\ **Abhi, Marta**\\ Project's state of the art \\ \\ **27.03.2018**\\ **Hanspeter**\\ Lecture: Numerics of Ordinary and Stochastic Differential Equations (ODEs and SDEs) \\ \\ **20.03.2018**\\ **Philipp**\\ Defense: Master's Thesis\\ **Patrick**\\ Manuscript discussion \\ \\ **06.03.2018**\\ **Elmir**\\ Project: state of the art \\ \\ **20.02.2018**\\ **Bharath**\\ Paper: Positive Feedback Promotes Oscillations in Negative Feedback Loops [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104761#abstract0]] \\ \\ **30.01.2018**\\ **Anton**\\ Introduction of himself & recent masters project \\ \\ **23.01.2018**\\ **Hanspeter**\\ Lecture: Harmonics and ultradian rhythms \\ \\ **16.01.2018**\\ **Christoph**\\ Choroid plexus as an important circadian clock \\ \\ **09.01.2018**\\ **Abhi**\\ Paper: DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition \\ \\ **02.01.2018**\\ **New Year 2018 Welcome, Group Meet**\\ \\ **19.12.2017**\\ **Hanspeter**\\ Lecture: Probability density\\ \\ **12.12.2017**\\ **Bharath**\\ Analysis of neuronal spikes data\\ \\ **05.12.2017**\\ **Hanspeter**\\ Lecture: Fat Fractals\\ \\ **27.11.2017**\\ **Takayuki**\\ TBA\\ \\ **14.11.2017**\\ **Abhishek**\\ State of the art of project mathematical modelling of //Neurospora// circadian clock\\ \\ **07.11.2017**\\ **Philipp**\\ Temperature entrainment in Neurospora crassa\\ \\ **24.10.2017**\\ **Lars**\\ Predictability of circadian transcripts via ChIP-seq analysis\\ \\ **17.10.2017**\\ **Marta**\\ TBA\\ \\ **10.10.2017**\\ **Adrian**\\ Circadian Clock & Cell Cycle: Effects on Breast Cancer Radio and Chemotherapy\\ \\ **26.09.2017**\\ **Wolfram**\\ Predicting ribosome stalling events and their linkage to protein secondary structure\\ \\ **05.09.2017**\\ **Christoph, Hanspeter**\\ Gordon, USA and EBRS, Amsterdam Meetings Reports\\ \\ **29.08.2017**\\ **Isao, Bharath, Hanspeter**\\ Gordon Meeting Report https://www.grc.org/chronobiology-conference/2017/ \\ \\ **22.08.2017**\\ **Abhi (Poster Abstract P142), Marta, Patrick**\\ Gordon and EBRS Meetings Reports http://www.nin-meeting.nl/\\ \\ **11.07.2017**\\ **Carl H. Johnson (USA)**\\ Temperature and Metabolic Compensation\\ \\ **07.07.2017**\\ **Everyone**\\ Their projects briefly to Carl Johnson\\ \\ **27.06.2017**\\ **Carl H. Johnson (USA)**\\ Is the TTFL the Core Circadian Pacemaker? An Alternative Perspective\\ \\ **30.05.2017**\\ **Abhishek**\\ Paper: The frequency natural antisense transcript first promotes, then represses, frequency gene expression via facultative heterochromatin \\ \\ **23.05.2017**\\ **Sarah**\\ Paper: Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver http://www.cell.com/cell-metabolism/abstract/S1550-41311630534-4 \\ \\ **09.05.2017**\\ **All**\\ Symposium on Theoretical Chronobiology, Lille, France\\ \\ **18.04.2017**\\ **Bharath**\\ Paper: Phosphorylation Is a Central Mechanism for Circadian Control of Metabolism and Physiology http://www.sciencedirect.com/science/article/pii/S1550413116305356 \\ \\ **28.03.2017**\\ **Patrick**\\ Snakemake\\ \\ **21.03.2017**\\ **Christoph**\\ Quantifying Coupling Strength of Circadian Oscillators\\ \\ **14.03.2017**\\ **Patrick**\\ Circadian clock and liver metabolism\\ \\ **07.03.2017**\\ **Isao Tokuda, Japan**\\ Variable entrainment property of //Arabidopsis// circadian clock by collective phase sensitivity\\ \\ **28.02.2017**\\ **Abhishek**\\ //Neurospora crassa//: introduction of its biology, circadian clock & mathematical models\\ \\ **14.02.2017**\\ **Layal**\\ RNA-seq data analysis, differential gene expression and alternative splicing\\ \\ **07.02.2017**\\ **All**\\ Literature Seminar\\ \\ **31.01.2017**\\ **Martin**\\ Circadian activity of two Drosophila species\\ \\ **17.01.2017**\\ **All**\\ Literature Seminar\\ \\ **20.12.2016**\\ **Jihwan Myung, Taiwan**\\ Philosophizing and Physiologizing on Time and Mood in the Brain\\ \\ **12.12.2016**\\ **Hanspeter**\\ Maximum-Entropy Principle\\ \\ **06.12.2016**\\ **Hanspeter**\\ Modeling diffusion processes\\ \\ **22.11.2016**\\ **All**\\ Literature Seminar\\ \\ **08.11.2016**\\ **Matthias**\\ TBA\\ \\ **02.11.2016**\\ **Bharath**\\ Analysis of Circadian Cellular Bioluminescence Recordings using a Kalman Smoother\\ \\ **25.10.2016**\\ **Sarah**\\ Mitochondrial Network Morphology\\ \\ **18.10.2016**\\ **Patrick**\\ Vectorfield Optimization\\ \\ **04.10.2016**\\ **Hanspeter, Patrick**\\ Impressions From the ICSB Spain Meeting http://www.crg.eu/sites/default/files/ICSB2016_anuncio%20A4_29-01-2016_0.jpg\\ \\ **27.09.2016**\\ **Bharath**\\ Quantifying firing properties of VIP neurons\\ \\ **12.07.2016**\\ **Felix**\\ Verteidigung Masterarbeit\\ \\ **28.06.2016**\\ **Hanspeter**\\ SRBR USA Summary https://srbr.org/wp-content/uploads/2015/10/SRBR-2016-Program-Book-with-abstracts.pdf\\ \\ **21.06.2016**\\ **Abhishek**\\ Masters presentation cum PhD interview\\ \\