August 10-11,2020, 1:00 PM to 6:30PM IST

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Inaugural Session ScheduleDay 1: Monday, August 10, 2020
IST

GMT+1

Title

Speaker

13:00-13:30

8:30-9:00

Registration of Participants

13:30-14:30

9:00-10:00

Inaugural program

13.30-13.40

9.00-9.10

Introduction to the SPARC program

Sharad K Soni

13.40-13.50

9.10-9.20

Welcome to participants andIntroduction to Partcipating Labs-I:

Shandar Ahmad

13,50-14.00

9.20-9.30

Introduction to Partcipating Labs-II:
Nicoletta Lab

Nicoletta Bobola

14.00-14.10

9.30-9.40

Introduction to Partcipating Labs-III:
Rakesh Bhatnagar’s lab

Rakesh Bhatnagar

14.10-14.20

9.40-9.50

Introduction to Partcipating Labs-IV:
Rupesh Chaturvedi’s lab

Rupesh Chaturvedi

14.20-14.30

9.50-10.00

Inaugual address by the Chief Guest

M Jagdesh Kumar

Inaugural Speakers

M Jagadesh Kumar
Vice-Chancellor, JNU,
(Chief Guest)

Shandar Ahmad
SCIS, JNU(SPARC PI & Host)

Nicoletta Bobola
The Univ. of Manchester(Principal collaborator)

Rakesh Bhatnagar(Vice-Chancellor, BHU)
SBT, JNU (SPARC Co-PI)

Sharad Soni
(InternationalCollaboration Unit, JNU)

Rupesh Chaturvedi
SBT, JNU(SPARC Co-PI)

Day 1 ScheduleDay 1: Monday, August 10, 2020
ISTGMT+1Title

Speaker

13:00-13:30

8:30-9:00

Registration of Participants

13:30-14:30

9:00-10:00

Inaugral program
Session-I (Chair: Shandar Ahmad)

14:30-15:15

10:00-10:45

Human embryonic development/organogenesis

Nicoletta Bobola

15:15-16:00

10:45-11:30

Rewiring of Transcriptional Regulators in the
Human Fungal Pathogen Candida albicans

Krishnamurthy
Natarajan

16:00-16:15

11.30-11:45

BREAK
Session-II (Chair: K. Natarajan)

16:15-17:00

11:45-12:30

Retinoic acid signaling regulates morphogenesis ofthe developing forebrain roof plate

Jonaki Sen

17:00-17:45

12:30-13:15

Transcriptional control and effects of mutations inregulatory elements during development

Araceli Garcia
Mora

17:45-18:30

Sequence, structure and conformational dynamics
13:15-14:00 signatures in genome wide regulatory programs of Shandar Ahmad
transcription factors

18:15-18:30

13:45-14:00

Valedictory Program

Session Chairs

Shandar Ahmad

Krishnamurthy Natarajan

Speakers

Nicoletta Bobola

KrishnamurthyNatarajan

Jonaki Sen

Araceli Garcia Mora

Shandar Ahmad

Day 2 ScheduleDay 2: Tuesday, August 11, 2020
Session-III (Chair: Mukesh Jain)
13:30-14:15

9:00-9:45

Patterning and morphogenesis/ molecular control

14:15-15:00

9:45-10:30

Sequence and structural variations in slow and fast
Manisha Kalsantranscription factor binding sites

15:00-15:45

10:30-11:15

15:45-16:00

11:15-11:30

Transcriptional signature modulating plantarchitectural traits enhances chickpea yield

Nicoletta Bobola

Swarup K Parida

BREAK

Session-IV (Chair: Brojen Singh)
16:00-16:45

11:30-12:15

Unified representation of single cells states withpathways and its utility for developmental biology
and stem cell studies

16:45-17:30

12:15-13:00

Identifying diversity in transcriptional regulationfrom high-throughput experiments

Leelavati Narlikar

17:30-18:15

13:00-13:45

Genomics and Molecular genetics approaches tostudy Transcription Factor function.

Arnab
Mukhopadhyay

18:15-18:30

13:45-14:00

Vibhor Kumar

Valedictory Program

Session Chairs

Mukesh Jain
SCIS, JNU

R.K.Brojen SinghSCIS, JNU

Speakers

Nicoletta Bobola

Manisha Kalsan

Swarup K Parida

Vibhor KumarLeelavati
Narlikar

Arnab
Mukhopadhyay

Inaugural Program Speakers

M Jagadesh Kumar Rakesh Bhatnagar Shandar Ahmad
Vice-Chancellor,(Vice-Chancellor,SCIS, JNU
JNU, (Chief Guest)
BHU), SBT, JNU(SPARC PI & Host)(SPARC Co-PI)

Nicoletta Bobola
The Univ. ofManchester, UK(Principalcollaborator)

Sharad Soni
Int. Collab Unit
(ICU), JNU

Rupesh Chaturvedi
SBT, JNU(SPARC Co-PI)

Technical Session Speakers
Nicoletta Bobola
The University ofManchester, UnitedKingdom

Jonaki Sen
Indian Institute ofTechnology, Kanpur

Krishnamurthy Natarajan
School of Life Sciences,
JNU

Arnab Mukhopadhyay
National Institute ofImmunology, New Delhi

Swarup K Parida
National Institute of Plantand Genomics Research,
New Delhi

Vibhor Kumar
Indraprastha Institute ofInformation Technology,
New Delhi

Leelavati Narlikar
CSIR- National ChemicalLaboratory, Pune
Araceli Garcia Mora
The University ofManchester, UnitedKingdom

Shandar Ahmad
School of Computational &Integrative Sciences, JNU
Manisha Kalsan
School of Computational &Integrative Sciences,
JNU

Introduction to Technical Session Speakers
SHANDAR AHMAD
Shandar Ahmad is a Computational Biologist interested in the role of genomic
DNA shape in transcription factor/ target interactions and he investigates thisusing machine learning and deep learning techniques. Currently, the Dean of
School of Computational & Integrative Sciences, Jawaharlal Nehru University, heheads SciWhyLab, which is involved in an integrated approach to study life
science and health related problems. Relevant to this workshop, his works on
predicting DNA-binding proteins, genomic DNA conformational ensemble
dictionaries, integrative functional annotations employing transcriptomic,
sequence and structure based signatures and clustering patterns of conserved
residues in transcription factors are some of the techniques he has developed.
NICOLETTA BOBOLA
Nicoletta Bobola is Professor of Developmental Biology and Genomics at the University ofManchester, UK. She obtained her PhD at the University of Genoa, Italy; as part of her
training and during her postdocs, she worked in Austria, Germany and the USA. She firstestablished her independent group at the Max-Plack Institute of Immunobiology in Freiburg(Germany) and later moved to the University of Manchester as Lecturer in 2006. She has a
career-long expertise in the field of transcriptional regulation. Her research aims atunderstanding how transcription factors instruct gene expression programs to generate
specific cell fates in vertebrate embryonic development, using mouse and zebrafish modelsystems (Development 2003, 2005 and 2008; Dev Biol 2009; MCB 2011, Nucleic AcidsResearch 2012; Development 2013; Dev Cell 2015; Elife 2017; Elife 2018). A complementaryarea of research investigates the role of the non-coding genome in instructing humandevelopment, and how changes in non-coding regulatory information lead to disease (Elife2016; Nat Comm 2020).
JONAKI SEN
Jonaki Sen completed her graduate studies from Albert Einstein College of Medicine, NewYork, where she studied the development of dorsal-ventral polarity in the Drosophila
embryo. This was followed by postdoctoral studies on vertebrate retinal development in thelaboratory of Prof. Constance Cepko in the Genetics Dept. at Harvard Medical School,Boston. At present, she is a Professor in the Department of Biological Sciences andBioengineering at IIT Kanpur. The research interest of her laboratory lies in understanding
various aspects of neuronal development. Her group studies the molecular mechanismsthat regulate morphogenesis, differentiation and neuronal migration, using the chick andmouse embryo as models.
KRISHNAMURTHY NATARAJANKrishnamurthy Natarajan is currently a Professor at the Laboratory of Eukaryotic Gene
Regulation in School of Life Sciences, JNU, Delhi. His broad area of research is Cell andMolecular biology/Molecular genetics: Transcription, chromatin and gene regulation withspecialized work in TAF complexes and Mechanism of Transcription in Saccharomyces
cerevisiae, Candida albicans; Gene regulation during Iron Homeostasis in Candida
albicans and Transcriptional Regulatory Network controlling Melanogenesis and pigment
disorders using Mouse Melanoma cell lines. He is also a Co-founder of Ahammune
Biosciences which focuses on translating scientific research to provide a treatment toimmunity based dermatological disorders such as vitiligo.
ARNAB MUKHOPADHYAY
Arnab Mukhopadhyay is currently Staff Scientist VI at the National Institute of Immunology(NII), New Delhi. He completed his MSc (1997) and PhD (2003) in Plant Molecular Biology
from Delhi University South Campus followed by a postdoctoral stint (2003-2008) atUMASS medical school, Worcester, Massachusetts, USA. Since 2009, his lab at NII has
been studying various molecular mechanisms of aging and longevity assurance usingCaenorhabditis elegans as the model system. He is an elected fellow of The National
Academy of Science, India (NASI) and Guha Research Conference (GRC) Society. He is arecipient of the Ramalingaswami Re-entry Fellowship (2009-2014), National BioscienceAward for Career Development (2016) and SERB-Science Technology Award for Research(STAR) award (2019).

SWARUP K PARIDA
Swarup Parida is currently a Staff Scientist IV at National Institute of Plant Genome
Research (NIPGR), New Delhi, India. He completed his Ph.D. in Biotechnology from Jamia
Hamdard University and National Research Centre on Plant Biotechnology (NRCPB), NewDelhi. He specializes in Agricultural Biotechnology, Plant Genomics, Genetics andMolecular Breeding. He is a recipient of several prestigious Young Scientist Awards,
including Indian National Science Academy (INSA), National Academy of Sciences India(NASI) and National Academy of Agricultural Sciences (NAAS), ELSEVIER-NASI-SCOPUS,
NAAS-Associateship, to name a few. He is also currently a member of Crop Science
Society of America and Editor of multiple international journals.

VIBHOR KUMAR
Vibhor Kumar received his PhD in Computational systems biology from Helsinki
University of Technology (now Aalto), Finland. During his PhD, he solved the first andhighest resolution (so far) structure of LDL (bad cholesterol) in native state at human bodytemperature. After completing PhD, he started applying computational approach togenomic data. He has worked at Genome Institute of Singapore (GIS) for more than 8 years
and published some fundamental research findings. At GIS, he was primarily working on
epigenome and gene regulation and applied his findings to other branches such as cancer
and stem cell study. Currently, he is working on deriving functional genomic insights fromsingle cell transcriptome and epigenome

LEELAVATI NARLIKARLeelavati Narlikar received her Bachelor's degree in Computer Engineering from Universityof Pune and a PhD in Computer Science from Duke University. She now works at theNational Chemical Laboratory, Pune and is a part of a group of scientists there who use
mathematics and computation to understand diverse aspects of biology. She is generallyinterested in designing new probabilistic models as well as algorithms to learn them, allwith the hope of solving fundamental problems in biology and healthcare.

ARACELI GARCIA MORA
Araceli Garcia Mora is originally from Valencia, Spain and studied her Bachelors degree inbiological sciences at the “Universidad Autónoma de Madrid”. Already at an undergraduatelevel she focused on bioinformatics and carried out her final year research project at theCentre for Molecular Biology Severo Ochoa (CBMSO), investigating the mitochondrial
genome of Leishmania. She continued her studies at The University of Manchester, whereshe completed an MSc in Bioinformatics and Systems Biology. During her masters shejoined the Bobola Lab group and decided to continue her research career in this group after
graduating in 2018. Currently she is halfway through her PhD in Genomics, funded by theMedical Research Council UK. Her research interests focus on understanding combinatorial
binding of Transcription Factors and investigating how disruptions in Transcription Factor
binding to enhancers can cause developmental disorders and misregulation oftranscription.

MANISHA KALSAN
Manisha Kalsan received her Master’s in Bioinformatics from Delhi Technological University
and, is currently a PhD student at School of Computational & Integrative Sciences, Jawaharlal
Nehru University. Her research interest lies in the applications of computational techniques tostudy the sequential and structural features of different transcription factors and their target
sites, and to predict the different states of a genome on the basis of the conformationalparameters of the DNA to annotate the genome for novel insights. She is also interested indeveloping predictors based on shape profiles for different types of target sites for atranscription factor, showing different temporal patterns.