11th International Conference on Pathways, Networks, and Systems Medicine


Wednesday, June 24


06:00 PM


Conference Registration


08:00 PM


Welcome Reception/Dinner

Thursday, June 25


07:30 AM




08:30 AM


Welcome and Opening Remarks

Shankar Subramaniam


Session I


Chair: Joe Nadeau


08:45 AM


Systems Biology of Stem Cells


09:15 AM


Adaptive Systems Biology of Mammalian Chromosome Rearrangements in Evolution

Harris Lewin, Jaebum Kim, Jian Ma, Denis Larkin and Marta Farre

09:45 AM


High altitude hypoxia adaptation may provide answers for sea level diseases

Gabriel Haddad, Tsering Stobdan, Roy  Ronen, Vineet Bafna, Pedro Cabrales and Dan Zhou

10:15 AM


Systems Biology of Cellular Stress

Sindhu Raghunandan, Srini Ramachandran, Eugene Ke, Ratnesh Lal, Shu Chien, John Shyy, Zhen Chen, Julie Li, Mark Wang, Traci Marin, Mano Maurya, Mano Maurya, Shakti Gupta and Shankar Subramaniam

10:45 AM


Systems Medicine in Oncology: Signaling-networks dynamic modeling, a possible tool for a better prediction of the behavior of associations of inhibitors of different pathways  in colorectal cancer

Silvio Parodi, Nicoletta Castagnino, Lorenzo Tortolina, Massimo Maffei, Gabriele Zoppoli, Alessio  Nencioni, Alberto  Ballestrero and Franco Patrone Franco Patrone


11:10 AM


Coffee Break & Poster Viewing


Session II


Chair: Harris Lewin


12:00 PM


A 'complement-ary' view on the human complement system in host defense, disease and therapy

Daniel Ricklin and John Lambris

12:30 PM


Molecular Identifier Clustering based Immune Repertoire Sequencing and Its Application in Studying Human Antibody Repertoire in Malaria

Ning Jiang

01:00 PM


RNA exosome regulation of noncoding transcripts and AID activity in the B cell genome

Evangelos Pefanis, Jiguang Wang, Gerson Rothschild, Junghyun Lim, Raul Rabadan, Aris Economides and Uttiya Basu

01:30 PM


Sensitive mapping of chromatin-altering polymorphisms reveals molecular drivers of autoimmune diseases

Shyam Prabhakar


02:00 PM


Lunch/Informal Discussions


07:30 PM


Dinner/Informal Discussions at a local Greek Restaurant

Friday, June 26


07:30 AM




Session III


Chair: Christian Metallo


08:30 AM


High throughput, functional genomics yields minimal sets of factors that can program cells into skeletal and cardiac muscle

Alexandre Colas, Michael Yu, Matthew Tierney, Wesley McKeithan, Peter  Andersen, Emily Berry, Sole Gatto, Thomas Cunningham, Sean Spiering, Florent Carrette, Trish Tran, Chun-Teng Huang, Jean-Francois Riou, Muriel  Umbhauer, Giovanni Paternostro, Deepak Srivastava, Dimitrios Zisoulis, Gregg Duester, Alessandra Sacco and Mark Mercola

09:00 AM


The Diversity and Complexity of Calcium Signaling in Cardiac Muscle

Raimond Winslow

09:30 AM


Engineered Cell-free Epicardium Activates Regeneration in the Adult Mammalian Heart

Pilar Ruiz-Lozano

10:00 AM


A computational infrastructure for multi-scale modelling

Peter Hunter, David  Nickerson, Alan Garny and Tommy Yu

10:30 AM


Acetyl Co-A: a Metabolic Junction Linking Metabolism and Cell Identity in Pluripotent Cells

Arieh Moussaieff, Eran Meshorer, Benedicte Herrmann, Daniel Aberdam and Yaakov Nahmias


11:00 AM


Coffee Break & Poster Viewing


Session IV


Chair: Peter Hunter


12:00 PM


Flow modulation of endothelial function: a multi-level regulation by AMPK/SIRT1

Zhen Chen, John  Shyy, Shankar Subramaniam and Shu Chien

12:30 PM


The pathway of collagen secretion

Vivek Malhotra

01:00 PM


Historeceptomics signatures to represent pharmacologic perturbations of biological systems

Sergey Shmelkov, Klara Felsovalyi, James Swetnam and Timothy Cardozo

01:30 PM


Significant Alterations in Gene Expression Within the Wnt Pathway Contribute to the Natural Variation in Bone Mechanical Function

Stephen Schlecht, Lauren Smith, Yueqin Yang, Erin Bigelow, Amber Cathey, Bonnie Nolan, Melissa Ramcharan, Eugene Manley Jr, Maureen Devlin, Joseph Nadeau and Karl Jepsen


02:00 PM


Lunch/Informal Discussions


07:30 PM


Dinner/Informal Discussions at a local Greek Restaurant

Saturday, June 27


07:30 AM




Session V


Chair: Dina Petranovic

08:30 AM


Probing cell metabolism using isotope tracers to understand disease mechanisms

Christian Metallo

09:00 AM


Studies of Metabolic Diseases and Cancer through Genome Scale Modeling of Human Metabolism

Jens Nielsen

09:30 AM


Re-wiring of mitochondrial metabolic pathways in response to genetic and environmental perturbations

Daniel Tennant

10:00 AM


Fatty acid metabolism in cancer cells: Are we looking at the right pathway?

Daniel Weindl, Xiangyi Dong, Thekla Cordes and Karsten Hiller

10:30 AM


Mechanistic modeling of metabolism and the Warburg effect in Hepatocellular carcinoma, using multi level -omics data and enzyme kinetics

Avlant Nilsson, Adil Mardinoglu and Jens Nielsen

10:45 AM


Temporal transcriptional response to insulin stimulation of myocytes: Impact of type 2 diabetes and obesity

Leif Väremo, Camilla Scheele, Christa Broholm, Adil Mardinoglu, Intawat Nookaew, Mathias Uhlén, Bente Klarlund Pedersen and Jens Nielsen


11:00 AM


Coffee Break & Poster Viewing


Session VI


Chair: Aris  Economides

11:30 AM


Using iPSCs to identify brain specific developmental gene regulatory pathways

Merril Gersten, Graham Cocks, Akshay Bhinge, Lawrence Stanton, Shankar Subramaniam and Noel Buckley

12:00 PM


Identification of Therapeutic Targets for Glioblastoma by Transcriptional Network Analysis

Vipul Bhargava

12:30 PM


In search of a common pathway for folic acid-responsive neural tube defects, neurodegeneration and cancer.  

Patrick Stover, Martha Field, Elena Kamynina and Ashley Palmer

01:00 PM


Role of Mutant Ubiquitin (UBB+1) in the yeast model of Alzheimer’s disease

Xin Chen, Ana Joyce Munoz, Andrea  Molt and Dina Petranovic


01:30 PM


Lunch/Informal Discussions


03:00 PM


City Tour (depart from the hotel lobby at 3:00PM)


07:30 PM


Dinner/Informal Discussions at a local Greek Restaurant

Sunday, June 28


07:30 AM




Session VII


Chair: Gabriel Haddad


08:30 AM


Quantifying acetate metabolism in hypoxic cancer cells

Vinay Bulusu, Sergey Tumanov and Jurre Kamphorst

09:00 AM


Integrating Genomic Layers to Understand Phenotypic Variation across Populations

Philip Awadalla

09:30 AM


Unraveling CRISPR-Cas9 genome engineering parameters in mammalian cells via a library-on-library approach

Prashant Mali

10:00 AM


Mendel 2.0: Revisiting genome organization and evolution, with epistasis, epigenetics and systems properties

Joseph Nadeau

10:30 AM


Research and Resource opportunities at the Heart, Lung and Blood Institute

Pankaj Qasba

11:00 AM


Gene correlation networks for the study of the hematopoietic stem cell niches

Charles Durand and Pierre Charbord


11:15 AM


Coffee Break & Poster Viewing


Session VIII


Chair: Shankar Subramaniam


12:00 PM


Enantiostasis rewiring of cellular networks & depigmenting disorder Vitiligo

Rajesh Gokhale

12:30 PM


Rapid, broad-based sequence profiling with digital PCR, High Resolution Melt, and Machine Learning

Stephanie Fraley

01:00 PM


Integrating multi-omic data analytics and health coaching to optimize wellness and minimize disease

Nathan Price

01:30 PM


Computational framework for elucidating the 3D spatial organization of chromatin from Hi-C experiments

Gaurav Arya


02:00 PM


Closing Remarks


02:15 PM


Lunch/Informal Discussions


08:00 PM


Farewell Dinner

Monday, June 29


07:30 AM




09:30 AM




Chair: Meghana Hemphill


A network-based scoring function for predicting protein complex structures

Edward Shih and Ming-Jing Hwang


Archetypal signatures of biological activities

Sergei Makarov, Alexander Medvedeva, Lioubov Medvedeva, Matt Moeser, Elena Martsen, Alexander Granick and Ming Zeng


Border-based quantification of molecule distribution in cell volume

Mikhail Paveliev, Agne Velthut-Meikas, Marko Crivaro, Mart Saarma and Heikki Rauvala


Calcium signaling pathway contributes to hypoxia adaptation in Tibetans

Changqing Zeng, Tianzi Liu and Basangzhuoma Basangzhuoma


Cancer mutations converge in the selection of deregulated arachidonate and xenobiotics metabolism

Francesco Gatto, Almut Schulze and Jens Nielsen


Dysregulated signaling hubs of lipid metabolism unravel mechanism underlying hepatocellular carcinoma

Sunjae Lee, Adil Mardinoglu, and Jens Nielsen


Exploring regulatory networks and interactions of the miR-96 cluster in the inner ear

Morag Lewis, Annalisa Buniello, Jennifer Hilton, Stijn van Dongen, Anton Enright and Karen Steel


FastGeneSL based on Logical Transformation of Genome-scale Model for Rapid Identification of Oncogenes as Targets for Cancer Treatment

Cheng Zhang, Boyang Ji, Adil Mardinoglu, Jens Nielsen and Qiang Hua


HCSD: the human cancer secretome database

Amir  Feizi and Jens  Nielsen


Highly parallel intracellular inhibition of protein-protein interaction networks identifies novel cancer drug leads

Philip Kim


Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

Pouyan Ghaffari, Adil Mardinoglu and Jens Nielsen


MalaCards - essential biomedical research tool

Noa  Rappaport, Michal Twik, Noam Nativ, Ella Buzhor, Tsippi  Iny Stein, Iris Bahir, Marilyn Safran and Doron Lancet


Quantitative analysis of CXCR3-ligand mediated cell-cell communication

Sarah Schrier, Abby Hill and Douglas Lauffenburger


Reconciling proteomic data into genome scale models

Benjamin Sanchez and Jens Nielsen


The Landscape of Metabolic Interactions in Human Gut Ecosystem

Boyang Ji and Jens Nielsen


Towards a Multi-scale Systems Biology Model of the Developing Heart.

Nazanin Ebrahimi, Gib Bogle, Christopher Bradley, Michael Cooling and Peter Hunter