Rutgers Center for Quantitative Biology

Welcome to The Rutgers Center of Quantitative Biology (CQB)The primary mission of the Rutgers Center for Quantitative Biology (CQB) is to enable scientific exchanges and collaborations between faculty residing in different academic departments who are interested in quantitative modeling of biological phenomena. Research interests of CQB faculty members comprise both experimental and theoretical approaches and range from evolutionary dynamics, stochastic processes in biology, and single-molecule biophysics to modeling onset and progression of cancer. CQB facilitates these activities by holding a weekly seminar series as well as providing travel support for faculty and affiliated students and postdoctoral researchers to attend national and international scientific meetings.

The members of CQB are:

Note: the Graduate Program in BioMaPS, or "Ph.D. in Computational Biology and Molecular Biophysics", has been renamed
the Graduate Program in Quantitative Biomedicine, and is now affiliated with
the Institute for Quantitative Biomedicine at Rutgers (IQB@R)

Upcoming Events

Click here to join the Center for Quantitative Biology Seminars mailing list

Click here for a list of past seminars, with abstracts

Fall 2018 CQB Seminars: Tue 12pm, Hill 260 unless indicated otherwise

(seminar details emailed to listserv subscribers)

09/11/2018 Tiberiu Tesileanu, Flatiron Institute "Environmental adaptation of olfactory receptor distributions" abstract

09/27/2018 CQB student seminar: Leonardo Santana "Analysis and modeling of cancer recurrence via birth-death processes" Thurs 12pm, Hill 260

10/09/2018 Amit Singer, Princeton University "Mathematics for cryo-electron microscopy" abstract

10/23/2018 Alexandra Zidovska, NYU "The "self-stirred" genome: Bulk and surface dynamics of the chromatin globule" abstract [postponed]

10/31/2018 Nir Yakoby, Rutgers University Camden "Patterning the Drosophila eggshell: mechanisms in cis and trans regulation" abstract

11/13/2018 Chris Wiggins, Columbia University "Just do the best you can: statistical physics approaches to reinforcement learning" abstract

11/20/2018 Tomas Gedeon, Montana State University "DSGRN: a bridge between network structure and network dynamics" abstract

11/27/2018 Gustavo Stolovitzky, IBM & Mount Sinal School of Medicine "Smaller, Faster and Chip-er: Isolation of exosomes by nanoDLD lab-on-a-chip technology and application to prostate cancer biomarker discovery" abstract

12/04/2018 Alexandra Zidovska, NYU "The "self-stirred" genome: Bulk and surface dynamics of the chromatin globule" abstract

12/11/2018 Sharad Ramanathan, Harvard University "Extracting reaction co-ordinates to understand the dynamics of early human and mouse development" abstract

Spring 2019 CQB Seminars: Tue 12pm, Hill 260 unless indicated otherwise

02/05/2019 Johannes Friedrich, Flatiron Institute "Goal-directed decision making with spiking neurons" abstract

02/19/2019 Luis Aparicio, Columbia University "Random Matrix Theory applications in single-cell biology" abstract

02/26/2019 Valentina Boeva, INSERM, Institut Cochin TBD [postponed]

04/02/2019 Bill Saidel, Rutgers University Camden "Insight into the activities of groups of birds" abstract

04/09/2019 Pablo Camara, UPenn "Going beyond cell-type identification with single-cell transcriptomics" abstract

04/23/2019 Jeanne Salje, Rutgers PHRI, Newark "Cells within cells: obligate intracellular bacteria and their differentiation within host cells" abstract

04/30/2019 Ioannis Androulakis, Rutgers University "Allostatic adaptation to stress and personalized physiological trade-offs in the circadian regulation of the HPA axis" abstract

Fall 2019 CQB Seminars: Tue 12pm, Serin 385 unless indicated otherwise [NOTE LOCATION CHANGE]

09/10/2019 Yanis Bahroun, Flatiron Institute "Exploration & Extension of The Similarity Matching Framework: Feature Learning & Nonlinear Methods & Transformation Learning" abstract

10/08/2019 Jae Kyoung Kim, KAIST/University of Michigan "Mathematical models to analyze dynamic data from molecule to behavior" abstract

10/22/2019 Nikolai Chapochnikov, Flatiron Institute "Neural computations for stimulus whitening by the olfactory system" abstract

11/19/2019 David Schwab, CUNY Graduate Center "How noise affects the Hessian spectrum in overparameterized neural networks" abstract

12/03/2019 Gabor Balazsi, Stony Brook University, "Interactions between gene network dynamics and evolution" abstract

Spring 2020 CQB Seminars: Mon 12pm, Hill 525 unless indicated otherwise [NOTE DATE AND LOCATION CHANGE]

02/17/2020 Paul Falkowski, Rutgers University, "Light to Life: The origin of metabolic catalysis" abstract [LOCATION: Serin 330W]

03/09/2020 Jason Yang, Rutgers University, "Interpretable machine learning insights into the coupling between antibiotic lethality and bacterial metabolism" abstract

Fall 2020 CQB Online Seminars: Mon 12.00-1.00 pm, Zoom links provided through the mailing list (email to This email address is being protected from spambots. You need JavaScript enabled to view it. to be added)

09/28/2020 Philipp Altrock, Moffitt Cancer Center and Research Institute, "Modeling eco-evolutionary interactions between engineered and wildtype T cells to quantify therapeutic success of anti-CD19 CAR T cell therapy" abstract

10/12/2020 Konstantin Mischaikow, Rutgers University, "DSGRN: An efficient tool for understanding regulatory networks" abstract

10/26/2020 Ilya Nemenman, Emory University, "Berg-Purcell bound, revisited" abstract

11/09/2020 Mohammad Kohandel, University of Waterloo, "From mechanistic to machine learning approaches in computational biology of cancer" abstract

12/07/2020 John Barton, UC Riverside, "Viral evolution through the lens of statistical physics" abstract

Spring 2021 CQB Online Seminars: Mon 12.00-1.00 pm, Zoom links provided through the mailing list (email to This email address is being protected from spambots. You need JavaScript enabled to view it. to be added)

01/25/2021 Tahir I. Yusafaly, UCSD, "Whole-Body PET/CT Radiomics to Predict Treatment Failure in Cervical Cancer Patients" abstract

02/08/2021 Jason Rocks, BU, "Memorizing without overfitting: Bias, variance and interpolation in over-parameterized models" abstract

03/08/2021 Kshitij Wagh, LANL, "Hitting the sweet spot - exploiting HIV glycan shield for effective AIDS vaccines" abstract

03/22/2021 Tal Korem, Columbia U, "The microbiome, metabolome, and host health" abstract

04/19/2021 James Greene, Clarkson U, "Induced drug resistance in cancer: modeling and control" abstract

05/03/2021 Sang-Hyuk Lee, Rutgers U, "Single-molecule study of DNA bending by mitochondrial transcription factor A (TFAM)" abstract

Fall 2021 CQB Online Seminars: Mon 12.00-1.00 pm, Zoom links provided through the mailing list (email to This email address is being protected from spambots. You need JavaScript enabled to view it. to be added)

10/04/2021 Shanshan Qin, Harvard U, "Unveiling the dynamics and structure of drifting neural representations" abstract

10/18/2021 Jamie Morton, Flatiron Institute, "Scalable estimation of microbial co-occurrence networks with Variational Autoencoders" abstract

Spring 2022 CQB Online Seminars: Mon 12.00-1.00 pm, Zoom links provided through the mailing list (email to This email address is being protected from spambots. You need JavaScript enabled to view it. to be added)

03/21/2022 Gyan Bhanot, Rutgers U, "Specialized ribosomes, in health and disease" abstract poster

04/04/2022 Shiva Farashahi, Flatiron Institute, "Coordinated drift of receptive fields during noisy representation learning" abstract [postponed]

04/18/2022 Anirvan Sengupta, Rutgers U and Flatiron Institute, "Neural optimal feedback control with local learning rules" abstract

05/09/2022 Kevin Ellis, Cornell U, "The role of higher-level knowledge in discovery problems: programs and hierarchical Bayes" abstract

Fall 2022 CQB Online Seminars: Mon 12.00-1.00 pm, Zoom links provided through the mailing list (email to This email address is being protected from spambots. You need JavaScript enabled to view it. to be added)

10/24/2022 David Lipshutz, Flatiron Institute, "Neuroscience-inspired online learning algorithms" abstract

11/07/2022 Yongfeng Zhang, Rutgers U, "Explainable AI for Science" abstract

11/14/2022 Siavash Golkar, Flatiron Institute, "Explorations in NeuroAI, paths less trod" abstract

12/05/2022 Elias Puchner, University of Minnesota, "Exploring intra-cellular processes at the nanoscopic length scale with quantitative single-molecule microscopy in living cells" abstract

News and Notable

(Please click on the "Publications" tab above to see complete publication lists for all CQB faculty)

Wilma Olson has been elected a 2018 Fellow of the American Physical Society.

Anirvan Sengupta and his collaborators showed that similarity-preserving networks of rectifying neurons, when presented with sensory inputs populating a low-dimensional manifold, learn localized receptive fields naturally. The paper, titled “Manifold-tiling Localized Receptive Fields are Optimal in Similarity-preserving Neural Networks”, will be presented at the Annual Conference on Neural Information Processing Systems (NIPS), to be held in Montreal in December 2018.

Alexandre Morozov gave a keynote talk at BELBI 2018 which took place June 18-22 in Belgrade, Serbia.

Morozov's group published a paper in Physical Review Letters which explains how sizes of large, complex networks can be reliably inferred by exploring only a small fraction of each network: link.

Khiabanian's lab recently published two papers on statistical modeling of noise in deep DNA sequencing data in the Journal of Statistical Physics (link) and BMC Bioinformatics (link). The application of these results to clinical data from cancer patients showed that age-related somatic mutation in infiltrated hematopoietic cells are often present within the solid tumor miroenvironment. This study was published in Blood (link) and was covered by GenomeWeb (link).

Jui Wan Loh, a PhD student in Khiabanian's lab, was awarded a pre-doctoral fellowship grant by the New Jersey Commission on Cancer Research to study clonal dynamics of leukemia under targeted gene-specific therapy.

In collaboration with researchers from the Vanderbilt Ingram Cancer Center and Cancer Institute of New Jersey, Gyan Bhanot's group has found that endogenous retroviruses transcripts are amplified by histone modification in a subset of kidney cancers, which causes an immune response blocked by the tumor, making the tumor susceptible to immune checkpoint therapy. This discovery was highlighted at the recent ASCO-SITC conference: link.

Under Gyan Bhanot's supervision, Anshuman Panda graduated from the Rutgers Department of Physics and Astronomy with a PhD thesis titled “Immune Checkpoint Therapy,” won an NJCCR Fellowship, and is now a post-doctoral associate at the Cancer Institute of New Jersey. 

Eduardo Sontag and collaborators have published a manuscript in PLoS Computational Biology on the dynamical responses of biological networks in Mycobacterium tuberculosis (link; in the news: "New theorem helps reveal tuberculosis' secret").