Chemical and Biological Systems Engineering Laboratory



CABSEL is engaged in a broad range of activities in the area of computational systems biology and bioinformatics. Our primary specializations include network inference, dynamical systems modeling and analysis, and design of experiments. Our research activities are driven by the mission to create enabling tools for extracting novel insights from heterogeneous biological data through the construction and analysis of biological network models, and to apply these tools to gain a better understanding of and to formulate interventions for human diseases and aging. Our research applications span multiple length- and time-scales in biology, from gene regulatory networks to signaling pathways to metabolic networks and from single cells to cell cultures. Our tools have been applied to give answers to biological questions of biotechnological, biomedical and biopharmaceutical significance.


For more information, go to Our Research page


The complete publication list can be found here.


Contact information:

Rudiyanto Gunawan

302 Furnas Hall

University at Buffalo 

Buffalo, NY 14260



Tel: +1 (716) 645-0952


Congrats Ravi!

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Congratulations Ravi for successfully defending his thesis on metabolic flux analysis applied to the understanding of aging biology.

Congrats to Qi Xin and Stephen Keegan!

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For successfully defending their Masters projects.

Three new people joined CABSEL!

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Shriram and Suting joined CABSEL as PhD students and Dr. Shilpi Aggarwal joined as Postdoctoral Fellow.

Check out our single-cell transcriptomic analysis tool CALISTA

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CALISTA is a numerically efficient and highly scalable toolbox for an end-to-end analysis of single-cell transcriptomic profiles. CALISTA includes four essential single-cell analyses for cell differentiation studies, including single-cell clustering, reconstruction of cell lineage specification, transition gene identification, and cell pseudotime ordering, which can be applied individually or in a pipeline. See CALISTA paper for more information.

A new publication...

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... on Alzheimer's disease C. elegans model will soon appear in the journal eLife

CABSEL receives its first NSF grant.

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The grant - $2 million over two years - funds a collaborative research team, led by Associate Professor Rudiyanto Gunawan, toward a brain-to-materials institute, translating neuroscience into a transformative neuromorphic computing platform. We are looking for motivated graduate students to participate in this exciting new research direction for the group.

Congratulations Jill!

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Jill successfully defended her Masters thesis on compartmental modeling of heat shock response dynamics in C. elegans.

We want you!

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CABSEL lab has an open position for a postdoctoral fellow in the area of computational systems biology and bioinformatics. The perfect candidate should hold a PhD degree in chemical engineering, bioengineering, bioinformatics, or related fields, with expertise in computational methods, mathematical modeling, optimization, network inference, and/or single cell analysis. We have numerous exciting projects in which the postdoctoral fellow can align him/herself. The position is available immediately. 

Congratulations to Nan!

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Nan successfully defended her thesis on single-cell transcriptional analysis. 

CABSEL welcomes new graduate students

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Panos, Xin Qi and Zhixin joined CABSEL to start their Ph.D. and Masters theses. Good luck and may the force be with you!

Two new graduate students join CABSEL.

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CABSEL welcomes two new graduate students Saber and Jill. Saber will carry on his PhD research on single-cell analysis of stem cell differentiation. Jill will investigate the tissue-to-tissue variability in the heat shock response in Caenorhabditis elegans for her  Masters thesis. 

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Nan Papili Gao's work on visualizing Waddington's epigenetic landscape using her bioinformatics tool CALISTA was selected as a winner of the Poster Presentation Award at the 2018 Foundation of Systems Biology in Engineering (FOSBE) meeting. 

Dr. Nadia Vertti Quintero!

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Nadia successfully defended her PhD thesis. Congratulations!​

CABSEL is moving to UBuffalo

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After 7 years at ETH Zurich, CABSEL is moving. Prof. Gunawan will start his new position as Associate Professor in the Chemical and Biological Engineering Department at UBuffalo in August 2018. Stay tuned for more update.

Our work on the cover page of Processes

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The work of a former PhD student of CABSEL (Thanneer Malai Perumal, Sage Bionetworks) was featured as the February cover page of Processes (in the special issue on Biological Networks).

Prof. Gunawan at the 1st IBSE Symposium

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Prof. Gunawan gave a keynote lecture titled "Pathway Analysis for Understanding the Biology of Aging" at the inaugural IBSE International Symposium at IIT Madras.

A new bioinformatics tool ProTINA

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ProTINA (Protein Target Inference by Network Analysis) is a bioinformatics tool to infer protein targets of drugs or diseases using gene transcriptional profiles. For more information, please check out ProTINA manuscript (Nucleic Acids Research, 2018). 

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Shilpi Aggarwal

Shilpi is a post-doc in CABSEL working on the development of network-based techniques for bioinformatics analysis with a specific focus on glycosylation and cellular metabolism.

Postdoctoral fellow

Mahasweta Bhattacharya

Mahasweta is working on building a neuronal activity decoder for Project MEMONET

PhD student

Panagiotis (Panos) Chrysinas

Panos is working on cross-tissue and cross-species prediction of gene expression.

PhD student

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Stephen Keegan

MS 2020

Qi Xin

MS 2020

Sudharshan Ravi

PhD 2020

Jillian Annis

MS 2019

Nan Papili Gao

PhD 2019

Nadia Sarait Vertti Quintero

PhD 2018

Anar Alshanbayeva

MS 2017

Sandro Hutter

PhD 2017

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How to find us

University at Buffalo North Campus
405 Furnas Hall
Buffalo, NY 14260
Tel: (716) 645-3518

© 2018 by Rudiyanto Gunawan