Announcements
Jason Cain successfully defends his thesis!
August 2023
Jacob Evarts receives an NSF Graduate Research Fellowship for his work on decomposing information sources in agent-based models.
April 2023
Jason Cain publishes The in silico lab: Improving academic code using lessons from biology.
January 2023
Kate Dray successfully defends her thesis!
October 2022
Alex Prybutok publishes Mapping CAR T-cell design space using agent-based models in collaboration with the Leonard lab.
July 2022
Alex Prybutok is awarded the inaugural Distinguished Graduate Service Award in the Department of Chemical and Biological Engineering at Northwestern University.
June 2022
Neda Bagheri is invited as the Plenary Speaker for the International Federation of Automatic Control symposium on Dynamics and Control of Process Systems in Busan, Korea.
June 2022
Alex Prybutok successfully defends her thesis!
April 2022
Alex Prybutok publishes a preprint of Mapping CAR T-cell design space using agent-based models in collaboration with the Leonard lab.
April 2022
Mugdha Sathe showcases her research in the ASCB Emerging Researcher Talk Series.
March 2022
Alex Prybutok and Jason Cain publish Fighting fire with fire: deploying complexity in computational modeling to effectively characterize complex biological systems in collaboration with the Leonard lab.
February 2022
Narasimhan Balakrishnan successfully defends his thesis!
February 2022
Neda Bagheri publishes The new era of quantitative cell imaging—challenges and opportunities.
January 2022
Kate Dray publishes GAMES: A dynamic model development workflow for rigorous characterization of synthetic genetic systems in collaboration with the Leonard and Mangan labs.
January 2022
Po-Hao Chiu, a National Taiwan University alumnus, joins the MODYLS team.
January 2022
Alex Prybutok showcases her research at the 2021 AIChE Annual Meeting.
November 2021
Jacob Evarts, a University of Oregon alumnus, joins the MODYLS team.
September 2021
Jessica Yu publishes Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model.
June 2021
Joshua Levy successfully defends his thesis!
June 2021
Joseph Muldoon publishes Model-guided design of mammalian genetic programs in collaboration with the Leonard lab.
February 2021
Sophia Jannetty, a Williams College alumnus, joins the MODYLS team.
September 2020
Joseph Muldoon receives an IBiS outstanding dissertation award.
September 2020
Narasimhan Balakrishnan receives a best poster award at the SysMod @ ISMB conference.
July 2020
Joseph Muldoon successfully defends his thesis!
July 2020
Jessica Yu successfully defends her thesis!
May 2020
Sebastian Bernasek publishes Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila in collaboration with the Carthew lab and the Amaral lab.
March 2020
Jessica Yu publishes Agent-based models predict emergent behavior of heterogeneous cell populations in dynamic microenvironments.
March 2020
Joseph Muldoon publishes The COMET toolkit for composing customizable genetic programs in mammalian cells in collaboration with the Leonard lab.
February 2020
Joseph Muldoon publishes Macrophages employ quorum licensing to regulate collective activation in collaboration with the Leonard lab.
February 2020
Sebastian Bernasek publishes Repressive gene regulation synchronizes development with cellular metabolism in collaboration with the Carthew lab and the Amaral lab.
July 2019
Jia Wu, Justin Finkle, and Sebastian Bernasek graduate!
June 2019
Albert Xue publishes DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data in collaboration with the Lucks lab.
May 2019
Prof. Bagheri is promoted to Associate Professor with tenure!
May 2019
Albert Xue publishes Exploration of the nanomedicine-design space with high-throughput screening and machine learning in collaboration with the Mrksich lab and Mirkin lab.
February 2019
Joseph Muldoon, Jessica Yu, and Mohammad-Kasim Fassia publish Network inference performance complexity: a consequence of topological, experimental, and algorithmic determinants.
February 2019
Prof. Bagheri publishes Energy-based descriptors to rapidly predict hydrogen storage in metal-organic frameworks in collaboration with the Snurr lab.
November 2018
Ty Yacoub publishes Multidimensional assessment of the host response in mechanically ventilated patients with suspected pneumonia in collaboration with the Budinger lab and Wunderink lab.
November 2018
Justin Finkle is selected to present at this year's IBiS retreat.
September 2018
Jessica Yu is selected as a runner-up for the 2018 Distinguished Graduate Researcher Award.
September 2018
Narasimhan Balakrishnan, Joseph Muldoon, and Jessica Yu showcase their research at the FOSBE conference.
August 2018
Jessica Yu receives a best poster award at the FOSBE conference.
August 2018
Jason Cain is awarded a Northwestern University Biotechnology Training Program fellowship.
August 2018
Slava Butkovich and Kate Dray are awarded Northwestern University Biotechnology Cluster awards.
August 2018
Prof. Bagheri is highlighted as a distinguished speaker for the Accelerated Discovery Forum at IBM Research-Almaden.
July 2018
Prof. Bagheri joins as a faculty member of the new NSF-Simons Center for Quantitative Biology at NU.
July 2018
Prof. Neda Bagheri and Prof. Josh Leonard are awarded an NIH synthetic biology research project grant for engineering cell-based devices.
July 2018
Justin Finkle and Jia Wu publish Windowed Granger causal inference strategy improves discovery of gene regulatory networks. Read more about the SWING algorithm here.
February 2018
Kate E. Dray, a University of Kentucky alumna, joins the MODYLS team joint with the Leonard Lab.
December 2017
Slava S. Butkovich, a Caltech alumna, joins the MODYLS team.
December 2017
Jason Y. Cain, a Northeastern University alumnus, joins the MODYLS team.
December 2017
Jia Wu is awarded an ASH abstract achievement award.
November 2017
Justin Finkle showcases his research at the RECOMB/ISCB Conference on Regulatory and Systems Genomics.
November 2017
Joseph Muldoon showcases his research at the Engineering Biology Research Consortium Fall 2017 retreat.
September 2017
Joseph Muldoon publishes Multiplexing engineered receptors for multiparametric evaluation of environmental ligands in collaboration with the Leonard lab.
August 2017
Ty Yacoub publishes Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span in collaboration with Northwestern University colleagues.
July 2017
Albert Xue publishes Machine learning on SAMDI mass spectrometry signal to noise ratio improves peptide array designs in collaboration with the Mrksich lab.
July 2017
Jessica S. Yu publishes Modulating and evaluating receptor promiscuity through directed evolution and modeling in collaboration with the Tyo lab.
May 2017
Jessica S. Yu showcases her research at the SIAM Conference on Applications of Dynamical Systems.
May 2017
Justin Finkle is awarded a Nicholson Fellowship from NU.
March 2017
Prof. Bagheri, Joseph Muldoon, and Jessica Yu showcase their research at the Engineering Biology Research Consortium Spring 2017 retreat.
March 2017
Prof. Bagheri is awarded an Northwestern Data Science Initiative based on Albert Xue's research in a supervised machine learning approach to characterize and predict enzyme activities.
January 2017
Prof. Bagheri is awarded a Faculty Early Career Development Program Award from the NSF.
January 2017
Alex Prybutok, an alumna of the University of Texas at Austin, joins the MODYLS team joint with the Leonard Lab.
December 2016
Josh Levy, an alumnus of Tufts University, joins the MODYLS team joint with the Kath Lab.
December 2016
Joseph Muldoon showcases his research at the RECOMB/ISCB Conference on Regulatory and Systems Genomics.
November 2016
Jessica S. Yu receives the 2015-2016 ChBE teaching assistant excellence award.
October 2016
Jessica S. Yu and Albert Y. Xue publish A support vector machine model provides an accurate transcript-level-based diagnostic for major depressive disorder in collaboration with Dr. Eva Redei.
October 2016
Joseph Muldoon receives the 2015-2016 IBiS teaching assistant excellence award.
September 2016
Jia Wu is awarded a Ruth Kirchstein National Service Award (F31) from the National Institutes of Health.
August 2016
Narasimhan Balakrishnan is appointed to the Northwestern University Biotechnology Cluster fellowship.
July 2016
Jessica Yu publishes Multi-class and multi-scale models of complex biological phenomena.
April 2016
The Northwestern Center for Synthetic Biology is launched. More news here.
March 2016
Jessica Yu receives an NSF Graduate Research Fellowship for her work on characterizing complex cancer dynamics using multi-scale agent-based models.
March 2016
Bagheri Lab publishes in Nature Methods with the HPN-DREAM Consortium, et al. The manuscript describes a community-based effort for causal inference of phosphoprotein signaling networks.
February 2016
Narasimhan Balakrishnan, an alumnus of the Indian Institute of Technology, Madras, joins the MODYLS team.
January 2016
Jessica Yu, an alumna of Northwestern University, joins the MODYLS team as a PhD student.
January 2016
Prof. Bagheri is awarded a Northwestern Data Science Initiative based on Ty Yacoub's research in uncovering molecular signatures of aging at the intersection of medicine and engineering.
January 2016
M. Kasim Fassia showcases his research at the 2015 AIChE Annual Meeting.
November 2015
Justin Finkle showcases his research at the annual BMES conference.
October 2015
Dr. Ty Yacoub joins the MODYLS team joint with the Szleifer Lab to conduct research on genetic causes of aging.
September 2015
Jia Wu is reappointed to the Northwestern University Biotechnology Cluster fellowship.
August 2015
Jessica Yu showcases her research at the annual FOSBE conference.
August 2015
Dr. Mark Ciaccio accepts a position as Senior Biology Data Scientist at AbbVie Biopharmaceuticals.
July 2015
Dr. Mark Ciaccio publishes The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets.
June 2015
Joseph Muldoon receives an honorable mention on his research proposal from the NSF graduate fellowship committee.
April 2015
Sebastian Bernasek, a UC Santa Barbara alumnus, joins the MODYLS team joint with the Amaral Lab.
December 2014
Prof. Neda Bagheri and Prof. Josh Leonard are selected to receive a Cornew Innovation Award from the Northwestern University Chemistry of Life Processes Institute.
November 2014
Jia Wu and Joseph Muldoon earn a Northwestern University Biotechnology Cluster fellowship.
August 2014
Dr. Mark Ciaccio is selected for the Hartwell Foundation Postdoctoral Fellowship.
July 2014
Jessica Yu graduates from Northwestern University with a B.S. in Chemical Engineering and a minor in Computer Science. She will be joining the Master of Biotechnology Program this fall.
June 2014
Joseph Muldoon, a University of Virginia alumnus, joins the MODYLS team joint with the Leonard Lab to conduct research on systems and synthetic biology of the immune system.
June 2014
Jessica Yu is awarded the Northwestern Alumnae Graduate Fellowship.
May 2014
Dr. Mark Ciaccio, Justin Finkle, and Albert Xue publish A systems approach to integrative biology: an overview of statistical methods to elucidate association and architecture.
May 2014
Aaron Oppenheimer showcases his research at the annual SIAM conference: Connecting Motifs and Molecular Mechanisms Toward Control of Complex Networks.
May 2014
Jia J. Wu publishes Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation along with Mark T. Duncan, Seungjin Shin, Zachary Mays, Stanley Weng, Neda Bagheri, William M. Miller, and Lonnie D. Shea.
May 2014
Justin Finkle and Albert Xue receive honorable mentions on their respective research proposals from the NSF graduate fellowship committee.
April 2014
Prof. Neda Bagheri and esteemed Northwestern colleagues are "breaking new ground" in the emerging field of synthetic and computational biology. Read about their work here.
March 2014
Albert Xue earns a Northwestern University Biotechnology Training Program fellowship.
December 2013
Jessica Yu's research is highlighted on the McCormick website.
November 2013
Jessica Yu showcases her research at the 2013 AIChE Annual Meeting.
November 2013
The MODYLS Lab competed in the 8th annual international Dialogue for Reverse Engineering Assessments and Methods (DREAM) Breast Cancer Network Inference Challenge.
• Placed 6th / 65 teams in the in silico network inference challenge.
• Placed 7th / 14 teams in the prediction of trajectories for new kinase inhibitors in four in vivo breast cancer cell lines.
• Placed 2nd / 14 teams in the high-dimensional visualization challenge.
October 2013
Justin Finkle earns a Northwestern University Biotechnology Training Program fellowship.
August 2013
Prof. Neda Bagheri is selected to participate in the 2013-2014 Searle Fellows Program.
August 2013
Dr. Mark Ciaccio is invited to present at the Global Analysis of Protein Dynamics Workshop.
June 2013
Jia Wu, a UCSD alumnus, joins the Bagheri Lab to investigate transcription factor activity involved in cell fate.
June 2013
Justin Finkle, a Cornell University alumnus, joins the Bagheri Lab to explore methods of inferring RNA expression from transcription factor abundance.
June 2013
Aaron Oppenheimer, a Case Western University alumnus, joins the Bagheri Lab to explore the analysis and control of emergent biological networks.
March 2013
Dr. Mark Ciaccio, joins the Bagheri Lab after having completed doctoral research with Prof. Richard Jones at the University of Chicago. An expert in microwestern array technology, Mark aims to integrate computational modeling with array data to gain insight on key regulatory networks governing cellular function.
February 2013
Albert Xue, a Case Western University alumnus, joins the Bagheri Lab to conduct research in integrated computational analysis of gene and protein regulatory networks.
November 2012
Jessica Yu showcases her research at the annual BMES conference: Probabilistic Markov models accurately predict T cell cytokine secretion dynamics.
October 2012