UW Bio UW ChemE eScience AICS
Lab Affiliations: NU CSB NU NICO UW CMB

Announcements

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

Prof. Bagheri is promoted to Associate Professor with tenure!
May 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

Joseph Muldoon, Jessica Yu, and Mohammad-Kasim Fassia publish Network inference performance complexity: a consequence of topological, experimental, and algorithmic determinants.
February 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

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

Prof. Bagheri publishes Energy-based descriptors to rapidly predict hydrogen storage in metal–organic frameworks in collaboration with the Snurr lab.
November 2018

Jessica Yu is selected as a runner-up for the 2018 Distinguished Graduate Researcher Award.
September 2018

Justin Finkle is selected to present at this year's IBiS retreat.
September 2018

Slava Butkovich and Kate Dray are awarded Northwestern University Biotechnology Cluster awards.
August 2018

Jason Cain is awarded a Northwestern University Biotechnology Training Program fellowship.
August 2018

Jessica Yu receives a best poster award at the FOSBE conference.
August 2018

Narasimhan Balakrishnan, Joseph Muldoon, and Jessica Yu showcase their research at the FOSBE conference.
August 2018

Prof. Neda Bagheri and Prof. Josh Leonard are awarded an NIH synthetic biology research project grant for engineering cell-based devices.
July 2018

Prof. Bagheri joins as a faculty member of the new NSF-Simons Center for Quantitative Biology at NU.
July 2018

Prof. Bagheri is highlighted as a distinguished speaker for the Accelerated Discovery Forum at IBM Research-Almaden.
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

Jason Y. Cain, a Northeastern University alumnus, joins the MODYLS team.
December 2017

Slava S. Butkovich, a Caltech alumna, joins the MODYLS team.
December 2017

Kate E. Dray, a University of Kentucky alumna, joins the MODYLS team joint with the Leonard Lab.
December 2017

Justin Finkle showcases his research at the RECOMB/ISCB Conference on Regulatory and Systems Genomics.
November 2017

Jia Wu is awarded an ASH abstract achievement award.
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

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

Ty Yacoub publishes Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the life span in collaboration with NU colleagues.
July 2017

Jessica S. Yu showcases her research at the SIAM Conference on Applications of Dynamical Systems.
May 2017

Jessica S. Yu publishes Modulating and evaluating receptor promiscuity through directed evolution and modeling in collaboration with the Tyo lab.
May 2017

Prof. Bagheri, Joseph Muldoon, and Jessica Yu showcase their research at the Engineering Biology Research Consortium Spring 2017 retreat.
March 2017

Justin Finkle is awarded a Nicholson Fellowship from NU.
March 2017

Prof. Bagheri is awarded a Faculty Early Career Development Program Award from the NSF.
January 2017

Prof. Bagheri is awarded an NU Data Science Initiative based on Albert Xue's research in a supervised machine learning approach to characterize and predict enzyme activities.
January 2017

Josh Levy, an alumnus of Tufts University, joins the MODYLS team joint with the Kath Lab.
December 2016

Alex Prybutok, an alumna of the University of Texas at Austin, joins the MODYLS team joint with the Leonard Lab.
December 2016

Joseph Muldoon showcases his research at the RECOMB/ISCB Conference on Regulatory and Systems Genomics.
November 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

Jessica S. Yu receives the 2015-2016 ChBE teaching assistant excellence award.
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 a review article in Current Opinion in Biotechnology, "Multi-class and multi-scale models of complex biological phenomena".
April 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

The NU Center for Synthetic Biology is launched. More news here.
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

Prof. Bagheri is awarded an NU Data Science Initiative based on Ty Yacoub's research in uncovering molecular signatures of aging at the intersection of medicine and engineering.
January 2016

Jessica Yu, an alumna of Northwestern University, joins the MODYLS team as a PhD student.
January 2016

Narasimhan Balakrishnan, an alumnus of the Indian Institute of Technology, Madras, joins the MODYLS team.
January 2016

M. Kasim Fassia showcases his research at the 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

Jessica Yu showcases her research at the annual FOSBE conference.
August 2015

Jia Wu is reappointed to the Northwestern University Biotechnology Cluster fellowship.
August 2015

Dr. Mark Ciaccio accepts a position as Senior Biology Data Scientist at AbbVie Biopharmaceuticals.
July 2015

Dr. Mark Ciaccio publishes in the journal Integrative Biology (cover). The manuscript describes DIONESUS, a scalable recursive algorithm based on partial least squares regression. On a millisecond time-scale, this algorithm reconstructs a large phosphoproteomic signaling network from microwestern array data.
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 NU 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

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 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

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, Jia J. Wu, Zachary Mays, Stanley Weng, Neda Bagheri, William M. Miller, and Lonnie D. Shea.
May 2014

Aaron Oppenheimer will present on Connecting Motifs and Molecular Mechanisms Toward Control of Complex Networks at the annual SIAM conference.
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

Jessica Yu is awarded the Northwestern Alumnae Graduate Fellowship.
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 NU 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

Dr. Mark Ciaccio is invited to give a seminar titled Connecting protein abundance, phosphorylation, phenotype, and drug discovery using the Microwestern Array at the National Research Council of Canada.
November 2013

Jessica Yu showcases her research at the annual AIChE conference: Agent Based Models of Heterogeneous Tumor Cell Populations.
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 phospho-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