Michelle Lynn Gill, Ph.D.

Biophysicist and Data Scientist

Current

Biophysicist and data scientist. Currently a data science fellow at Metis. Eager to apply my superb computational, statistical, and communication skills to solve challenging problems in team-focused settings.

Education

2003-2006 Yale University, New Haven, CT
Ph.D., Molecular Biophysics & Biochemistry
Advisors: J. Patrick Loria and Scott Strobel

2001-2003 Yale University, New Haven, CT
M.Phil., Molecular Biophysics & Biochemistry

1997-2001 University of Kansas, Lawrence, KS
B.S., Biochemistry, Summa Cum Laude

Experience

2016 Metis, Data Science Fellow
Member of the Summer Cohort of the Data Science Bootcamp in New York. I am concurrently serving as a teaching assistant while attending the bootcamp.

2014-2016 National Cancer Institute, National Institutes of Health, Scientist
Developed robust and extremely fast methods for reconstruction of non-uniformly sampled NMR data.

2008-2014 Columbia University, Department of Biochemistry and Molecular Biophysics, Postdoctoral Research Fellow
Part of a collaboration that demonstrated conformational selection is critical in the highly concerted mechanism of the DNA methyltransferase, AlkB. Developed multiple quantum NMR spin relaxation experiments for quantifying the slow timescale (microsecond – millisecond) motions of methyl sidechains.
Advisor: Professor Arthur G. Palmer, III

2007-2008 University of Kansas, Department of Pharmaceutical Chemistry, Postdoctoral Research Fellow
Examined the role of dynamics in IgG and vaccine stability.
Advisor: Professor C. Russell Middaugh

2006-2007 The Boston Consulting Group, Consultant
Worked with clients in the finance and pharmaceutical sectors to streamline organizational structure and identify novel investment opportunities. I was part of the case team that won the 2007 Global BCG Strategy Olympics for our work with a pharmaceutical client.

2001-2006 Yale University, Department of Molecular Biophysics and Biochemistry, Graduate Research Fellow
Developed methods for the study of monovalent metal binding in nucleic acids using 205Thallium NMR.
Advisors: Professor J. Patrick Loria and Professor Scott A. Strobel

1998-2001 University of Kansas, Department of Pharmaceutical Chemistry, Undergraduate Research Fellow
Characterized cationic lipid-DNA complexes for non-viral gene therapy.
Advisor: Professor C. Russell Middaugh

Projects

Blog

Personal blog, themodernscientist, discusses data visualization, optimization, automation, and various other computationally-related interests. Posts frequently incorporate Jupyter notebooks and shell scrips. The blog itself is created using Pelican, a Python-based static blogging engine, and the website is hosted on GitHub.

NESTA-NMR

Developed and currently maintain a program, called NESTA-NMR, that enables the acquisition of experimental data to be completed up to 100X faster. This project uses a compressed sensing algorithm, called NESTA. The program is written in C, highly parallelized, and best-in-class for speed and optimization accuracy. Associated scientific (GSL and FFTW) and parallelization (pthreads) libraries were also used.

I built the website using Flask and created the documentation using Sphinx.

pdLSR

pdLSR is a library for performing least squares regression. It attempts to seamlessly incorporate this task in a Pandas-focused workflow. Input data are expected in dataframes, and multiple regressions can be performed using functionality similar to Pandas groupby.

MFOutParser

MFOutParser is a Python library developed during my postdoctoral research that parses a particularly challenging text format and performs preliminary analysis on the resulting data using Pandas.

Python Book

Co-author of an in-progress, introductory Python book, called “Unix and Python to the Rescue!”, geared towards life scientists who want to learn Unix and Python. I wrote a blog post announcing the project and have also written posts on the book’s website.

Technical Skills

Teaching

2003 Yale University, Graduate Teaching Fellow
Course: Medical Impact of Basic Science
Role: Led discussion sessions where undergraduates discussed primary scientific literature, helped them develop and write research proposals based on topics covered

2002-2003 Yale University, Graduate Teaching Fellow
Course: Biochemistry II
Role: Led discussion sessions and reviews, designed quizzes and homework questions

Publications

Peer Reviewed

Gill, M.L., Byrd, R.A., Palmer, A.G. “Detection of Chemical Exchange in Methyl Groups of Macromolecules”, in preparation.

Gill, M.L., Sun, S., Byrd, R.A., “Highly Quantitative Reconstruction of Sparsely Sampled, Low Dimensionality NMR Spectra”, in preparation.

2016 Gill, M.L., Byrd, R.A., Palmer, A.G. “Dynamics of GCN4 Facilitate DNA Interaction: A Model-Free Analysis of an Intrinsically Disordered Region”, Phys. Chem. Chem. Phys. 2016, 18, 5839–5849. [pdf]

2015 *Sun, S., *Gill, M.L., Li, Y., Huang, M., Byrd, R.A. “Efficient and generalized processing of multidimensional NUS NMR Data: the NESTA algorithm and comparison of regularization terms”, J. Biomol. NMR 2015, 62, 105–117. [pdf]
* Authors contributed equally

2014 Gill, M.L., Palmer, A.G. “Local isotropic diffusion approximation for coupled internal and overall molecular motions in NMR spin relaxation”, J. Phys. Chem. B 2014, 118, 11120–11128. [pdf]

2014 Ergel, B., Gill, M.L., Brown, L., Yu, B., Palmer, A.G., Hunt, J.F. “Protein dynamics control the progression and efficiency of the catalytic reaction cycle of AlkB”, J. Biol. Chem. 2014, 289, 29584–29601. [pdf]

2011 Gill, M.L. and Palmer, A.G. “Multiplet-filtered and gradient-selected zero-quantum TROSY experiments for 13C1H3 methyl groups in proteins”, J. Biomol. NMR, 2011, 51, 245–251. [pdf]

2009 Ramsey, J.D., Gill, M.L., Kamerzell, T.J., Price, E.S., Joshi, S.B., Bishop, S.M., Oliver, C.N., Middaugh, C.R. “Using empirical phase diagrams to understand the role of intramolecular dynamics in immunoglobulin G stability”, J. Pharm. Sci. 2009, 98, 2432–2447. [pdf]

2006 Gill, M.L., Strobel, S.A., and Loria, J.P. “Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex”, Nucleic Acids Res. 2006, 34, 4506–4514. [pdf]

2005 Gill, M.L., Strobel, S.A., and Loria, J.P. “205Tl NMR methods for the study of monovalent metal binding sites in nucleic acids”, J. Am. Chem. Soc. 2005, 127, 16723–16732. [pdf]

2005 Beach, H., Cole, R., Gill, M.L., and Loria, J.P. “Conservation of µs-ms enzyme motions in the apo- and substrate-mimicked state”, J. Am. Chem. Soc. 2005, 127, 9167–9176. [pdf]

2004 Adams, P.L., Stahley, M.R., Gill, M.L., Kosek, A.B., Wang, J., and Strobel, S.A. “Crystal structure of a group I intron splicing intermediate”, RNA 2004, 12, 1867–1887. [pdf]

2003 Wiethoff, C.M., Gill, M.L., Koe, G.S., Koe, J.G., and Middaugh, C.R. “A fluorescence study of the structure and accessibility of plasmid DNA condensed with cationic gene delivery vehicles”, J. Pharm. Sci. 2003, 92, 1272–1285. [pdf]

2002 Wiethoff, C.M., Gill, M.L., Koe, G.S., Koe, J.G., and Middaugh, C.R. “The structural organization of cationic lipid-DNA complexes”, J. Biol. Chem. 2002, 277, 44980–44987. [pdf]

2000 Silchenko, S., *Sippel, M.L., Kuchment, O., Benson, D.R., Mauk, A.G., Altuve, A., and Rivera, M. “Hemin is kinetically trapped in cytochrome b5 from rat outer mitochondrial membrane”, Biochem. Biophys. Res. Commun. 2000, 273, 467–472. [pdf]
* M.L. Gill is formerly M.L. Sippel

Other

2014 Gill, M.L., Byrd, R.A. “Dynamic activation of apoptosis: conformational ensembles of cIAP1 are linked to a spring-loaded mechanism”, Nat. Struct. Mol. Biol 2014, 21, 1022–1023. [pdf]

Selected Presentations

2015 Gill, M.L., Sun, S., Li, Y., Huang, M., Byrd, R.A. “NESTA-NMR: efficient and generalized processing of multidimensional NUS NMR data”, Poster, 56th Experimental Nuclear Magnetic Resonance Conference, 2015, Monterrey, CA.

2014 Gill, M.L., Byrd, R.A., Palmer, A.G. “The role of GCN4 conformational dynamics in DNA binding and recognition”, Poster, International Conference of Magnetic Resonance in Biological Sciences, 2014, Dallas, TX.

2012 Gill, M.L., Ergel, B., Brown, L., Yu, B., Palmer, A.G., Hunt, J.F., “Protein dynamics control the progression and efficiency of the catalytic reaction cycle of AlkB”, Poster, International Conference of Magnetic Resonance in Biological Sciences, 2012, Lyon, France.

2011 Gill, M.L., and Palmer, A.G., “Gradient-selected zero-quantum experiments for the study of 1H—13C correlations in protonated methyl groups”, Poster, 52nd Experimental Nuclear Magnetic Resonance Conference, 2011, Monterrey, CA.

2005 Gill, M.L., Strobel, S.A., and Loria, J.P., “Direct study of 205Tl binding to a G-quadruplex by detection of 1H–205Tl scalar couplings”, Selected Oral Presentation, 46th Experimental Nuclear Magnetic Resonance Conference, 2005, Providence, RI.

Awards

2009–2012 NIH Postdoctoral Research Fellowship (F32 GM089047)

2007 Global BCG Strategy Olympics Winning Team

2002–2006 NSF Graduate Research Fellowship

2003 Outstanding Graduate Teaching Assistant

2000–2001 Barry M. Goldwater Scholar

2001 Outstanding Undergraduate Honors Research Thesis

1997–2001 Kansas Board of Regents Full Tuition Scholarship

Online Education

Links are to completion certificates. Only machine learning and statistics courses are listed. A comprehensive list is also available.