@article{dicks2025rapids,title={Accelerating single-cell analysis with GPU-enabled RAPIDS-singlecell},author={Dicks, S. and Heumos, L. and Jimenez, S. and Angerer, P. and Gold, I. and Virshup, I. and Fischer, F. and May, L. and Nolet, C. J. and Gill, M. and Boerries, M. and Theis, F.},journal={In preparation},year={2025},}
E. Sevgen, J. Moller, A. Lange, J. Parker, S. Quigley, J. Mayer, P. Srivastava, S. Gayatri, D. Hosfield, M. Korshunova, M. Livne, M. Gill, R. Ranganathan, A.B. Costa, and A.L. Ferguson
ProT-VAE: Protein transformer variational autoencoder for functional protein design.
Proceedings of the National Academy of Sciences122 (2025)
@article{sevgen2025protvae,title={ProT-VAE: Protein transformer variational autoencoder for functional protein design},author={Sevgen, E. and Moller, J. and Lange, A. and Parker, J. and Quigley, S. and Mayer, J. and Srivastava, P. and Gayatri, S. and Hosfield, D. and Korshunova, M. and Livne, M. and Gill, M. and Ranganathan, R. and Costa, A.B. and Ferguson, A.L.},journal={Proceedings of the National Academy of Sciences},volume={122},number={41},year={2025},doi={10.1073/pnas.2408737122},recent={true},}
2024
P. St. John, D. Lin, P. Binder, M. Greaves, V. Shah, J. St. John, A. Lange, P. Hsu, R. Illango, A. Ramanathan, A. Anandkumar, D.H. Brookes, A. Busia, A. Mahajan, S. Malina, N. Prasad, S. Sinai, L. Edwards, T. Gaudelet, C. Regep, M. Steinegger, B. Rost, A. Brace, K. Hippe, L. Naef, K. Kamata, G. Armstrong, K. Boyd, Z. Cao, H.Y. Chou, S. Chu, A. Santos Costa, S. Darabi, E. Dawson, K. Didi, C. Fu, M. Geiger, M. Gill, D.J. Hsu, G. Kaushik, M. Korshunova, S. Kothen-Hill, Y. Lee, M. Liu, M. Livne, Z. McClure, J. Mitchell, A. Moradzadeh, O. Mosafi, Y. Nashed, S. Paliwal, Y. Peng, S. Rabhi, F. Ramezanghorbani, D. Reidenbach, C. Ricketts, B.C. Roland, K. Shah, T. Shimko, H. Sirelkhatim, S. Srinivasan, A.C. Stern, D. Toczydlowska, S.P. Veccham, N.A.E. Venanzi, A. Vorontsov, J. Wilber, I. Wilkinson, W.J. Wong, E. Xue, C. Ye, X. Yu, Y. Zhang, G. Zhou, B. Zandstein, A. Chacon, P. Sohani, M. Stadler, C. Hundt, F. Zhu, C. Dallago, B. Trentini, E. Kucukbenli, T. Rvachov, E. Calleja, J. Israeli, H. Clifford, R. Haukioja, N. Haemel, K. Tretina, N. Tadimeti, and A.B. Costa
BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery.
@article{stjohn2024bionemo,title={BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery},author={St. John, P. and Lin, D. and Binder, P. and Greaves, M. and Shah, V. and St. John, J. and Lange, A. and Hsu, P. and Illango, R. and Ramanathan, A. and Anandkumar, A. and Brookes, D.H. and Busia, A. and Mahajan, A. and Malina, S. and Prasad, N. and Sinai, S. and Edwards, L. and Gaudelet, T. and Regep, C. and Steinegger, M. and Rost, B. and Brace, A. and Hippe, K. and Naef, L. and Kamata, K. and Armstrong, G. and Boyd, K. and Cao, Z. and Chou, H.Y. and Chu, S. and dos Santos Costa, A. and Darabi, S. and Dawson, E. and Didi, K. and Fu, C. and Geiger, M. and Gill, M. and Hsu, D.J. and Kaushik, G. and Korshunova, M. and Kothen-Hill, S. and Lee, Y. and Liu, M. and Livne, M. and McClure, Z. and Mitchell, J. and Moradzadeh, A. and Mosafi, O. and Nashed, Y. and Paliwal, S. and Peng, Y. and Rabhi, S. and Ramezanghorbani, F. and Reidenbach, D. and Ricketts, C. and Roland, B.C. and Shah, K. and Shimko, T. and Sirelkhatim, H. and Srinivasan, S. and Stern, A.C. and Toczydlowska, D. and Veccham, S.P. and Venanzi, N.A.E. and Vorontsov, A. and Wilber, J. and Wilkinson, I. and Wong, W.J. and Xue, E. and Ye, C. and Yu, X. and Zhang, Y. and Zhou, G. and Zandstein, B. and Chacon, A. and Sohani, P. and Stadler, M. and Hundt, C. and Zhu, F. and Dallago, C. and Trentini, B. and Kucukbenli, E. and Rvachov, T. and Calleja, E. and Israeli, J. and Clifford, H. and Haukioja, R. and Haemel, N. and Tretina, K. and Tadimeti, N. and Costa, A.B.},journal={arXiv},year={2024},doi={10.48550/arXiv.2411.10548},recent={true},}
M.T. Strauss, I. Bludau, W.F. Zeng, E. Voytik, C. Ammar, J. Schessner, R. Illango, M.L. Gill, F. Meier, S. Willems, and M. Mann
AlphaPept, a modern and open framework for MS-based proteomics.
@article{strauss2024alphapept,title={AlphaPept, a modern and open framework for MS-based proteomics},author={Strauss, M.T. and Bludau, I. and Zeng, W.F. and Voytik, E. and Ammar, C. and Schessner, J. and Illango, R. and Gill, M.L. and Meier, F. and Willems, S. and Mann, M.},journal={Nature Communications},volume={15},year={2024},doi={10.1038/s41467-024-46485-4},recent={true},}
2022
M.L. Gill
The rise of the machines in chemistry.
Magnetic Resonance in Chemistry60, 1044–1051 (2022)
@article{gill2022risemachines,title={The rise of the machines in chemistry},author={Gill, M.L.},journal={Magnetic Resonance in Chemistry},volume={60},pages={1044--1051},year={2022},doi={10.1002/mrc.5304},}
D. Reidenbach, M. Livne, R.K. Illango, M.L. Gill, and J.I. Israeli
Improving small molecule generation using mutual information machine.
Poster presented at ICLR Machine Learning for Drug Discovery Workshop, 2023PosterAbstract
@article{reidenbach2022smallmolecule,title={Improving small molecule generation using mutual information machine},author={Reidenbach, D. and Livne, M. and Illango, R.K. and Gill, M.L. and Israeli, J.I.},journal={arXiv},year={2022},doi={10.48550/arXiv.2208.09016},}
2019
M.L. Gill, A. Hsu, and A.G. Palmer
Detection of chemical exchange in methyl groups of macromolecules.
Poster presented at 57th Experimental Nuclear Magnetic Resonance Conference, Pittsburgh, PA, 2016Poster
@article{gill2019methylexchange,title={Detection of chemical exchange in methyl groups of macromolecules},author={Gill, M.L. and Hsu, A. and Palmer, A.G.},journal={Journal of Biomolecular NMR},volume={73},pages={443--450},year={2019},doi={10.1007/s10858-019-00240-w},}
2017
M. Tong, J. Pelton, M.L. Gill, W. Zhang, F. Picart, and M. Seeliger
Survey of solution dynamics in Src kinase reveals cross talk between the ligand binding and regulatory sites.
@article{tong2017srckinase,title={Survey of solution dynamics in Src kinase reveals cross talk between the ligand binding and regulatory sites},author={Tong, M. and Pelton, J. and Gill, M.L. and Zhang, W. and Picart, F. and Seeliger, M.},journal={Nature Communications},volume={8},pages={2160},year={2017},doi={10.1038/s41467-017-02240-6},}
2016
M.L. Gill, R.A. Byrd, and A.G. Palmer
Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region.
Physical Chemistry and Chemical Physics18, 5839–5849 (2016)
Poster presented at International Conference on Magnetic Resonance in Biological Systems, Dallas, TX, 2014Poster
Poster presented at 57th Experimental Nuclear Magnetic Resonance Conference, Pittsburgh, PA, 2016Poster
@article{gill2016gcn4,title={Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region},author={Gill, M.L. and Byrd, R.A. and Palmer, A.G.},journal={Physical Chemistry and Chemical Physics},volume={18},pages={5839--5849},year={2016},doi={10.1039/c5cp06197k},}
2015
S. Sun, M.L. Gill, Y. Li, M. Huang, and R.A. Byrd
Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms.
Poster presented at 56th Experimental Nuclear Magnetic Resonance Conference, Monterey, CA, 2015Poster
Poster presented at 57th Experimental Nuclear Magnetic Resonance Conference, Pittsburgh, PA, 2016Poster
@article{sun2015nesta,title={Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms},author={Sun, S. and Gill, M.L. and Li, Y. and Huang, M. and Byrd, R.A.},journal={Journal of Biomolecular NMR},volume={62},pages={105--117},year={2015},doi={10.1007/s10858-015-9923-x},}
2014
B. Ergel, M.L. Gill, L. Brown, B. Yu, A.G. Palmer, and J.F. Hunt
Protein dynamics control the progression and efficiency of the catalytic reaction cycle of AlkB.
Journal of Biological Chemistry289, 29584–29601 (2014)
Poster presented at International Conference on Magnetic Resonance in Biological Systems, Lyon, France, 2012Poster
@article{ergel2014alkb,title={Protein dynamics control the progression and efficiency of the catalytic reaction cycle of AlkB},author={Ergel, B. and Gill, M.L. and Brown, L. and Yu, B. and Palmer, A.G. and Hunt, J.F.},journal={Journal of Biological Chemistry},volume={289},pages={29584--29601},year={2014},doi={10.1074/jbc.M114.575647},}
M.L. Gill and R.A. Byrd
Dynamic activation of apoptosis: conformational ensembles of cIAP1 are linked to a spring-loaded mechanism.
@article{gill2014ciap1,title={Dynamic activation of apoptosis: conformational ensembles of cIAP1 are linked to a spring-loaded mechanism},author={Gill, M.L. and Byrd, R.A.},journal={Nature Structural Molecular Biology},volume={21},pages={1022--1023},year={2014},doi={10.1038/nsmb.2925},}
M.L. Gill and A.G. Palmer
Local isotropic diffusion approximation for coupled internal and overall molecular motions in NMR spin relaxation.
Journal of Physical Chemistry B118, 11120–11128 (2014)
@article{gill2014localisotropic,title={Local isotropic diffusion approximation for coupled internal and overall molecular motions in NMR spin relaxation},author={Gill, M.L. and Palmer, A.G.},journal={Journal of Physical Chemistry B},volume={118},pages={11120--11128},year={2014},doi={10.1021/jp506580c},}
2011
M.L. Gill and A.G. Palmer
Multiplet-filtered and gradient-selected zero-quantum TROSY experiments for 13C1H3 methyl groups in proteins.
Poster presented at 52nd Experimental Nuclear Magnetic Resonance Conference, Monterey, CA, 2011Poster
@article{gill2011methyltrosy,title={Multiplet-filtered and gradient-selected zero-quantum TROSY experiments for $^{13}$C$^{1}$H$_{3}$ methyl groups in proteins},author={Gill, M.L. and Palmer, A.G.},journal={Journal of Biomolecular NMR},volume={51},pages={245--251},year={2011},doi={10.1007/s10858-011-9533-1},}
2009
J.D. Ramsey, M.L. Gill, T.J. Kamerzell, E.S. Price, S.B. Joshi, S.M. Bishop, C.N. Oliver, and C.R. Middaugh
Using empirical phase diagrams to understand the role of intramolecular dynamics in immunoglobulin G stability.
Journal of Pharmaceutical Sciences98, 2432–2447 (2009)
@article{ramsey2009immunoglobulin,title={Using empirical phase diagrams to understand the role of intramolecular dynamics in immunoglobulin G stability},author={Ramsey, J.D. and Gill, M.L. and Kamerzell, T.J. and Price, E.S. and Joshi, S.B. and Bishop, S.M. and Oliver, C.N. and Middaugh, C.R.},journal={Journal of Pharmaceutical Sciences},volume={98},pages={2432--2447},year={2009},doi={10.1002/jps.21619},}
2006
M.L. Gill, S.A. Strobel, and J.P. Loria
Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex.
@article{gill2006gquadruplex,title={Crystallization and characterization of the thallium form of the \textit{Oxytricha nova} G-quadruplex},author={Gill, M.L. and Strobel, S.A. and Loria, J.P.},journal={Nucleic Acids Research},volume={34},pages={4506--4514},year={2006},doi={10.1093/nar/gkl616},}
2005
H. Beach, R. Cole, M.L. Gill, and J.P. Loria
Conservation of µs-ms enzyme motions in the apo- and substrate-mimicked state.
Journal of the American Chemical Society127, 9167–9176 (2005)
@article{beach2005enzyme,title={Conservation of µs-ms enzyme motions in the apo- and substrate-mimicked state},author={Beach, H. and Cole, R. and Gill, M.L. and Loria, J.P.},journal={Journal of the American Chemical Society},volume={127},pages={9167--9176},year={2005},doi={10.1021/ja0514949},}
M.L. Gill, S.A. Strobel, and J.P. Loria
205Tl NMR methods for the study of monovalent metal binding sites in nucleic acids.
Journal of the American Chemical Society127, 16723–16732 (2005)
@article{gill2005tl205nmr,title={$^{205}$Tl NMR methods for the study of monovalent metal binding sites in nucleic acids},author={Gill, M.L. and Strobel, S.A. and Loria, J.P.},journal={Journal of the American Chemical Society},volume={127},pages={16723--16732},year={2005},doi={10.1021/ja055358f},}
2004
P.L. Adams, M.R. Stahley, M.L. Gill, A.B. Kosek, J. Wang, and S.A. Strobel
Crystal structure of a group I intron splicing intermediate.
@article{adams2004groupi,title={Crystal structure of a group I intron splicing intermediate},author={Adams, P.L. and Stahley, M.R. and Gill, M.L. and Kosek, A.B. and Wang, J. and Strobel, S.A.},journal={RNA},volume={10},pages={1867--1887},year={2004},doi={10.1261/rna.7140504},}
@article{wiethoff2003fluorescence,title={A fluorescence study of the structure and accessibility of plasmid DNA condensed with cationic gene delivery vehicles},author={Wiethoff, C.M. and Gill, M.L. and Koe, G.S. and Koe, J.G. and Middaugh, C.R.},journal={Journal of Pharmaceutical Sciences},volume={92},pages={1272--1285},year={2003},doi={10.1002/jps.10391},}
@article{wiethoff2002lipiddna,title={The structural organization of cationic lipid-DNA complexes},author={Wiethoff, C.M. and Gill, M.L. and Koe, G.S. and Koe, J.G. and Middaugh, C.R.},journal={Journal of Biological Chemistry},volume={277},pages={44980--44987},year={2002},doi={10.1074/jbc.M207758200},}
2000
S. Silchenko, M.L. Sippel, O. Kuchment, D.R. Benson, A.G. Mauk, A. Altuve, and M. Rivera
Hemin is kinetically trapped in cytochrome b5 from rat outer mitochondrial membrane.
Biochemical and Biophysical Research Communications273, 467–472 (2000)
@article{silchenko2000hemin,title={Hemin is kinetically trapped in cytochrome b$_5$ from rat outer mitochondrial membrane},author={Silchenko, S. and Sippel, M.L. and Kuchment, O. and Benson, D.R. and Mauk, A.G. and Altuve, A. and Rivera, M.},journal={Biochemical and Biophysical Research Communications},volume={273},pages={467--472},year={2000},doi={10.1006/bbrc.2000.2968},}