Most of these videos are on
microrobotics and
nanoscience.
While a lot of our work now is on
structural and computational biology, we have not made many videos
on those topics yet. However, we have
written a textbook and plenty of papers you can read on
structural and computational biology and biochemistry.
However, OspreyTube
is growing.
Please note that not all of our videos above are on YouTube because
some, for example, are hosted
in a lecture series at MIT. Some of our videos are copyrighted by the music
publisher (because of
the music) and therefore
are here, here,
or here,
or here. Or Here
(Siggraph 1990).
Indexes* and Reviews of Our Papers
*Indicates indexes and reviews of our papers not written/compiled
by our group.
*Please note: Most indexes and collections of our papers are incomplete since the
computer science indexes do not list the biomedical journals, and
Medline does not list the computer science and robotics papers. Only Google Scholar
"Probabilistic Disease Classification of
Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum,"
(with R. Lilien and H. Farid), Journal of Computational Biology,
10(6) 2003, pp. 925-946.
"HASH: a Program to Accurately Predict Protein Hα (H-alpha)
Shifts from Neighboring Backbone Shifts" (with J. Zeng, and
P. Zhou). Journal of Biomolecular NMR 2012; Dec
16.
Computational Design of a PDZ Domain Peptide Inhibitor that
Rescues CFTR Activity (with K. Roberts, P. Cushing, P. Boisguerin,
and D. Madden). PLoS Computational Biology 2012;
8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
Improved HIV-1 Neutralization Breadth and Potency of V2-Apex
Antibodies by In Silico Design (with G. Holt, J. Gorman,
S. Wang, A. Lowegard, B. Liu, T. Lin, B. Zhang, M. Louder,
M. Frenkel, K. McKee, S. Rawi, O'Dell R., C.-H. Shen, N. Doria-Rose,
and P. Kwong). Cell Reports (2023).
LUTE (Local Unpruned Tuple Expansion): Accurate
continuously flexible protein design with general energy functions
and rigid-rotamer-like efficiency (with M. Hallen and J. Jou).
Journal of Computational Biology
2016 Sep 28. PMID: 27681371
This journal paper is a revised paper based on the earlier Conference version:
LUTE (Local Unpruned Tuple Expansion): Accurate continuously
flexible protein design with general energy functions and
rigid-rotamer-like efficiency (with M. Hallen and
J. Jou). Proceedings of the Annual International Conference on
Research in Computational Molecular Biology (RECOMB), Los
Angeles, CA, April, 2016.
In Research in Computational Molecular Biology, Lecture Notes in
Bioinformatics (LNBI), Springer-Verlag (Berlin), Volume 9649, 2016,
pp. 122-136.
A compact representation of continuous energy surfaces for
more efficient protein design (with M. Hallen and P. Gainza).
Journal of Chemical Theory and Computation.
2015; 11(5):2292-2306.
The Compass That Steered Robotics. In Logic and
Program Semantics, Lecture Notes in Computer Science (LNCS) 7230,
Springer-Verlag (Berlin) 2012. pp. 50-65.
Practical
Mobile Robot Self-Localization (with J. Howell) Proceedings,
International Conference on Robotics and Automation, San Francisco, CA,
April 24-28, 2000. pp. 3485-3492.
Movie, 4:30, Quicktime w/Sorenson codec, max 250 kb/s
(42MB)
B. R. Donald, J. Jennings, and D. Rus, Minimalism +
Distribution = Supermodularity [TR FTP], Journal
of Experimental and Theoretical Artificial Intelligence (JETAI), Special
issue on Software Architectures for Hardware Agents; Vol. 9 No. 2-3 (1997) pp.
293-321.
Proc. IEEE/Robotics Society of Japan International Workshop on Intelligent
Robots and Systems, (IROS) Pittsburgh, PA (1995).
. Program
Mobile Robots in Scheme
(with J. Rees)
Proc. IEEE International Conference on Robotics and Automation Nice,
France (May, 1992), pp. 2681-2688.
[PDF]
Many people do not realize that the title of this paper is in the
hortatory subjunctive mode. It should be read as: Program
Mobile Robots in Scheme! Note the exclamation point.
Towards a Theory of Information Invariants for Cooperating Autonomous
Mobile Robots, (with J. Jennings and D. Rus) International Symposium of
Robotics Research (ISRR). Hidden Valley, PA (October 2, 1993).
Sensor Interpretation and Task-Directed Planning Using
Perceptual Equivalence Classes (with J. Jennings). Proc. IEEE
International Conference on Robotics and Automation, Sacramento,
CA (April, 1991), pp. 190-197.
``The Motion of Planar Compliantly-Connected Rigid
Bodies in Contact, with Applications to Automatic Fastening,'' B. R. Donald
and D. Pai. International Journal of Robotics Research12(4), August 1993, pp. 307-338.
``Symbolic Methods for the Simulation of Planar Mechanical Systems in
Design,'' B. R. Donald and D. Pai. in Symbolic and
Numerical Computation for Artificial Intelligence, (ed. B. Donald
et al.) Academic Press, Harcourt Jovanovich, (London: 1992), pp.
245-258.
Planning Multi-Step Error Detection and Recovery Strategies.
International Journal of Robotics Research, 9(1),
1990. pp. 3-60.
Planning and Control
for Microassembly of Structures
Composed of Stress-Engineered MEMS Microrobots (with C. Levey,
C. McGray, I. Paprotny, and D. Rus). International Journal of
Robotics Research 2013; 32(2):
218-246.
Turning-rate Selective Control: A New Method for Independent
Control of Stress-engineered MEMS Microrobots (with C. Levey and
I. Paprotny). Proceedings of Robotics: Science and
Systems Conference (RSS), University of Sydney, Sydney, NSW,
Australia. July 9-13, 2012 (In press).
The Compass That Steered Robotics. In Logic and
Program Semantics, Lecture Notes in Computer Science (LNCS) 7230,
Springer-Verlag (Berlin) 2012. pp. 50-65.
Ultra-sharp metal and nanotube-based probes for applications
in scanning microscopy and neural recording (with I. Borzenets,
I. Yoon, M. Prior, R. Mooney, and G. Finkelstein). Journal of
Applied Physics 2012; 111(7):74703-747036.
doi: 10.1063/1.3702802.
Simultaneous Control of Multiple MEMS Microrobots (with C. Levey,
I. Paprotny, and D. Rus). Proceedings of the Eighth International
Workshop on the Algorithmic Foundations of Robotics (WAFR),
Guanajuato, Mexico, December 7-9, 2008. Book chapter version (final) appears in:
Springer Tracts on Advanced Robotics, 57,
Springer-Verlag (Berlin), (2010), pp. 69-84.
Planar Microassembly by Parallel Actuation of MEMS
Microrobots (with C. Levey and I. Paprotny). Journal of
Microelectromechanical Systems 2008;
17(4): 789-808.
Assembly of Planar Structures by Parallel Actuation of MEMS
Microrobots (with C. Levey and I. Paprotny). Hilton Head
Workshop: A Solid-State Sensors, Actuators and Microsystems
Workshop pp. 202-207.
June 1-2, 2008, Hilton Head, SC.
A Steerable, Untethered MEMS Mobile Micro-Robot (with
C. Levey, C.McGray, I. Paprotny, and D. Rus). In
Robotics Research, Springer Tracks in Advanced Robotics 28,
ed. S. Thrun, et al., Springer-Verlag (Berlin) 2007,
pp. 337-356.
An Untethered, Electrostatic, Globally-Controllable MEMS Micro-Robot (with
C. Levey, C.McGray, I. Paprotny, and D. Rus). Journal of
Microelectromechanical Systems, 2006; 15(1):1-15.
A Steerable, Untethered, 250 x 60 µm MEMS Mobile Micro-Robot (with C.
Levey, C.McGray, I. Paprotny, and D. Rus). 12th International Symposium of
Robotics Research (ISRR), October 12-15, 2005, San Francisco, CA.
Power Delivery and Locomotion of Untethered Micro-Actuators (with C.
Levey, C. McGray, D. Rus, and M. Sinclair). Journal of
Microelectromechanical Systems 2003; 10(6):947-959.
Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design,
Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and
M. Sinclair). in Robotics Research eds. P. Dario and R. Chatila.
Springer-Verlag (London) 2005, pp.502--516.
Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design,
Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and
M. Sinclair) 11th
International Symposium of Robotics Research (ISRR), October 19-22,
2003, Siena, Italy.
Computational
Methods for the Design and Control of MEMS Micromanipulator Arrays (with K.-F.
Böhringer, G. Kovacs, N. MacDonald, and J. Suh) IEEE Computational
Science and Engineering, Vol. 4, No. 1. Special Issue on Computational
MEMS (Jan-March 1997). pp. 17-29.
Improved HIV-1 Neutralization Breadth and Potency of V2-Apex
Antibodies by In Silico Design (with G. Holt, J. Gorman,
S. Wang, A. Lowegard, B. Liu, T. Lin, B. Zhang, M. Louder,
M. Frenkel, K. McKee, S. Rawi, O'Dell R., C.-H. Shen, N. Doria-Rose,
and P. Kwong). Cell Reports (2023).
Disruptor: Computational identification of oncogenic mutants
disrupting protein interactions (with N. Guerin, V.Kugler, A. Lieb,
E. Stefan, and T. Kaserer). Communications Biology (Nature
Publishing Group)
(2023)
Protocol for predicting drug-resistant protein mutations to an ERK2 inhibitor using RESISTOR
(with N. Guerin and T. Kaserer).
Cell STAR (Structured Transparent Accessible Reproducible)
Protococols 2023; 4(2):102170. doi: 10.1016/j.xpro.2023.102170.
RESISTOR: An algorithm for predicting
resistance mutations using Pareto optimization over multistate
protein design and mutational signatures
(with N. Guerin
and
T. Kaserer).
Journal: Cell Systems 2022; (13)10:
830-843 [PDF,
at journal],
and Video
from Conference: RECOMB (May, 2022), San Diego.
Computational Design of a PDZ Domain Peptide Inhibitor that
Rescues CFTR Activity (with K. Roberts, P. Cushing, P. Boisguerin,
and D. Madden). PLoS Computational Biology 2012;
8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
"Probabilistic Disease Classification of
Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum,"
(with R. Lilien and H. Farid), Journal of Computational Biology,
10(6) 2003, pp. 925-946.
Phylogenetic Classification of Protozoa Based on the
Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate
Reductase-Thymidylate Synthase (with R. O'Neil, R. Lilien, R. Stroud, and A.
Anderson) Journal of Biological Chemistry 2003;
278(52):52980-52987.
R. Mettu, R. Lilien, and B. R. Donald. High-Throughput Inference of
Protein-Protein Interfaces from Unassigned NMR Data. Bioinformatics
2005; 21(Suppl. 1):i292-i301.
The version on the Oxford (Bioinformatics) website is messed up,
and this version is easier to read. (They did not
correct a printer's error, and the SI has
vanished). This version
corrects both of the journal's errors.
Below you can read the whole story:
Here is the accepted
manuscript, which does not contain the error
that Bioinformatics introduced in the abstract. The error is
corrected in the published Erratum.
"Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by
Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) The Journal of
Computational Biology, 8(1):19-36, 2001.
"Phase-Independent Rhythmic Analysis of Genome-Wide Expression
Patterns", (with C. Langmead, A. Yan, and C. R. McClung), Journal of
Computational Biology 10(3-4) 2003, pp. 521-536.
DexDesign: an osprey-based algorithm for designing
de novo D-peptide inhibitors. (with N. Guerin, H. Childs and
P. Zhou). Protein Engineering, Design, and Selection. 2024;
37:gzae007. doi: 10.1093/protein/gzae007. PMID: 38757573
DexDesign: A new OSPREY-based algorithm for designing de
novo D-peptide inhibitors (with N. Guerin, H. Childs, and
P. Zhou). Proceedings of the Annual International Conference on
Research in Computational Molecular Biology (RECOMB),
Boston. (April 29-May 2, 2024). In Lecture Notes in Computer
Science 14758, Springer (Cham,
Schweizerische Eidgenossenschaft) pp. 336-249.
Improved HIV-1 Neutralization Breadth and Potency of V2-Apex
Antibodies by In Silico Design (with G. Holt, J. Gorman,
S. Wang, A. Lowegard, B. Liu, T. Lin, B. Zhang, M. Louder,
M. Frenkel, K. McKee, S. Rawi, O'Dell R., C.-H. Shen, N. Doria-Rose,
and P. Kwong). Cell Reports (2023).
Disruptor: Computational identification of oncogenic mutants
disrupting protein interactions (with N. Guerin, V.Kugler, A. Lieb,
E. Stefan, and T. Kaserer). Communications Biology (Nature
Publishing Group) (2023).
Non-canonical inhibitors target the CAL binding site: new
approaches to stabilize functional ΔF508-CFTR (with N. Gill,
J. Amacher, P. Cushing, Y. Zhao, L. Wallace, A. Pletnev, M. Spaller,
S. Cullati, S. Gerber, P. Boisguerin, D. Casalena, D. Auld, S. Wang, and
D. Madden). 2023 European Cystic Fibrosis Society
Conference. Dubrovnik, Croatia March 29-April 1 2023.
Discovery, characterization, and redesign of potent antimicrobial
thanatin orthologs from Chinavia ubica and Murgantia
histrionica targeting E. coli LptA (with K. Huynh,
A. Kibrom and P. Zhou).
American Society for Biochemistry and
Molecular Biology, Discover BMB Conference, Seattle, WA. March,
2023.
Journal of Biological Chemistry (2023) 299:(3):S640.
Some Geometric and Computational Challenges Arising in Structural
Molecular Biology (Invited Talk). 35th International Symposium on
Computational Geometry (SoCG 2019). Leibniz International
Proceedings in Informatics (LIPIcs), vol. 129. pp. 2:1. Schloss
Dagstuhl -- Leibniz-Zentrum für Informatik. doi:
10.4230/LIPIcs.SoCG.2019.2
OSPREY 3.0: Open-Source Protein Redesign for You,
with Powerful New Features (with J. Martin, A. Lowegard,
M. Frenkel, M.. Hallen, A. Ojewole, J. Jou, S. Wang, and G. Holt).
Journal of Computational Chemistry 2018; 39(30):
2494-2507 Cover article.
Available here:
This work was presented at: Structural Bioinformatics and Computational Biophysics (3DSIG) track
of ISMB. Chicago, Il. July 6-12, 2018. (Selected for Oral
Presentation).
A critical analysis of computational protein design with sparse
residue interaction graphs (with
S. Jain, J. Jou, and I. Georgiev).
PLoS Comput. Biol. 2017 Mar 30;13(3):e1005346. doi:
10.1371/journal.pcbi.1005346.
OSPREY Predicts Resistance Mutations Using Positive and Negative
Computational Protein Design
(with Ojewole A, Lowegard A, Gainza P, Reeve SM, Georgiev I, and Anderson AC).
Methods Mol. Biol. 2017; 1529:291-306.
PMID: 27914058
Crystal structure, conformational fixation and entry-related
interactions of mature ligand-free HIV-1 Env (with
Do Kwon Y, Pancera M, Acharya P, Georgiev IS, Crooks ET, Gorman J,
Joyce MG, Guttman M, Ma X, Narpala S, Soto C, Terry DS, Yang Y, Zhou
T, Ahlsen G, Bailer RT, Chambers M, Chuang GY, Doria-Rose NA, Druz
A, Hallen MA, Harned A, Kirys T, Louder MK, O'Dell S, Ofek G, Osawa
K, Prabhakaran M, Sastry M, Stewart-Jones GB, Stuckey J, Thomas PV,
Tittley T, Williams C, Zhang B, Zhao H, Zhou Z, Lee LK,
Zolla-Pazner S, Baxa U, Schon A, Freire E, Shapiro L, Lee KK,
Arthos J, Munro JB, Blanchard SC, Mothes W, Binley JM, McDermott AB,
Mascola JR, and Kwong PD).
Nature Structural Molecular
Biology.
2015; (22): 522-531. doi: 10.1038/nsmb.3051.
PMID: 26098315
Enhanced potency of a broadly neutralizing HIV-1 antibody
in vitro improves protection against lentiviral infection
in vivo (with R. Rudicell, Y. Kwon, S.Y. Ko,
A. Pegu, M. Louder, I. Georgiev,
X. Wu, J. Zhu, J. Boyington, X. Chen, W. Shi, Z. Yang,
N. Doria-Rose, K. McKee, S. O'Dell, S. Schmidt, G.Y. Chuang, A. Druz,
C. Soto, Y. Yang, B. Zhang, T. Zhou, J.P. Todd, K. Lloyd, J. Eudailey,
K. Roberts,
R. Bailer, J. Ledgerwood, NISC
Comparative Sequencing Program, J. Mullikin, L. Shapiro, R. Koup,
B. Graham, M. Nason, M. Connors, B. Haynes, S. Rao, M. Roederer,
P. Kwong, J. Mascola, and G. Nabel).
Journal of Virology 2014; 88(21):12669-82.
Structure of an HIV-1 Neutralizing Antibody Target: A Lipid
Bound gp41 Envelope Membrane Proximal Region Trimer
(with P. Reardon, H. Sage,
D. Moses, J. Martin,
A. Munir,
B. Haynes, and
L. Spicer). Proc. Nat. Acad. Sci. U.S.A. (PNAS) 2014; 111(4):1391-6.
[Read the
open-access PDF
(PNAS website); View the structure:
PDB
Deposition 2m7w,
NMR Solution Structure of gp41-M-MAT, a membrane
associated MPER trimer from HIV-1 gp41,
(with
J. Martin,
P. Reardon, H. Sage, D. Moses, A. Munir,
B. Haynes,
L. Spicer).]
Design of Epitope-Specific Probes for Sera Analysis and Antibody
Isolation (with I. Georgiev, P. Acharya, S. Schmidt, Y. Li,
D. Wycuff, G. Ofek, N. Doria-Rose, T. Luongo, Y, Yang, T. Zhou, J.
Mascola, P. Kwong).
Retrovirology 2012; 9(Suppl.2):P50. From
AIDS Vaccine. Boston, MA. Sep. 9-12 (2012).
Computational Design of a PDZ Domain Peptide Inhibitor that
Rescues CFTR Activity (with K. Roberts, P. Cushing, P. Boisguerin,
and D. Madden). PLoS Computational Biology 2012;
8(4): e1002477. doi:10.1371/journal.pcbi.1002477.
Predicting resistance mutations using protein design algorithms
(with K. Frey, I. Georgiev, and A. Anderson).
Proc. Nat. Acad. Sci. U.S.A.(PNAS)
2010; 107(31):13707-12.
PubMed PMID: 20643959.
High-Resolution Protein Structure Determination Starting with a
Global Fold Calculated from Exact Solutions to the RDC Equations,
(with J. Zeng, J. Boyles, C. Tripathy, L. Wang, A. Yan, and P. Zhou).
Journal of Biomolecular NMR 2009;
45(3):265-281. PMID: 19711185
Computational Structure-Based Redesign of Enzyme Activity (with
C. Chen, I. Georgiev, and A. Anderson).
Proc. Nat. Acad. Sci. U.S.A. (PNAS) 2009; 106(10):3764-3769.
Automated NMR Assignment and Protein Structure Determination
using Sparse Dipolar Coupling Constraints (with
J. Martin). Progress in NMR Spectroscopy 2009; 55(2):101-127.
"Allosteric Inhibition of the Protein-Protein Interaction Between
the Leukemia-Associated Proteins RUNX1 and CBFβ"
(with R. Lilien
and M. Sridharan)
Chemistry & Biology 2007; 14(10):1186-1197.
Redesigning the PheA Domain of Gramicidin Synthetase Leads to a
New Understanding of the Enzyme's Mechanism and Selectivity (with
B. Stevens, R. Lilien, I. Georgiev, and A. Anderson).
Biochemistry 2006; 45 (51):15495-15504.
Structure Determination of Symmetric Homo-oligomers by a Complete Search
of Symmetry Configuration Space Using NMR Restraints and van der Waals
Packing (with S. Potluri, A. Yan, J. Chou, and C. Bailey-Kellogg).
Proteins 2006; 65(1):203-219.
A Novel Ensemble-Based Scoring and Search Algorithm
for Protein Redesign, and its Application to Modify the Substrate
Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme
(with R. Lilien, B. Stevens, and A. Anderson). Journal of Computational
Biology 2005; 12(6-7):740-761.
Phylogenetic Classification of Protozoa Based on the
Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate
Reductase-Thymidylate Synthase (with R. O'Neil, R. Lilien, R. Stroud, and A.
Anderson) Journal of Biological Chemistry 2003;
278(52):52980-52987.
The Crystal Structure of Dihydrofolate Reductase-Thymidylate Synthase
from Cryptosporidium hominis Reveals a Novel Architecture for the
Bifunctional Enzyme, (with R. O'Neil, R. Lilien, R. Stroud, and A. Anderson)
Journal of Eukaryotic Microbiology 2003;
50(6):555-556. Cover
article.
Intracellular neural recording with pure carbon nanotube probes
(with
I. Yoon,
K. Hamaguchi, I. Borzenets, G. Finkelstein, and R. Mooney).
PLoS One 8(6):e65715 (2013)
Ultra-sharp metal and nanotube-based probes for applications
in scanning microscopy and neural recording (with I. Borzenets,
I. Yoon, M. Prior, R. Mooney, and G. Finkelstein). Journal of
Applied Physics 2012; 111(7):74703-747036.
doi: 10.1063/1.3702802.
Crystal Structure of E. coli LptA in complex with Murgantia histrionica Thanatin
(with K. Huynh,
A. Kibrom and
P. Zhou). PDB
ID: 8GAL.
Crystal Structure of E. coli LptA in complex
with Chinavia Ubica Thanatin
(with K. Huynh,
A. Kibrom and
P. Zhou). PDB
ID: 8GAK
Crystal Structure of E. coli LptA in complex with Podisus
maculiventris Thanatin
(with K. Huynh,
A. Kibrom and
P. Zhou). PDB
ID: 8GAJ
Inhibitor R-27 in complex with Staph. aureus DHFR and tricyclic-NADPH (tNADPH)
(with
S. Reeve, S. Wang, and
D. Wright). PDB ID:
7T7S.
Inhibitor R-27 in complex with Staph. aureus DHFR and α-NADPH (with
S. Reeve, S. Wang, and
D. Wright). PDB ID:
7T7Q.
Independently verified structure of gp41-M-MAT, a membrane
associated MPER trimer from HIV-1 gp41, (with
J. Martin, P. Reardon, H. Sage, D. Moses, A. Munir,
B. Haynes, and L. Spicer) PDB ID: 2m7w .
Solution structure of the FF Domain 2 of human transcription
elongation factor CA150, (with M. Zeng, C. Tripathy, J. Boyles,
A. Yan, and P. Zhou), PDB ID: 2KIQ (2009).
Complete ensemble of NMR structures of Unphosphorylated Human
Phospholamban Pentamer, (with S. Potluri, A. Yan, J. Chou, and C.
Bailey-Kellogg), PDB ID: 2HYN.
Crystal structure of Dihydrofolate Reductase-Thymidylate Synthase
(DHFR-TS) from Cryptosporidium hominis, (with R. O'Neil, R. Lilien,
R. Stroud, and A. Anderson), PDB ID: 1QZF.
Algorithms in Structural Molecular Biology and Computational Chemistry
DexDesign: an osprey-based algorithm for designing
de novo D-peptide inhibitors. (with N. Guerin, H. Childs and
P. Zhou). Protein Engineering, Design, and Selection. 2024;
37:gzae007. doi: 10.1093/protein/gzae007. PMID: 38757573
DexDesign: A new OSPREY-based algorithm for designing de
novo D-peptide inhibitors (with N. Guerin, H. Childs, and
P. Zhou). Proceedings of the Annual International Conference on
Research in Computational Molecular Biology (RECOMB),
Boston. (April 29-May 2, 2024). In Lecture Notes in Computer
Science 14758, Springer (Cham,
Schweizerische Eidgenossenschaft) pp. 336-249.
RESISTOR: A New OSPREY Module to Predict Resistance Mutations
(with N. Guerin and T. Kaserer). Journal of Computational
Biology (Accepted, In press) 2022.
RESISTOR: An algorithm for predicting
resistance mutations using Pareto optimization over multistate
protein design and mutational signatures (with N. Guerin and
T. Kaserer). Proceedings of the Annual International Conference
on Research in Computational Molecular Biology (RECOMB), San
Diego. (May 22-25, 2022).
In Research in Computational Molecular Biology, RECOMB 2022,
Lecture Notes in Computer Science, vol. 13278. Springer (Cham,
Schweizerische Eidgenossenschaft). pp. 387-389.
Minimization-Aware Recursive K* (MARK*): A Novel, Provable
Algorithm that Accelerates Ensemble-based Protein Design and
Provably Approximates the Energy Landscape (with J. Jou, G. Holt,
and A. Lowegard).
Proceedings of the Annual International
Conference on Research in Computational Molecular Biology (RECOMB),
Washington, DC. (May 5-8, 2018). Springer Nature Switzerland AG (2019)
RECOMB 2019, Lecture Notes in Bioinformatics (LNBI) 11467, pp. 101–119.
[PDF, Supporting
Material ]
Protein Design by Provable Algorithms (with
M. Hallen). Communications of the ACM,
2019; 61(10): 76-84. DOI: 10.1145/3338124.
OSPREY 3.0: Open-Source Protein
Redesign for You, with Powerful New Features.
(with M. Hallen, J. Martin, et al).
Journal of Computational Chemistry 2018; 39(30):
2494-2507 Cover article.
Available here:
CATS (Coordinates of Atoms by Taylor Series): Protein design with
backbone flexibility in all locally feasible directions (with
M. Hallen). Proc. International Conference on Intelligent Systems
for Molecular Biology (ISMB), Prague (July, 2017). Journal
version: Bioinformatics (2017) 33 (14): i5-i12. DOI: https://doi.org/10.1093/bioinformatics/btx277
BBK* (Branch and Bound over K*): A Provable and
Efficient Ensemble-Based Protein Design Algorithm to Optimize
Stability and Binding Affinity over Large Sequence Spaces (with
A. Ojewole, J. Jou, and V. Fowler). Journal of Computational
Biology 2018; 25(7): 726–739.
This journal paper is based on our RECOMB (2017) conference paper:
BBK* (Branch and Bound over K*): A Provable and
Efficient Ensemble-Based Algorithm to Optimize
Stability and Binding Affinity over Large Sequence Spaces (with
A. Ojewole, J. Jou, and V. Fowler).
Proceedings of the Annual International Conference on Research in
Computational Molecular Biology (RECOMB), Hong Kong. (May 3-7, 2017).
In: Research in
Computational Molecular Biology,
Lecture
Notes in Computer Science (LNCS), Springer-Verlag
(Berlin) vol. 10229, pp. 157-172.
LUTE (Local Unpruned Tuple Expansion): Accurate
continuously flexible protein design with general energy functions
and rigid-rotamer-like efficiency (with M. Hallen and J. Jou).
Journal of Computational Biology
2016 Sep 28. PMID: 27681371
This journal paper is a revised paper based on the earlier Conference version:
LUTE (Local Unpruned Tuple Expansion): Accurate continuously
flexible protein design with general energy functions and
rigid-rotamer-like efficiency (with M. Hallen and
J. Jou). Proceedings of the Annual International Conference on
Research in Computational Molecular Biology (RECOMB), Los
Angeles, CA, April, 2016.
In Research in Computational Molecular Biology, Lecture Notes in
Bioinformatics (LNBI), Springer-Verlag (Berlin), Volume 9649, 2016,
pp. 122-136.
COMETS (Constrained Optimization of Multistate Energies by Tree
Search): A provable and efficient protein design algorithm to
optimize binding affinity and specificity with respect to sequence
(with M. Hallen). Journal of Computational Biology 2015
23(5):311-21. doi: 10.1089/cmb.2015.0188. Epub 2016 Jan 13..
This journal paper is a revised paper based on the earlier Conference version:
COMETS (Constrained Optimization of Multistate Energies by Tree
Search): A provable and efficient algorithm to optimize binding
affinity and specificity with respect to sequence (with
M. Hallen). Proceedings of the Annual International Conference
on Research in Computational Molecular Biology (RECOMB),
Warsaw, April 12-15, 2015.
In Research in Computational Molecular Biology Lecture Notes in
Computer Science, Springer-Verlag (Berlin), Volume 9029, 2015,
pp 122-135.
A compact representation of continuous energy surfaces for
more efficient protein design (with M. Hallen and P. Gainza).
Journal of Chemical Theory and Computation.
2015; 11(5):2292-2306.
Parallel Computational Protein Design (with Zhou Y and Zeng J.)
Methods Mol Biol. 2017;1529:265-277. PMID: 27914056
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming
Algorithm for Sparse Approximations of Computational Protein Design
(with J. Jou, S. Jain, and I. Georgiev).
Journal of Computational Biology 2015
doi: 10.1089/cmb.2017.0267. .
This journal paper is a revised paper based on the earlier Conference version:
BWM*: A Novel, Provable, Ensemble-based Dynamic Programming
Algorithm for Sparse Approximations of Computational Protein Design
(with J. Jou, S. Jain, and I. Georgiev). Proceedings of the
Annual International Conference on Research in Computational
Molecular Biology (RECOMB), Warsaw, April 12-15, 2015.
In Research in Computational Molecular Biology
Lecture Notes in Computer Science, Springer-Verlag (Berlin), Volume 9029, 2015, pp 154-166.
Fast search algorithms for Computational Protein Design (with
S.
Traore, K.
Roberts, D. Allouche,
I. Andre, T. Schiex, and S. Barbe).
Journal of Computational Chemistry 2016;
37(12):1048-58. doi: 10.1002/jcc.24290. Epub 2016 Feb 2. Cover Article.
Fast Gap-Free Enumeration of Conformations and Sequences for
Protein Design (with K. E. Roberts, P. Gainza, and M. A. Hallen).
Proteins (2015)
doi: 10.1002/prot.24870 volume 83 issue 10 pages 1859-1877.
Improved Energy Bound Accuracy Enhances the Efficiency of
Continuous Protein Design (with K. Roberts). Proteins:
Structure, Function, and Bioinformatics.
2015; 83(6):1151-64.
An efficient parallel algorithm for accelerating computational
protein design (with Y. Zhou, W. Xu, and J Zeng).
Bioinformatics. 2014 Jun 15;30(12):i255-i263. Proceedings
of ISMB, Boston, MA. doi: 10.1093/bioinformatics/btu264.
"OSPREY: Protein Design with Ensembles, Flexibility,
and Provable Algorithms" (with P. Gainza, K. Roberts, I. Georgiev,
R. Lilien, D. Keedy, C.-Y. Chen, F. Reza, A. Anderson,
D. Richardson, and J. S. Richardson).
Methods in Enzymology 2013; 523:87-107
"Simultaneous determination of subunit and complex structures of
symmetric homo-oligomers from ambiguous NMR data" (with H. Chandola
and C. Bailey-Kellogg). Proceedings of the 4th ACM
International Conference on Bioinformatics, Computational Biology,
and Biomedical Informatics (ACM BCB). Washington,
DC. September, 2013. ACM Press. pp. 171-180.
"Extracting Structural Information from Residual Chemical
Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations
and Applications to Determine Protein Structure" (with C. Tripathy,
A. Yan, and P. Zhou). Proceedings of the Annual
International Conference on Research in Computational Molecular
Biology (RECOMB), Beijing, China (2013). In: Research in
Computational Molecular Biology, Lecture Notes in Computer
Science (LNBI), Springer-Verlag (Berlin), Volume 7821 (2013).
pp. 271-284.
The Role of Local Backrub Motions in Evolved and Designed
Mutations (with D. Keedy, I. Georgiev, E. Triplett, D. Richardson,
and J. Richardson). PLoS Computational Biology
2012; 8(8):
e1002629. doi:10.1371/journal.pcbi.1002629.
"HASH: a Program to Accurately Predict Protein Hα (H-alpha)
Shifts from Neighboring Backbone Shifts" (with J. Zeng, and
P. Zhou). Journal of Biomolecular NMR 2012; Dec
16.
"Protein Design using Continuous Rotamers" (with P. Gainza and
K. Roberts). PLoS Computational Biology (2012)
8(1): e1002335. doi:10.1371/journal.pcbi.1002335.
Protein Side-Chain Resonance Assignment and NOE Assignment
Using RDC-Defined Backbones without TOCSY Data, (with J. Zeng and
P. Zhou). Journal of Biomolecular NMR 2011:
45(3):265-281.
A graphical method for analyzing distance restraints using
residual dipolar couplings for structure determination of symmetric
protein homo-oligomers (with J. Martin, A. Yan, C Bailey-Kellogg,
and P. Zhou). Protein Science 20(6):970-985 (2011) Mar
16. doi: 10.1002/pro.620. PMID: 21413097
A geometric arrangement algorithm for structure determination of
symmetric protein homo-oligomers from NOEs and RDCs
(with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou).
Journal of Computational Biology 2011; 18(11):1507-23.
NMR Structural Inference of Symmetric Homo-Oligomers (with
H. Chandola, A. Yan, S. Potluri, and C. Bailey-Kellogg). Journal
of Computational Biology 2011; 18(12):1757-75.
PMID: 21718128.
A Bayesian Approach for Determining Protein
Side-chain Rotamer Conformations using Unassigned NOE Data (with
J. Zeng, K. Roberts, and P. Zhou). Journal of Computational
Biology 2011; 18(11):1661-79.
Design of protein-protein interactions with a novel
ensemble-based scoring algorithm (with K. Roberts, P. Cushing,
P. Boisguerin, and D. Madden). In Proceedings of the Annual
International Conference on Research in Computational Molecular
Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes in
Computer Science, Springer (Berlin), Volume 6577, pp. 361-376 (2011), DOI:
10.1007/978-3-642-20036-6
A geometric arrangement algorithm for structure determination of
symmetric protein homo-oligomers from NOEs and RDCs
(with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou).
In Proceedings of the Annual International Conference on
Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes
in Computer Science, Springer (Berlin),
Volume 6577, pp. 222-237 (2011), DOI:
10.1007/978-3-642-20036-6.
Protein loop closure using orientational restraints from
NMR data
(with C. Tripathy, J. Zeng, and P. Zhou).
In Proceedings of the Annual International Conference on
Research in Computational Molecular Biology (RECOMB), Vancouver, CA (2011). In Lecture Notes
in Computer Science, Springer (Berlin),
Volume 6577, pp. 483-498 (2011), DOI:
10.1007/978-3-642-20036-6
A Bayesian approach for determining protein side-chain rotamer
conformations using unassigned NOE data (with J. Zeng, K. Roberts,
and P. Zhou). In Proceedings of the Annual International
Conference on Research in Computational Molecular Biology
(RECOMB), Vancouver, CA (2011). In Lecture Notes in Computer
Science, Springer (Berlin),
Volume 6577, pp. 563-578 (2011), DOI:
10.1007/978-3-642-20036-6
A Markov Random Field Framework for Protein Side-Chain Resonance
Assignment (with J. Zeng and P. Zhou). International Conference on
Research in Computational Molecular Biology (RECOMB), Lisbon,
Portugal. April/August, 2010.
In Lecture Notes in Computer Science, Springer
(Berlin) Volume LNBI 6044/2010, pp. 550-570. ISBN 978-3-642-12682-6.
Algorithms and Analytic Solutions using Sparse Residual
Dipolar Couplings for High-Resolution Automated Protein Backbone
Structure Determination by NMR (with A. Yershova, C. Tripathy, and
P. Zhou), Workshop on the Algorithmic Foundations of Robotics (WAFR),
Singapore (2010).
Algorithm for Backrub Motions in Protein Design (with
I. Georgiev, D. Keedy, J. Richardson, and D. Richardson).
Bioinformatics 2008; 4(13):i196-i204.
Proc. International Conference on Intelligent
Systems for Molecular Biology (ISMB), Toronto CA (July, 2008)
Structure Determination of Symmetric Protein Complexes by a
Complete Search of Symmetry Configuration Space Using NMR Distance
Restraints (with S. Potluri, A. Yan, J. Chou, and
C. Bailey-Kellogg). In Algorithmic Foundation of Robotics
VII. Springer Tracts in Advanced Robotics (vol. 47), Ed. S. Akella
et al. Springer-Verlag (Berlin) 2008 pp. 335-340.
A Hausdorff-Based NOE Assignment Algorithm Using Protein
Backbone Determined from Residual Dipolar Couplings and Rotamer
Patterns, (with J. Zeng, C. Tripathy, and P. Zhou). The
Computational Systems Bioinformatics Conference (CSB), Stanford
CA. (August, 2008) pp. 169-181.
Structure-Based Protein NMR Assignments using Native Structural
Ensembles (with S. Apaydin and V. Conitzer). Journal of
Biomolecular NMR 2008; 40(4):263-276.
PMID: 18365752.
The Minimized Dead-End Elimination Criterion and Its Application
to Protein Redesign in a Hybrid Scoring and Search Algorithm for
Computing Partition Functions over Molecular Ensembles (with
I. Georgiev and R. Lilien). Journal of Computational
Chemistry 2008;29(10):1527-42. PMID: 1829329
Dead-End Elimination with Backbone Flexibility (with I.
Georgiev). Proc. International Conference on Intelligent
Systems for Molecular Biology (ISMB), Vienna, Austria:
July 21-25, 2007. Appears in in
Bioinformatics 2007; 23(13):i185-i195.
A Complete Algorithm to Resolve Ambiguity for Inter-subunit NOE
Assignment in Structure Determination of Symmetric Homo-oligomers
(with S. Potluri, A. Yan, and C. Bailey-Kellogg). Protein
Science 2007; 16(1):69-81.
A Polynomial-Time Algorithm for De Novo Protein Backbone Structure
Determination from NMR Data (with L. Wang and R. Mettu). Journal of
Computational Biology 2006; 13(7): 1276-1288.
A Data-Driven, Systematic Search Algorithm for Structure Determination
of Denatured or Disordered Proteins (with L. Wang). The Computational
Systems Bioinformatics Conference (CSB), Stanford CA. (August, 2006)
Pages 67-78. ISBN 1-86094-700-X.
Improved Pruning Algorithms and Divide-and-Conquer Strategies for
Dead-End Elimination, with Application to Protein Design (with I. Georgiev
and R. Lilien), Proc. International Conference on Intelligent Systems
for Molecular Biology (ISMB), Fortaleza, Brazil (2006).
Bioinformatics 2006; 22(14):e174-183.
A Novel Minimized Dead-End Elimination Criterion and Its Application to
Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing
Partition Functions over Molecular Ensembles, (with I. Georgiev and R.
Lilien). Proceedings of the Tenth Annual International Conference on
Research in Computational Molecular Biology (RECOMB), Venice, Italy
(April 2-5, 2006). In Springer Berlin, Lecture Notes in Computer Science,
RECOMB 2006, LNBI 3909, pp. 530-545, 2006.
R. Mettu, R. Lilien, and B. R. Donald. High-Throughput Inference of
Protein-Protein Interfaces from Unassigned NMR Data. Bioinformatics
2005; 21(Suppl. 1):i292-i301.
Here is the accepted
manuscript, which does not contain the error
that Bioinformatics introduced in the abstract. The error is
corrected in the published Erratum.
L. Wang and B. R. Donald. An Efficient and Accurate Algorithm for
Assigning Nuclear Overhauser Effect Restraints Using a Rotamer Library
Ensemble and Residual Dipolar Couplings. The IEEE Computational Systems
Bioinformatics Conference (CSB), Stanford CA. (August, 2005) pp.
189-202.
L. Wang, R. Mettu, and B. R. Donald. An Algebraic Geometry Approach to
Protein Backbone Structure Determination from NMR Data. The IEEE
Computational Systems Bioinformatics Conference (CSB), Stanford CA.
(August, 2005) pp. 235-246.
High-Throughput Inference of Protein-Protein Interfaces from Unassigned
NMR Data (with R. Mettu and R. Lilien), Proc. International Conference
on Intelligent Systems for Molecular Biology (ISMB), Detroit, MI
(2005).
A Novel Ensemble-Based Scoring and Search Algorithm
for Protein Redesign, and its Application to Modify the Substrate
Specificity of the Gramicidin Synthetase A Phenylalanine Adenylation Enzyme
(with R. Lilien, B. Stevens, and A. Anderson). Journal of Computational
Biology 2005; 12(6-7):740-761.
Exact Solutions for Internuclear Vectors and
Backbone Dihedral Angles from NH Residual Dipolar Couplings in Two Media,
and Their Application in a Systematic Search Algorithm for Determining
Protein Backbone Structure (with L. Wang), Journal of Biomolecular
NMR 2004; 29(3):223-242.
An Expectation/Maximization Nuclear Vector
Replacement Algorithm for Automated NMR Resonance Assignments (with C.
Langmead). Journal of Biomolecular NMR 2004;
29(2):111-138.
A Subgroup Algorithm to Identify Cross-Rotation Peaks Consistent with
Non-Crystallographic Symmetry (with R. Lilien, C. Bailey-Kellogg, and A.
Anderson). Acta Crystallographica D: Biological Crystallography
2004; D60, 1057-1067.
Symmetry, Goniometers and
RDCs
(with A. Yan). Tutorial,
Donald Laboratory, Departments of Computer Science and Chemistry,
Dartmouth College, Hanover NH (2004).
Analysis of a Systematic Search-Based Algorithm for Determining Protein
Backbone Structure from a Minimal Number of Residual Dipolar Couplings (with
L. Wang). The IEEE
Computational Systems Bioinformatics Conference (CSB), Stanford CA
(August, 2004) pp. 319-330.
"A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated
NMR Resonance Assignments," (with C. Langmead, A. Yan, R. Lilien, and L.
Wang), Journal of Computational Biology 2004;
11(2--3):277-298.
A Probability-Based Similarity Measure for Saupe Alignment Tensors with
Applications to Residual Dipolar Couplings in NMR Structural Biology (with
A. Yan and C. Langmead). The International Journal of Robotics
Research Special Issue on Robotics Techniques Applied to Computational
Biology, 2005; (29)(2-3):165-182.
"An Exact Algorithm For Determining Protein Backbone Structure From NH
Residual Dipolar Couplings," (with L. Wang, R. Mettu, and R.Lilien), Proc. IEEE
Computational Systems Bioinformatics Conference (CSB), Stanford
University, Palo Alto (August 10, 2003) pp. 611-612. ISBN 0-7695-2000-6.
"Modeling Protein Flexibility for Structure-Based
Active Site Redesign", (with R.
Lilien and A.
Anderson), The Sixth Annual International Conference on Research in
Computational Molecular Biology (RECOMB), Washington DC (April 18-21,
2002). In Currents in Computational Molecular Biology, 2002 (ed. L.
Florea et al.) pp 122-123.
"Modeling of Protein Flexibility for Computational Active Site
Redesign," (with R. Lilien
and A. Anderson)
The 16th Annual National MD/PhD Conference, Given Institute, Aspen,
Colorado, July 13-15, 2001.
"Reducing Mass Degeneracy in SAR by MS (Structure-Activity Relation by
Mass Spectrometry) by Stable Isotopic Labeling," (with C. Bailey-Kellogg, J. Kelley, and C. Stein) The Journal of
Computational Biology, 8(1):19-36, 2001.
"The NOESY Jigsaw: Automated Protein Secondary
Structure and Main-Chain Assignment from Sparse, Unassigned NMR Data," (with
C. Bailey-Kellogg, A. Widge,
J. Kelley, M.
Berardi, and J. Bushweller), The Journal of Computational
Biology, 7(3-4) (2000) pp. 537-558.
Automated NMR Assignment and Protein Structure Determination
using Sparse Dipolar Coupling Constraints (with
J. Martin). Progress in NMR Spectroscopy 2009; 55(2):101-127.
Algorithmic Challenges in Structural Molecular Biology and
Proteomics, Plenary lecture at WAFR, Utrecht/Zeist, The Netherlands.
July 11-13, 2004. Appears in Springer
Tracts in Advanced Robotics (vol. 17), Springer (Berlin) 2005, pp. 1-10.
"Physical Geometric Algorithms for Structural Molecular Biology" (with
C. Bailey-Kellogg, J. Kelley, and R. Lilien) invited paper at the Special
Session on Computational Biology & Chemistry, Proc. International
Conference on Robotics and Automation (2001), Seoul, Korea, pp.
940-947.
Scientific
papers (with some pointers to videos) are provided for you here, in the list immediately below:
Intracellular neural recording with pure carbon nanotube probes
(with
I. Yoon,
K. Hamaguchi, I. Borzenets, G. Finkelstein, and R. Mooney).
PLoS One 8(6):e65715 (2013)
Planning and Control
for Microassembly of Structures
Composed of Stress-Engineered MEMS Microrobots (with C. Levey,
C. McGray, I. Paprotny, and D. Rus). International Journal of
Robotics Research 2013; 32(2):
218-246.
Turning-rate Selective Control: A New Method for Independent
Control of Stress-engineered MEMS Microrobots (with C. Levey and
I. Paprotny). Proceedings of Robotics: Science and
Systems Conference (RSS), University of Sydney, Sydney, NSW,
Australia. July 9-13, 2012 (In press).
The Compass That Steered Robotics. In Logic and
Program Semantics, Lecture Notes in Computer Science (LNCS) 7230,
Springer-Verlag (Berlin) 2012. pp. 50-65.
Ultra-sharp metal and nanotube-based probes for applications
in scanning microscopy and neural recording (with I. Borzenets,
I. Yoon, M. Prior, R. Mooney, and G. Finkelstein). Journal of
Applied Physics 2012; 111(7):74703-747036.
doi: 10.1063/1.3702802.
Simultaneous Control of Multiple MEMS Microrobots (with C. Levey,
I. Paprotny, and D. Rus). Proceedings of the Eighth International
Workshop on the Algorithmic Foundations of Robotics (WAFR),
Guanajuato, Mexico, December 7-9, 2008. Book chapter version (final) appears in:
Springer Tracts on Advanced Robotics, 57,
Springer-Verlag (Berlin), (2010), pp. 69-84.
Planar Microassembly by Parallel Actuation of MEMS
Microrobots (with C. Levey and I. Paprotny). Journal of
Microelectromechanical Systems 2008;
17(4): 789-808.
Assembly of Planar Structures by Parallel Actuation of MEMS
Microrobots (with C. Levey and I. Paprotny). Hilton Head
Workshop: A Solid-State Sensors, Actuators and Microsystems
Workshop pp. 202-207.
June 1-2, 2008, Hilton Head, SC.
A Steerable, Untethered MEMS Mobile Micro-Robot (with
C. Levey, C.McGray, I. Paprotny, and D. Rus). In
Robotics Research, Springer Tracks in Advanced Robotics 28,
ed. S. Thrun, et al., Springer-Verlag (Berlin) 2007,
pp. 337-356.
An Untethered, Electrostatic, Globally-Controllable MEMS Micro-Robot (with
C. Levey, C.McGray, I. Paprotny, and D. Rus). Journal of
Microelectromechanical Systems, 2006; 15(1):1-15.
A Steerable, Untethered, 250 x 60 µm MEMS Mobile Micro-Robot (with C.
Levey, C.McGray, I. Paprotny, and D. Rus). 12th International Symposium of
Robotics Research (ISRR), October 12-15, 2005, San Francisco, CA.
Power Delivery and Locomotion of Untethered Micro-Actuators (with C.
Levey, C. McGray, D. Rus, and M. Sinclair). Journal of
Microelectromechanical Systems 2003; 10(6):947-959.
Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design,
Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and
M. Sinclair). in Robotics Research eds. P. Dario and R. Chatila.
Springer-Verlag (London) 2005, pp.502--516.
Untethered Micro-Actuators for Autonomous Micro-robot Locomotion: Design,
Fabrication, Control, and Performance (with C. Levey, C. McGray, D. Rus, and
M. Sinclair) 11th
International Symposium of Robotics Research (ISRR), October 19-22,
2003, Siena, Italy.
Computational
Methods for the Design and Control of MEMS Micromanipulator Arrays (with K.-F.
Böhringer, G. Kovacs, N. MacDonald, and J. Suh) IEEE Computational
Science and Engineering, Vol. 4, No. 1. Special Issue on Computational
MEMS (Jan-March 1997). pp. 17-29.
K.-F.
Böhringer, B. R. Donald, and N. C. MacDonald, Classification
and Lower Bounds for MEMS Arrays and Vibratory Parts Feeders: What
Programmable Vector Fields Can (and Cannot) Do, IEEE
International Conference on Robotics and Automation (ICRA), Minneapolis,
Minnesota (April 1996).
Distributed Robotic
Manipulation: Experiments in Minimalism [TR FTP], in
International Symposium on Experimental Robotics, (ISER) Stanford, CA
(1995). Appears in: in Experimental Robotics IV, Lecture Notes in Control
and Information Sciences 223, ed. O. Khatib et al., Springer Verlag
(Berlin) 1997 pp. 11-25.
A Theory of
Manipulation and Control for Microfabricated Actuator Arrays,
Proceedings of the IEEE Workshop on Micro Electro Mechanical
Systems (MEMS), Oiso, Japan (January 1994).
Scientific
papers (with some pointers to videos) are provided for you here, in the list immediately below:
The Compass That Steered Robotics. In Logic and
Program Semantics, Lecture Notes in Computer Science (LNCS) 7230,
Springer-Verlag (Berlin) 2012. pp. 50-65.
Practical
Mobile Robot Self-Localization (with J. Howell) Proceedings,
International Conference on Robotics and Automation, San Francisco, CA,
April 24-28, 2000. pp. 3485-3492.
Movie, 4:30, Quicktime w/Sorenson codec, max 250 kb/s
(42MB)
B. R. Donald, J. Jennings, and D. Rus, Minimalism +
Distribution = Supermodularity [TR FTP], Journal
of Experimental and Theoretical Artificial Intelligence (JETAI), Special
issue on Software Architectures for Hardware Agents; Vol. 9 No. 2-3 (1997) pp.
293-321.
Proc. IEEE/Robotics Society of Japan International Workshop on Intelligent
Robots and Systems, (IROS) Pittsburgh, PA (1995).
. Program
Mobile Robots in Scheme
(with J. Rees)
Proc. IEEE International Conference on Robotics and Automation Nice,
France (May, 1992), pp. 2681-2688.
[PDF]
Many people do not realize that the title of this paper is in the
hortatory subjunctive mode. It should be read as: Program
Mobile Robots in Scheme! Note the exclamation point.
Towards a Theory of Information Invariants for Cooperating Autonomous
Mobile Robots, (with J. Jennings and D. Rus) International Symposium of
Robotics Research (ISRR). Hidden Valley, PA (October 2, 1993).
Sensor Interpretation and Task-Directed Planning Using
Perceptual Equivalence Classes (with J. Jennings). Proc. IEEE
International Conference on Robotics and Automation, Sacramento,
CA (April, 1991), pp. 190-197.
``The Motion of Planar Compliantly-Connected Rigid
Bodies in Contact, with Applications to Automatic Fastening,'' B. R. Donald
and D. Pai. International Journal of Robotics Research12(4), August 1993, pp. 307-338.
``Symbolic Methods for the Simulation of Planar Mechanical Systems in
Design,'' B. R. Donald and D. Pai. in Symbolic and
Numerical Computation for Artificial Intelligence, (ed. B. Donald
et al.) Academic Press, Harcourt Jovanovich, (London: 1992), pp.
245-258.
Planning Multi-Step Error Detection and Recovery Strategies.
International Journal of Robotics Research, 9(1),
1990. pp. 3-60.
Scientific
papers (with some pointers to videos) are provided for you here, in the list immediately below:
"Accessible
Animation and Customizable Graphics via Simplicial Configuration Modeling"
(with T. Ngo, D. Cutrell, J. Dana, L. Loeb, and S. Zhu), in Proc. ACM
SIGGRAPH (New Orleans) July, 2000, pp. 403-410.
Real-Time Robot Motion Planning Using Rasterizing Computer Graphics
Hardware, (with J.
Lengyel, M. Reichert, and D. Greenberg), Proc. SIGGRAPH '90,
Dallas, TX (Aug 1990), pp. 327-336.
The EIGHT Manual: An Introduction to Geometric Modelling and
Three-Dimensional Graphics on the Lisp Machine. Working Paper
262, MIT Artificial Intelligence Laboratory, Cambridge, MA (1984); and Cornell
Computer Science Department Technical Report TR 91-1186, Cornell
University, Ithaca NY (1991).
BUILDER: A Database and Display Program for Computer-aided
Architectural Design. Harvard Computer Graphics Conference, (Session 17,
Architectural Practice) July 27, 1982. Cambridge, MA.
A
Familiar Space in Two Dimensions: Piper Auditorium Computer-aided
Design (CAD) Study (with Paul Stevenson Oles). Design
Exhibition. Graduate School of Design, Harvard University (1982).
A geometric arrangement algorithm for structure determination of
symmetric protein homo-oligomers from NOEs and RDCs
(with J. Martin, A. Yan, C. Bailey-Kellogg, and P. Zhou).
Journal of Computational Biology 2011; 18(11):1507-23.
A graphical method for analyzing distance restraints using
residual dipolar couplings for structure determination of symmetric
protein homo-oligomers'' (with J. Martin, A. Yan, C Bailey-Kellogg,
and P. Zhou). Protein Science 20(6):970-985 (2011) Mar
16. doi: 10.1002/pro.620. PMID: 21413097
A
Rational Rotation Method for Robust Geometric Algorithms, (with J. Canny
and E. Ressler). Annual Symposium on Computational Geometry, Proceedings of
the Eighth Annual Symposium on Computational Geometry, (1992) Berlin, Germany
pp. 251-260.
I started putting my papers on the Web around 1994. For books and papers
before that, most are available at the publishers' web sites. I have
added a few pre-1994 papers to the list above, after getting a lot of requests..
Error
Detection and Recovery for Robot Motion Planning with
Uncertainty (1987). A revised version was published by Springer as
my
first book at Cornell:
Error Detection and Recovery in Robotics, Lecture Notes in
Computer Science, Vol. 336, Springer-Verlag, New York (1989). 314 pp. ISBN
0387969098