D.H. Mathews, J. Sabina, M. Zuker & D.H. Turner. Expanded Sequence
Dependence of Thermodynamic Parameters Improves Prediction of RNA
Secondary Structure J. Mol. Biol. 288, 911-940 (1999)
R.B. Lyngsø, M. Zuker & C.N.S. Pedersen. Fast evaluation
of internal loops in RNA secondary structure prediction. Bioinformatics
15, 440-445, (1999).
M. Zuker. Calculating nucleic acid secondary structure. Curr Opin
Struct Biol. 10, 303-310, (2000)
V. Moulton, M. Zuker, M. Steel, R. Pointon & D. Penny. Metrics
on RNA secondary structures. J. Computational Biology 7, 277-292,
(2000)
K. Kidd-Ljunggren, M. Zuker, I.L. Hofacker & A.H. Kidd. The
Hepatitis B Virus Pregenome: Prediction of RNA Structure and Implications
for the Emergence of Deletions. Intervirology 43, 154-164, (2000)
J.-M. Rouillard, C.J. Herbert & M. Zuker. OligoArray: Genome-scale
oligonucleotide design for microarrays. Bioinformatics 18 (3), 486-487,
(2002)
A. Waugh, P. Gendron, R. Altman, J.W. Brown, D. Case, D. Gautheret,
S.C. Harvey, N. Leontis, J. Westbrook, E. Westhof, M. Zuker, F.
Major RNAML: A standard syntax for exchanging RNA information. RNA
8 (6), 707-717, (2002)
back to Prof. Zuker's biography page
McCue L, Thompson
W, Carmack C, Lawrence C. 2002. Factors influencing the identification
of transcription factor binding sites by cross-species comparison
Genome Res 2002 Oct;12(10):1523-32.
Bayesian Clustering
with variable and transformation selection, Jiu, JS. Zhang, JL,
Palumbo, MJ and Lawrence, CE., Bayesian Statistics, 2002 (to appear)
BALSA: Bayesian
algorithm for local sequence alignment, Webb BJ, Liu JS, Lawrence
CE, Nucleic Acids Res. 2002 Mar 1;30(5):1268-77.
Statistical Prediction of Single-Stranded Regions in RNA Secondary
Structure and Application to Predicting Effective Antisense Target
Sites and Beyond., Ding Y. Lawrence C.E. Nucleic Acids Research,.
2001 Mar 1;29(5):1034-46, 2001
Human-Mouse
Genome Comparison to Locate Human Regulatory Sites, Wasserman, WW.
Palumbo MJ., Thompson, W. Fickett JW. and Lawrence C., Nature-Genetics
26(2):225-228, 2000
Functional Classification
of cNMP-Binding Proteins and Nucleotide Cyclases with Implications
for Novel Regulatory Pathways in Mycobacterium Tuberculosis. McCue,
L.A. McDonough, K.A. and Lawrence, C.E. Genome Research, 10:204-219,
2000.
Markovian Structures
in Biological Sequence Alignments, Liu, JS. Neuwald, AF. and Lawrence,
CE. J. American Statistical Association, 94:1-15,1999 (Awarded the
Mitchell prize the most outstanding paper in applied Bayesian statistics
in 2000)
Bayesian Adaptive
Sequence Alignment Algorithms, Zhu, J, Liu, JS, and Lawrence, CE.
Bioinformatics, 14:25-39, 1998
Bayesian Models
for Multiple Local Sequence Alignment and Gibbs Sampling Strategies,
Liu, JS. Neuwald, AF. and Lawrence, CE. J. American Statistical
Association, 90:1156-1170, 1995.
Detecting Subtle
Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment.
Lawrence, C. Altschul, S. Boguski, M. Liu, J. Neuwald, A. and Wootton,
J. Science, 262:208-214, 1993
Bayesian Models
for Multiple Local Sequence Alignment and Gibbs Sampling Strategies,
Liu, JS. Neuwald, AF. and Lawrence, CE. J. American Statistical
Association, 90:1156-1170, 1995.
back to Prof.Lawrence's biography page
Frank, J., Wagenknecht,
T., McEwen, B.F., Marko, M., Hsieh, C.-E., Mannella, C.A. (2002)
J. Struct. Biol. 138, 85-91. Three-dimensional imaging of biological
complexity.
Mannella, C.A.,
Pfeiffer, D.R., Bradshaw, P.C., Moraru, I.I., Slepchenko, B., Loew,
L.M., Hsieh, C., Buttle, K., Marko, M. (2001) IUBMB Life 52, 1-7.
Topology of the mitochondrial inner membrane: dynamics and bioenergetic
implications [with cover].
Verschoor, A.,
Tivol, W.F., Mannella, C.A. (2001) J. Struct. Biol. 133, 254-265.
Single-particle approaches in the analysis of small 2D crystals
of the mitochondrial channel, VDAC.
Frey, T, Mannella,
C.A. (2000) Trends Biochem. Sci. 25, 319-324. The internal structure
of mitochondria [with cover].
Deng, Y., Marko,
M., Buttle, K.F., Leith, A., Mieczkowski, M., Mannella, C.A. (1999)
J. Struct. Biol. 127, 231-239. Cubic membrane structure in amoeba
(Chaos carolinensis) mitochondria determined by electron microscopic
tomography [with cover].
Mannella, C.A.,
Neuwald, A.F., Lawrence, C.E. (1996) J. Bioenerg. Biomembr. 28,
163-169. Detection of likely transmembrane b-strand regions in sequences
of mitochondrial pore proteins using the Gibbs sampler.
Guo, X.W., Mannella,
C.A. (1992) Biophys. J. 63, 418-427. Classification of projection
images of crystalline arrays of the mitochondrial channel, VDAC,
embedded in aurothioglucose.
Forte, M., Guy,
H.R., Mannella, C.A. (1987) J. Bioenerg. Biomembr. 19, 341-350.
Molecular genetics of the VDAC ion channel: structural model and
sequence analysis.
Mannella, C.A.,
Frank, J. (1987) J. Molec. Evol. 24, 228-235. Interrelatedness of
5S RNA sequences investigated by correspondence analysis.
back to Dr. Mannella's biography page
Professor
Kristin P. Bennett
back to Prof. Bennett's biography page
"Regression Error Characteristic Curves ", Jinbo Bi and K. P. Bennett,
Proceedings of the 20th International Conference on Machine Learning, 2003.
"A Geometric Approach to Support Vector Regression", Jinbo Bi and
K. P. Bennett, to appear in Neurocomputing (special issue on support vector
machines), 2003.
Sparse Kernel Partial Least Squares Regression.
M. Momma and K.P. Bennett, Proceedings of Conference on Learning Theory, 2003.
K. P. Bennett and M. J. Embrechts, "An Optimization Perspective on Partial
Least Squares", in J.A.K. Suykens, G. Horvath, S. Basu, C.
Micchelli, J. Vandewalle (Eds.) Advances in Learning Theory: Methods,
Models and Applications, NATO Science Series III: Computer &
Systems Sciences, Volume 190, IOS Press Amsterdam, 2003,p. 227-250.
M. Song, C. Breneman, J. Bi, N. Sukumar, K. Bennett, S. Cramer, and N. Tugcu,
"Prediction of Protein Retention Times in Anion-Exchange Chromatography
Systems Using Support Vector Regression", September 2002, Journal of Chemical
Information and Computer Sciences.
K. Bennett, M. Momma, and J. Embrechts, MARK: A Boosting Algorithm for Heterogeneous
Kernel Models, Proceedings of SIGKDD International Conference on Knowledge Discovery
and Data Mining, 2002.
"Exploiting Unlabeled Data in Ensemble Methods", with A. Demiriz,
and R. Maclin, to appear in Proceedings of SIGKDD International Conference on
Knowledge Discovery and Data Mining, 2002.
C. Breneman, K. Bennett, M. Embrechts, S. Cramer, M. Song, and J. Bi, "Descriptor Generation, Selection and Model Building in Quantitative Structure-Property Analysis", in Chapter 11 of Experimental Design for Combinatorial and High Throughput Materials Development, J. Crawse editor, Wiley, 2002.
back to Prof. Bennett's biography page
Professor
Curt Breneman
back to Prof. Breneman's biography page
C. E. Whitehead,
N. Sukumar and C.M. Breneman, "Transferable Atom Equivalent Multi-Centered
Multipole Expansion Method", J. Comp. Chem. (Special Issue on
electron densities and electrostatic potentials) - S. R. Gadre, Ed.
(Invited 4/02 Accepted 8/02, In Press) 2002. (29 manuscript pages,
plus 8 tables, 13 figures and supplemental material) M. Embrechts,
F. Arciniegas, M. Ozdemir, C.M. Breneman, and K. Bennett, "Data
Mining Using 2-D Neural Network Sensitivity Analysis for Molecules"
ASME ANNIE Proceedings, C. Dagli, Ed. 2001. (6 pages)
Mark J. Embrechts, C. M. Breneman, Fabio Arciniegas, Muhsin Ozdemir,
and Kristin P. Bennett, "Data Mining Using 2-D Neural Network
Sensitivity Analysis for Molecules," in Intelligent Engineering
Systems through Artificial Neural Networks: Smart Engineering System
Design: Vol. 11, C. H. Dagli et al., Eds., pp. 345 - 350, ASME Press
(2001). (A Peer-Reviewed Edited Compilation)
C.M. Breneman, Mark J. Embrechts, Muhsin Ozdemir, Larry Lockwood,
Kristin Bennett, and Dirk DeVogelaere, "Feature Selection Methods
Based on Genetic Algorithms for In Silico Drug Design," Chapter
15 (26 pages) in Evolutionary Computation in Bioinformatics, Corne,
D. W., and Fogel, G.B., Eds., Morgan Kaufmann, San Francisco (2002)
(A Peer-Reviewed Edited Compilation)
Demiriz, A., Bennett, K. P., Breneman, C. M., Embrechts, M. J.
"Support Vector Machine Regression in Chemometrics". In
Computing Science and Statistics: Proceedings of Interface, "Frontiers
in Data Mining and Bioinformatics" Volume 33, Arnold Goodman
and Padhraic Smyth, Eds. 2001. (Refereed - 9 pages - published on
CD)
J. Bi, K.P Bennett, M. Embrechts and C.M. Breneman, "Dimensionality
Reduction via Sparse Support Vector Machines", JMLR (Journal
of Machine Learning Research - Special Issue on variable/feature
selection), (In Press) 2002. (15 manuscript pages, including figures
and tables)
Robert Kewley, Mark J. Embrechts, and Curt Breneman, "Neural
Network Sensitivity Analysis and Cross-Validation for Data Strip
Mining Problems," in Intelligent Engineering Systems through
Artificial Neural Networks, Vol. 8, Cihan Dagli et al., eds., pp.
391 - 396, ASME Press (1998).
Mark J. Embrechts, Robert Kewley, Jr., and Curt Breneman, "Computationally
Intelligent Data Mining for the Automated Discovery of Novel Pharmaceuticals,"
in Intelligent Engineering Systems through Artificial Neural Networks,
Vol. 8, Cihan Dagli et al., eds., pp. 397 - 403, ASME Press (1998).
C.M. Breneman, T.R. Thompson, M. Rhem, and M. Dung, "Electron
Density Modeling of Large Systems Using the Transferable Atom Equivalent
Method" Computers & Chemistry, 1995, 19(3), 161-179.
back to Prof. Breneman's biography page
Professor
Chris Bystroff
back to Prof. Bystroff''s biography page
Bystroff, C.
& Baker, D. (1997). Blind predictions of local protein structure
in CASP2 targets using the I-sites library. Proteins Suppl 1, 167-71.
Bystroff, C.
& Baker, D. (1998). Prediction of local structure in proteins
using a library of sequence-structure motifs. J Mol Biol 281, 565-77.
Bystroff, C.
& Garde, S. (2003). Helix propensitites of short peptides: Molecular
dynamics versus Bioinformatics. Proteins 50, (in press).
Bystroff, C.
& Shao, Y. (2002). Fully automated ab initio protein structure
prediction using I-SITES, HMMSTR and ROSETTA. Bioinformatics 18,
S54-61.
Bystroff, C.,
Simons, K. T., Han, K. F. & Baker, D. (1996). Local sequence-structure
correlations in proteins. Curr Opin Biotechnol 7, 417-21.
Bystroff, C.,
Thorsson, V. & Baker, D. (2000). HMMSTR: A hidden markov model
for local sequence-structure correlations in proteins. Journal of
Molecular Biology 301, 173-90.
Han, K. F.,
Bystroff, C. & Baker, D. (1997). Three-dimensional structures
and contexts associated with recurrent amino acid sequence patterns.
Protein Sci 6, 1587-90.
Hu, J., Shen,
X., Shao, Y., Bystroff, C. & Zaki, M. J. (2002). BIOKDD 2002,
Edmonton, Canada.
Simons, K. T.,
Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C. & Baker,
D. (1999). Improved recognition of native-like protein structures
using a combination of sequence-dependent and sequence-independent
features of proteins. Proteins 34, 82-95.
Thayer, E. C.,
Bystroff, C. & Baker, D. (2000). Detection of protein coding
sequences using a mixture model for local protein amino acid sequence.
J Comput Biol 7, 317-27.
Yi, Q., Bystroff,
C., Rajagopal, P., Klevit, R. E. & Baker, D. (1998). Prediction
and structural characterization of an independently folding substructure
in the src SH3 domain. J Mol Biol 283, 293-300.
Zaki, M. J.
& Bystroff, C. (2001). Mining Residue Contacts in Proteins.
In Data Mining for Scientific and Engineering Applications (R. Grossman,
C. Kamath, P. Kegelmeyer, Kumar, V. & Namburu, R., eds.), pp.
141-164.
Kluwer Academic Publishers,, Boston, MA.
Zaki, M. J.,
Shan, J. & Bystroff, C. (2000). Proceedings IEEE International
Symposium on Bio-Informatics and Biomedical Engineering, Arlington,
VA, USA.
back to Prof. Bystroff's biography page
Dr.
Ye Ding
back to Dr. Ding's biography page
Ding, Ye and Lawrence, C.E. (2003) Statistical algorithms for folding
and target accessibility prediction and design of nucleic acids.
Pending U.S. Patent, filed on January 28, 2003.
Ding, Ye (2002).
Rational statistical design of antisense oligonucleotides for high
throughput functional genomic and drug target validation. Statistica
Sinica 12, 273-296.
Ding, Ye and
Charles E. Lawrence (2001). Statistical prediction of single-stranded
regions in RNA secondary structure with application to predicting
effective antisense target sites and beyond. Nucleic Acids Research,
29, 1034-1046.
Ding, Ye and
Lawrence, C.E. (1999) A Bayesian statistical algorithm for RNA secondary
structure prediction. Computers & Chemistry 23, 387-400.
back to Dr. Ding's biography page
Professor Mark Embrechts
back to Prof. Embrects's biography page
Embrechts, M. J., Arciniegas, F., Ozdemir. [2003] "Data Mining
Using 2-D Neural Network Sensitivity Analysis for Molecules,"
Smart Engineering Systems Design (in print).
Breneman, C. M., Bennett, K. P., Embrechts, M., Cramer, S., Song,
M., and Bi, J. [2002] "Descriptor Generation, Selection and Model
Building in Quantitative Structure-Property Analysis," Chapter
11 in QSAR Developments, Crawse, J. N., Ed., John Wiley.
Embrechts, M. J., Ozdemir, M., Lockwood, L. Breneman, C., Bennett,
C. and DeVogelaere, D. [2002] "Feature Selection Methods Based
on Genetic Algorithms for In-Silico Drug Design," Chapter 13
in Evolutionary Computation in Bioinformatics, David W. Corne and
Gary B. Fogel, Eds., Morgan Kaufmann, San Francisco, CA.
Demiriz, A., Bennett, K. P., and Embrechts, M. [2002] "A Genetic
Algorithm Approach for Semi-Supervised Clustering," Smart Engineering
Systems Design, Vol. 4, pp 35-44.
Kewley, R. H., Embrechts, M. J. and Breneman, C. [2000] "Data
Strip Mining for the Virtual Design of Pharmaceuticals with Neural
Networks," IEEE Transactions on Neural Networks, Vol. 11 (3),
pp. 668-679.
Non-Project Related Publications
Alan Bivens, J. A., Szymanski, B., Embrechts, M. J. [2002] "Network
Congestion Arbitration and Source problem Prediction Using Neural
Networks," Smart Engineering Systems Design, Vol. 4, pp. 243-252.
Kewley, R. H., Jr. and Embrechts, M. J. [2002] "Computational
Military Tactical Planning Systems," IEEE Transactions on Systems,
Man, and Cybernetics Part C, Vol. 32 (2) pp. 161-171.
Embrechts, M. J. and Harsson, L. E. [2001] "A Neural Network
Controller of Nonholonomic Systems using a Specialized Training Technique,"
International Journal of Smart Systems Design, Vol. 3, pp. 203-216.
Eklund, N., and Embrechts, M. J., [2001] "Multi-Objective Optimization
of Spectra Using Genetic Algorithms," Journal of the Illuminating
Engineering Society, Vol. 30 (2), pp. 65-72.
Bengio, Y., Buhman, J. M., Embrechts, M., J. and Zurada, J. M. [2000]
"Introduction to the Special Issue on Neural Networks for Data
Mining and Knowledge Discovery," Guest Editorial, IEEE Transactions
on Neural Networks, Vol. 11, No 3, pp. 545 - 549.
Professor
Shekhar Garde
back to Prof. Garde's biography page
C. Bystroff and S. Garde, "Helix Propensities of Short Peptides:
Molecular Dynamics versus Bioinformatics", Proteins (in press)
(2003).
T. Ghosh, S. Garde, and Angel E. Garcia, "Molecular Evidence
for Alpha-helix Stabilization by Shielding of the Backbone Hydrogen
Bonds by Side Chains", submitted, (2003).
T. Ghosh, Angel E. Garcia, and S. Garde, "Water-Mediated Three-Particle
Hydrophobic Interactions Between Hydrophobic Solutes: Size, Pressure,
and Salt Dependences", J. Phys. Chem. B, 107, 612-617 (2003).
S. Garde, L. Yang, J. S. Dordick, and M. E. Paulaitis, "Molecular
Dynamics Simulation of C_8E_5 Micelle in Explicit Water: Structure
and Hydrophobic Solvation Thermodynamics", Molecular Physics,
100, 2299-2306 (2002).
T. Ghosh, Angel E. Garcia, and S. Garde, "Enthalpy and Entropy
Contributions to the Pressure Dependence of Hydrophobic Interactions",
J. Chem. Phys., 116, 2480-2486 (2002). [abstract]
T. Ghosh, Angel E. Garcia, and S. Garde, "Molecular Dynamics
Simulations of Pressure Effects on Hydrophobic Interactions",
J. Am. Chem. Soc., 123, 10997-11003 (2001). [abstract]
A. Kalra, N. Tugcu, S. Cramer, and S. Garde, "Salting-in and
Salting-out of Hydrophobic Solutes in Aqueous Salt Solutions",
Journal of Physical Chemistry B., 105, 6380-6386 (2001). [abstract]
S. Garde and H. S. Ashbaugh, "Temperature Dependence of Hydrophobic
Hydration and Entropy Convergence in an Isotropic Model of Water",
Journal of Chemical Physics, 115, 977-982 (2001). [abstract]
G. Hummer, A. E. García, and S. Garde, "Helix nucleation
kinetics using molecular simulations in explicit solvent",
Proteins: Struct. Funct. Genet., 42, 77-84 (2001). [abstract]
back to Prof. Garde's biography page
Dr. Lee Ann McCue
back to Dr. Lee Ann McCue's biography page
Publications related to Bioinformatics:
Qin, Z.S., McCue, L.A., Thompson, W., Mayerhofer, L., Lawrence, C.E., and Liu, J.S. (2003) Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nature Biotech. 21:435-439.
McCue, L.A., Thompson, W., Carmack, C.S., and Lawrence, C.E. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res. 12:1523-1532.
McCue, L.A., Thompson, W., Carmack, C.S., Ryan, M.P., Liu, J.S., Derbyshire, V., and Lawrence, C.E. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nuc. Acids Res. 29:774-782.
Florczyk, M.A., McCue, L.A., Purkayastha, A., Currenti, E., Wolin, M.J., and McDonough, K.A. (2003) A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression. Infect. Immun. 71:5332-5343.
Purkayastha, A., McCue, L.A., and McDonough, K.A. (2002) Identification of
a Mycobacterium tuberculosis putative classical nitroreductase
gene whose expression is coregulated with that of the acr
gene within macrophages, in standing versus shaking cultures, and
under low oxygen conditions. Infect. Immun. 70:1518-1529
Florczyk, M.A., McCue, L.A., Stack, R.F., Hauer, C.R., and McDonough, K.A. (2001) Identification of mycobacterial proteins differentially expressed under standing versus shaking culture conditions using MALDI-TOF mass spectrometry. Infect. Immun. 69:5777-5785.
McCue, L.A., McDonough, K.A., and Lawrence, C.E. (2000) Functional classification of cNMP-binding proteins and nucleotide cyclases with implications for novel regulatory pathways in Mycobacterium tuberculosis. Genome Res. 10:204-219.
Qu, K., McCue, L.A., and Lawrence, C.E. (1998) Bayesian protein family classifier.
Proc. Int. Conf. Intell. Syst. Mol. Biol. 6:131-139.
Publications in Gene Expression:
Qin, Z.S., McCue, L.A., Thompson, W., Mayerhofer, L., Lawrence,
C.E., and Liu, J.S. (2003) Identification of co-regulated genes
through Bayesian clustering of predicted regulatory binding sites.
Nature Biotech. 21:435-439.
McCue, L.A., Thompson, W., Carmack, C.S., and Lawrence, C.E. (2002)
Factors influencing the identification of transcription factor binding
sites by cross-species comparison. Genome Res. 12:1523-1532.
McCue, L.A., Thompson, W., Carmack, C.S., Ryan, M.P., Liu, J.S.,
Derbyshire, V., and Lawrence, C.E. (2001) Phylogenetic footprinting
of transcription factor binding sites in proteobacterial genomes.
Nuc. Acids Res. 29:774-782.
Florczyk, M.A., McCue, L.A., Purkayastha, A., Currenti, E., Wolin,
M.J., and McDonough, K.A. (2003) A family of acr-coregulated
Mycobacterium tuberculosis genes shares a common DNA motif
and requires Rv3133c (dosR or devR) for expression.
Infect. Immun. 71:5332-5343.
back to Dr. Lee Ann McCue's biography page
Professor
Lee Newberg
back to Prof. Newberg's biography page
L. A. Newberg.
The number of clone orderings. Discrete Applied Mathematics, 69:233--245,
1996. R. M. Karp and L. A. Newberg. An algorithm for analyzing probed
partial digestion experiments. Computer Applications in the Biosciences,
11(3):229--235, June 1995.
R. M. Karp and L. A. Newberg. An algorithm for analyzing probed
partial digestion experiments. Computer Applications in the Biosciences,
11(3):229-235, June 1995.
F. Alizadeh,
R. M. Karp, L. A. Newberg, and D. K. Weisser. Physical mapping of
chromosomes: A combinatorial problem in molecular biology. Algorithmica,
13(1-2):52-76, January-February 1995.
L. A. Newberg. Finding a most likely clone ordering from oligonucleotide
hybridization data. Genomics, 21(3):602--611, June 1994.
L. A. Newberg.
Finding a most likely clone ordering from oligonucleotide hybridization
data. Genomics, 21(3):602--611, June 1994.
L. A. Newberg
and D. Naor. A lower bound on the number of solutions to the probed
partial digest problem. Advances in Applied Mathematics, 14(2):172--183,
June 1993.
F. Alizadeh,
R. M. Karp, L. A. Newberg, and D. K. Weisser. Physical mapping of
chromosomes: A combinatorial problem in molecular biology. In Proceedings
of The Fourth Annual ACM-SIAM Symposium on Discrete Algorithms,
Austin, TX, January 1993. ACM Press.
E. S. Lander,
P. Green, J. Abrahamson, A. A. Barlow, M. J. Daly, S. E. Lincoln,
and L. A. Newberg. MAPMAKER: An interactive computer package for
constructing primary genetic linkage maps of experimental and natural
populations. Genomics, 1(2):174--181, October 1987.
back to Prof.Newberg's biography page
Professor
John Salerno
back to Prof. Salerno's biography page
Salerno,J.C. et al (1997) An autoinhibitory control element defines
calcium regulated isoforms of NO synthase J. Biol. Chem. 272, 29769-29777
Salerno, J. C., Martasek, P., Williams, R. F., and Masters, B. S.
S. (1997) Substrate And Substrate Analog Binding To Endothelial
Nitric Oxide Synthase - Electron Paramagnetic Resonance As An Isoform-Specific
Probe Of The Binding Mode Of Substrate Analogs. Biochemistry 36:
11821 - 11827.
Migita, C. T., Salerno, J. C., Masters, B. S. S., Martasek, P. Mcmillan,
K. and Ikedasaito, M. (1997) Substrate Binding-Induced Changes In
The Epr Spectra Of The Ferrous Nitric Oxide Complexes Of Neuronal
Nitric Oxide Synthase. Biochemistry 36: 10987 -10992.
Zehr, J. P., Harris, D., Dominic, B., and Salerno, J. (1997) Structural
Analysis Of The Trichodesmium Nitrogenase Iron Protein - Implications
For Aerobic Nitrogen Fixation Activity. FEMS Microbiology Letters
153: 303 - 309.
Martasek P, Miller RT, Liu Q, Roman LJ, Salerno JC, Migita CT, Raman
CS, Gross SS, Ikeda-Saito M, (1998) The Cys331A mutant of neuronal
nitric oxide synthase is defective in arginine binding J. Biol.
Chem. 273(52), 34799-34805
Martasek, P., Roman, L.J., Raman, C.S., Liu, Q., Salerno, J.C.,
Ikeda-Saito, M., Gross, S.S., and Masters, B.S.S. (1998) The Cys331A
mutant of nNOS is defective in arginine binding Portland Press Proceedings:
Biology of Nitric Oxide, vol 6
Hunter, D.J., Salerno, J.C. and Ingledew, W.J. (1998) Angular dependence
of electron paramagnetic resonances of an azide-NO complex of cytochrome
c oxidase: orientation of the haem-copper axis in cytochrome aa3
from ox heart. B.B.A. 1364, 55-62
Hastings SF, Kaysser, Jiang F., SalernoJ.C. , Gennis R.B., Ingledew
WJ (1998) Identification of a stable semiquinone intermediate in
the purified and membrane bound ubiquinol oxidase-cytochrome bd
from Escherichia coli. Eur J Biochem 255, 317-2
Masters, B.S.S., Miller, R.T., Roman, L.J., Nishmura, J.S., Panda,
S., Harris, D.E., Horowitz, P., Shea, T.M., Zhang, J., Kim, J.-J.,
and Salerno, J.C. ( 1999) Structural Aspects of the Flavoprotein
Domains of Isoforms of Nitric Oxide Synthase in: Flavins and Flavoproteins
1999: Proc. 13th Int. Symp., Konstanz, Germany; Ghisla S, Kroneck
P, Macheroux P, Sund H, Editors; Agency for Scientific Publ., Berlin
Hunter, D. J., Oganesyan, V. S. Salerno, J. C. Butler, C. S. Ingledew,
W. J. Thomson, A. J. (2000). Angular dependence of perpendicular
and parallel mode electron paramagnetic resonance of oxidized beef
heart cytochrome c oxidase. Biophys J 78: 439-450.
Smith, S.M.E., Sham, C., Roman, L. , Martasek, P., and Salerno,
J.C. (2001) Titration of low Kd binding sites: binding of arginine
analogs to nitric oxide synthases Nitric Oxide Journal 5(5), 442-452
Ingledew, W.J., Salerno, J.C., Smith, SM.E. and Rich, P. (2002)
Neuronal nitric oxide synthase ligand and protein vibrations at
the substrate binding site. A study by FTIR. Biochemistry.;41(26):8377-84.
Ghosh, D.K. and Salerno J.C. (2003) Nitric oxide synthases: domain
structure and alignment in enzyme function and control. Front Biosci.
8: 193-209.
back to Prof. Salerno's biography page
Professor
Mark Wentland
back to Prof. Wentlands biography page
Wentland, M.
P.; Ye, Y.; Cioffi, C. L.; Lou, R.; Zhou, Q.; Xu, G.; Duan, W.;
Dehnhardt, C. M.; Sun, X.; Cohen, D. J.; Bidlack, J. M. "Syntheses
and Opioid Receptor Binding Affinities of 8-Amino-2,6-methano-3-benzazocines."
J. Med. Chem. 2003, 46, 838-849.
Lou, R.; VanAlstine, M.; Sun, X.; Wentland, M. P. "Preparation
of N-Hydroxysuccinimido Esters via Palladium-Catalyzed Carbonylation
of Aryl Triflates and Halides." Tetrahedron Lett. 2003, 44,
2477 - 2480.
Bidlack, J. M.; Cohen, D. J.; McLaughlin, J. P.; Lou, R.; Ye, Y.;
Wentland, M. P. "8-Carboxamidocyclazocine: A Long-Acting, Novel
Benzomorphan." J. Pharmacol. Exp. Ther. 2002, 302, 374-380.
Wentland, M. P.; Lou, R.; Dehnhardt, C. M.; Duan, W.; Cohen, D.J.;
Bidlack, J. M. "3-Carboxamido Analogues of Morphine and Naltrexone:
Synthesis and Opioid Receptor Binding Properties." Bioorgan.
Med. Chem. Lett. 2001, 11, 1717-1721.
Wentland, M. P.; Lou, R.; Ye, Y.; Cohen, D. J.; Richardson, G. P.;
Bidlack, J. M. "8-Carboxamidocyclazocine Analogues: Redefining
the Structure-Activity Relationships of 2,6-Methano-3-benzazocines."
Bioorgan. Med. Chem. Lett. 2001, 11, 623-626.
Wentland, M.P.; Duan, W.; Cohen, D.J.; Bidlack, J.M. "Selective
Protection and Functionalization of Morphine: Synthesis and Opioid
Receptor Binding Properties of 3-Amino-3-desoxymorphine Derivatives."
J. Med. Chem. 2000, 43, 3558-3565.
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to Prof. Wentlands biography page
Professor
Mohammed J. Zaki
back to Prof. Zaki's biography page
Jason Wang,
Mohammed J. Zaki, Hannu Toivonen, Dennis Shasha (editors), Data
Mining in Bioinformatics, Springer London Ltd., to appear late 2003
(collection of invited chapters).
Mohammed J.
Zaki, Mining Data in Bioinformatics, to appear in Nong Ye (ed.),
Handbook of Data Mining, Lawrence Earlbaum Associates, 2003.
Mohammed J.
Zaki, Shan Jin and Chris Bystroff, Mining Residue Contacts in Proteins
Using Local Structure Predictions, to appear in IEEE Transactions
on Systems, Man and Cybernetics, special issue on Bioengineering
and Bioinformatics, N. Boubakis (ed.), 2003.
Mohammed J.
Zaki, Hannu T.T. Toivonen, and Jason T.L. Wang (editors), Proceedings
of the 2nd BIOKDD Workshop on Data Mining in Bioinformatics (with
SIGKDD02), ACM Press, July 2002.
Jingjing Hu,
Xioalan Shen, Yu Shao, Chris Bystroff, Mohammed J. Zaki, Mining
Protein Contact Maps, 2nd BIOKDD Workshop on Data Mining in Bioinformatics,
Edmonton, Canada, July 2002.
Yu Shao, Malik
Magdon-Ismail, Danial Freedman, Srinivas Akella, Mohammed Zaki,
Chris Bystroff, Compression of Protein Conformational Space (Poster),
in 6th Annual International Conference on Research in Computational
Molecular Biology (RECOMB02), Washington, DC, April 2002.
Mohammed J.
Zaki, Hannu T.T. Toivonen, and Jason T.L. Wang (editors), Proceedings
of the 1st BIOKDD Workshop on Data Mining in Bioinformatics (with
SIGKDD01), San Francisco, CA, August 2001.
Mohammed J.
Zaki, Shan Jin, Chris Bystroff, Mining Residue Contacts in Proteins
Using Local Structure Predictions, in IEEE International Symposium
on Bioinformatics and Biomedical Engineering, pp 168-175, Washington,
DC, November 2000.
Vineet Gupta,
Srinivasan Parthasarathy, Mohammed J. Zaki, Arithmetic and Logic
Operations with DNA, 3rd DIMACS Workshop on DNA Based Computers,
Philadelphia, Pennsylvania, June 1997.
back to Prof. Zaki's biography page
Prof. Zuker