Publications

[2008] [2007] [2006] [2005] [2004] [2003] [2002] [2001] [2000] [1999] [1998] [1997] [1996]

2008

Ward, R.M., S. Erdin, T.A. Tran, D.M. Kristensen, A.M. Lisewski, and O. Lichtarge.
De-Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features. PLoS ONE. 2008 May 7;3(5):e2136.
[Abstract]. [PDF].

Kristensen, D.M., R.M. Ward, A.M. Lisewski, S. Erdin, B.Y. Chen, V.Y. Fofanov, M. Kimmel, L.E. Kavraki, and O. Lichtarge.
Prediction of Enzyme Function Based on 3D Templates of Evolutionarily Important Amino Acids. BMC Bioinformatics. 2008 Jan 11;9(1):17.
[Abstract]. [PDF]. [Supplementary Material].

Mihalek, I., I. Res and O. Lichtarge.
Background frequencies for residue variability estimates: BLOSUM revisited. BMC Bioinformatics. 2007 Dec 27;8(1):488 [Epub ahead of print].
[Abstract]. [PDF]. [Data Set].

2007

Shin, H., A. M. Lisewski and O. Lichtarge
Graph sharpening plus graph integration: a synergy that improves protein functional classification. Bioinformatics 2007 23: 3217-3224; doi:10.1093/bioinformatics/btm511. Advance Access Oct 31.
[Abstract]. [PDF]. [Supplementary Material].

Chen, B. Y., V. Y. Fofanov, D. H. Bryant, B. D. Dodson, D. M. Kristensen, A. M. Lisewski, M. Kimmel, O. Lichtarge, and L. E. Kavraki.
The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs. J Comput Biol. 2007 Jul-Aug;14(6):791-816.
[Abstract].

Chen, B. Y., D. H. Bryant, A. E. Cruess, J. H. Bylund, V. Y. Fofanov, D. M. Kristensen, M. Kimmel, O. Lichtarge, and L. E. Kavraki.
Composite motifs integrating multiple protein structures increase sensitivity for function prediction. Comput Syst Bioinformatics Conf. 2007;6:343-55.
[Abstract].

Mihalek, I., I. Res, O. Lichtarge.
On itinerant waters and detectability of protein-protein interfaces through comparative analysis of homologues. J. Mol. Biol. 2007 Jun 1;369(2):584-95. Epub 2007 Mar 24.
[Abstract]. [PDF]. [Data Set].

Ribes-Zamora, A., I. Mihalek, O. Lichtarge, and A. A. Bertuch.
Distinct faces of the Ku heterodimer mediate DNA repair versus telomeric functions. Nature Structural and Molecular Biology. 2007 Apr;14(4):301-7. Epub 2007 Mar 11.
[Abstract]. [PDF].

Chen B.Y, Bryant D.H., Fofanov V.Y., Kristensen D.M., Cruess A.E., Kimmel M., Lichtarge O., Kavraki L.E.
Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction. J Bioinform Comput Biol. 2007 Apr;5(2):353-82.
[Abstract]. [PDF].

Item C.B., Mihalek I., Lichtarge O., Jalan A., Vodopiutz J., Muhl A., Bodamer O.A.
Manifestation of hawkinsinuria in a patient compound heterozygous for hawkinsinuria and tyrosinemia III. Mol Genet Metab. 2007 Jun 6; [Epub ahead of print].
[Abstract]. [PDF].

Lisewski, A.M. and O. Lichtarge.
Rapid detection of similarity in protein structure and function through contact metric distances. Nucl. Acids Res. 2006 34: e152; doi:10.1093/nar/gkl788.
[Abstract]. [PDF].

Chen, BY, DH Bryant, VY Fofanov, DM Kristensen, AE Cruess, M Kimmel, O Lichtarge, and LE Kavraki.
Cavity-aware motifs reduce false positives in protein function prediction. Comput. Syst. Bioinformatics Conf. 2006;:311-23 PMID: 17369649
[Abstract]. [PDF].

2006

Rajagopalan L, Patel N, Madabushi S, Goddard JA, Anjan V, Lin F, Shope C, Farrell B, Lichtarge O, Davidson AL, Brownell WE, Pereira FA.
Essential Helix Interactions in the Anion Transporter Domain of Prestin Revealed by Evolutionary Trace Analysis. J Neurosci. 2006 Dec 6;26(49):12727-12734.
[Abstract]. [PDF].

Morgan, D.H., D.M. Kristensen, D. Mittleman, and O. Lichtarge.
ET Viewer: An Application for Predicting and Visualizing Functional Sites in Protein Structures. Bioinformatics. 2006 Aug 15;22(16):2049-50. Epub 2006 Jun 29.
[Abstract]. [PDF].

Yao, H.S., I. Mihalek, and O. Lichtarge.
Rank Information: a Structure-independent Measure of Evolutionary Trace Quality that Improves Identification of Protein Functional Sites. Proteins. 2006 Oct 1;65(1):111-23.
[Abstract]. [PDF].

Mihalek I., I. Res and O. Lichtarge.
"Evolutionary Trace Report Maker: a new type of service for comparative analysis of proteins." Bioinformatics. 2006 Jul 1;22(13):1656-7. Epub 2006 Apr 27.
[Abstract]. [PDF].

Raviscioni M., Q. He, E.M. Salicru, C.L. Smyth, and O. Lichtarge.
"Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors." Proteins. 2006 Sep 1;64(4):1046-57.
[Abstract]. [PDF].

Chen, B.Y., V.Y. Fofanov, D.H. Bryant, B.D. Dodson, D.M. Kristensen, A.M. Lisewski, M. Kimmel, O. Lichtarge and L.E. Kavraki.
"Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction." Lecture Notes in Computer Science 3909: 500-515 2006. Presented at Research in Computational Molecular Biology: 10th Annual International Conference, 2006.
[Abstract].

Kristensen, D.M., B.Y. Chen, V.Y. Fofanov, R.M. Ward, A.M. Lisewski, M. Kimmel, L.E. Kavraki, and O. Lichtarge.
"Recurrent Use of Evolutionary Importance for Functional Annotation of Proteins Based on Local Structural Similarity." Protein Science. 2006 Jun;15(6):1530-6. Epub 2006 May 2.
[Abstract]. [PDF].

Chiba P., I. Mihalek, G.F. Ecker G.F, S. Kopp, and O. Lichtarge.
"Role of transmembrane domain/transmembrane domain interfaces of P-glycoprotein (ABCB1) in solute transport. Convergent information from photoaffinity labeling, site directed mutagenesis and in silico importance prediction." Current Medicinal Chemistry 13 (7): 793-805 2006.
[Abstract].

Mihalek, I., I. Res, and O. Lichtarge.
"Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins." Proteins. 2006 Apr 1;63(1):87-99.
[Abstract]. [PDF].

Mihalek, I., I. Res, and O. Lichtarge.
"A structure and evolution guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins." Bioinformatics. 2006 Jan 15;22(2):149-56. Epub 2005 Nov 22.
[Abstract]. [PDF]. [Supplementary Material].

Shenoy, S.K., M.T. Drake, C.D. Nelson, D.A. Houtz, K. Xiao, S. Madabushi, E. Reiter, R.T. Premont, O. Lichtarge, and R.J. Lefkowitz.
"beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor." J. Biol. Chem. 2006 Jan 13;281(2):1261-73. Epub 2005 Nov 9.
[Abstract]. [PDF].

2005

Gu, P., D.H. Morgan, M. Sattar, X. Xu, R. Wagner, M. Ravisconi, O. Lichtarge, and A.J. Cooney.
"Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptors." J. Biol. Chem. 280(36):31818-29.
[Abstract]. [PDF].

Raviscioni, M., P. Gu, M. Sattar, A.J. Cooney, O. Lichtarge. (2005).
"Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity." J. Mol. Biol. 350(3) : 402-15.
[Abstract]. [PDF].

Res, I. and O. Lichtarge. (2005).
"Character and Evolution of Protein-Protein Interfaces" Phys. Bio. 2 : S36-S43.
[Abstract]. [PDF].

Res, I., I. Mihalek, O. Lichtarge. (2005).
"An evolution based classifier for prediction of protein interfaces without using protein structures." Bioinformatics 21(10) : 2496-501.
[Abstract]. [PDF].

Chen, B.Y., V.Y. Fofanov, D.M. Kristensen, M. Kimmel, O. Lichtarge, L.E. Kavraki. (2005)
"Algorithms for Structural Comparison and Statistical Analysis of 3-D Protein Motifs." Pac. Symp. Biocomputing. 334-45.
[Abstract]. [PDF].

2004

Cushman, I., B.R. Bowman, M.E. Sowa, O. Lichtarge, F.A. Quiocho, M. Moore. (2004).
"Computational and Biochemical Identification of a Nuclear Pore Complex Binding Site on the Nuclear Transport Carrier NTF2" J. Mol. Biol. 344(2): 303-10.
[Abstract]. [PDF].

Quan, X.J., T. Denayer, J. Yan, H. Jafar-Nejad, A. Philippi, O. Lichtarge, K. Vleminckx, B.A. Hassan. (2004).
"Evolution of neural precursor selection: functional divergence of proneural proteins" Development. Apr;131(8):1679-89. Epub 2004 Mar 17.
[Abstract]. [PDF]

Mihalek, I., I. Res, O. Lichtarge. (2004).
"A Family of Evolution-Entropy Hybrid Methods for Ranking of Protein Residues by Importance" J. Mol. Bio. 336(5): 1265-82.
[Abstract]. [PDF].

Madabushi, S., A.K. Gross, A. Philippi, E.C. Meng, T.G. Wensel, O. Lichtarge. (2004).
"Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions" J. Biol. Chem. 279(9): 8126-32
[Abstract]. [PDF]. [Supplementary Material].

2003

Lichtarge, O., H. Yao, D.M. Kristensen, S. Madabushi and I. Mihalek. (2003).
"Accurate and scalable identification of functional sites by evolutionary tracing" J. Struct. Func. Gen. 4(2-3): 159-166.
[Abstract]. [PDF].

Mihalek, I., H. Yao, I. Res, O. Lichtarge. (2003).
"Combining inference from evolution and geometric probability in protein structure evaluation." J. Mol. Biol. 331: 263-279.
[Abstract]. [PDF].

Lin, C.Y., M.G. Varma, A. Joubel, S. Madabushi, O. Lichtarge and D.L. Barber. (2003).
"Conserved motifs in somatostatin, D2-dopamine, and Alpha2B-adrenergic receptors for inhibiting the Na-H exchanger NHE1." J Biol Chem. 278(17): 15128-35.
[Abstract].

Yao, H., D.M. Kristensen, I. Mihalek, M.E. Sowa, C. Shaw, M. Kimmel, L. Kavraki and O. Lichtarge (2003).
"An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures." J. Mol. Biol. 326: 255-261.
[Abstract]. [PDF]. [Supplementary Material].

2002

Yang, M., W. Wang, M. Zhong, A. Philippi, O. Lichtarge and B.M. Sanborn (2002).
"Lysine 270 in the third intracellular domain of the oxytocin receptor is an important determinant for G alpha(q) coupling specificity." Mol. Endocrinol. 16(4): 814-23.
[Abstract]. [PDF].

Imanishi, Y., N. Li, I. Sokal, M.E. Sowa, O. Lichtarge, T.G. Wensel, D.A. Saperstein, W. Baehr and K. Palczewski (2002).
"Characterization of retinal guanylate cyclase-activating protein 3 (GCAP3) from zebrafish to man." Eur. J. Neurosci. 15(1): 63-78.
[Abstract]. [PDF].

Lichtarge, O. and M.E. Sowa (2002).
"Evolutionary predictions of binding surfaces and interactions." Curr. Opin. Struct. Biol. 12(1): 21-7.
[Abstract]. [PDF].

Madabushi, S., H. Yao, M. Marsh, D.M. Kristensen, A. Philippi, M.E. Sowa and O. Lichtarge (2002).
"Structural clusters of evolutionary trace residues are statistically significant and common in proteins." J. Mol. Biol. 316(1): 139-54.
[Abstract]. [PDF]. [Supplementary Material]

Lichtarge, O., M.E. Sowa and A. Philippi (2002).
"Evolutionary traces of functional surfaces along G protein signaling pathway." Methods Enzymol. 344: 536-56.
[Abstract].

2001

Lichtarge, O. (2001).
"Getting past appearances: the many-fold consequences of remote homology." Nat. Struct. Biol. 8(11): 918-20.
[PubMed]. [PDF].

Sowa, M.E., W. He, K.C. Slep, M.A. Kercher, O. Lichtarge and T.G. Wensel (2001).
"Prediction and confirmation of a site critical for effector regulation of RGS domain activity." Nat. Struct. Biol. 8(3): 234-7.
[Abstract]. [PDF].

2000

Geva, A., T.B. Lassere, O. Lichtarge, S.K. Pollitt and T.J. Baranski (2000).
"Genetic mapping of the human C5a receptor. Identification of transmembrane amino acids critical for receptor function." J. Biol. Chem. 275(45): 35393-401.
[Abstract]. [PDF].

Amir, R.E., I.B. Van den Veyver, R. Schultz, D.M. Malicki, C.Q. Tran, E.J. Dahle, A. Philippi, L. Timar, A.K. Percy, K.J. Motil, O. Lichtarge, E.O. Smith, D.G. Glaze and H.Y. Zoghbi (2000).
"Influence of mutation type and X chromosome inactivation on Rett syndrome phenotypes." Ann. Neurol. 47(5): 670-9.
[Abstract]. [PDF].

Lloyd, T.E., P. Verstreken, E.J. Ostrin, A. Phillippi, O. Lichtarge and H.J. Bellen (2000).
"A genome-wide search for synaptic vesicle cycle proteins in Drosophila." Neuron 26(1): 45-50.
[Abstract].

Sowa, M.E., W. He, T.G. Wensel and O. Lichtarge (2000).
"A regulator of G protein signaling interaction surface linked to effector specificity." Proc. Natl. Acad. Sci. U S A 97(4): 1483-8.
[Abstract]. [PDF].

1999

Sheikh, S.P., J.P. Vilardarga, T.J. Baranski, O. Lichtarge, T. Iiri, E.C. Meng, R.A. Nissenson and H.R. Bourne (1999).
"Similar structures and shared switch mechanisms of the beta2-adrenoceptor and the parathyroid hormone receptor. Zn(II) bridges between helices III and VI block activation." J. Biol. Chem. 274(24): 17033-41.
[Abstract]. [PDF].

Baranski, T.J., P. Herzmark, O. Lichtarge, B.O. Gerber, J. Trueheart, E.C. Meng, T. Iiri, S.P. Sheikh and H.R. Bourne (1999).
"C5a receptor activation. Genetic identification of critical residues in four transmembrane helices." J. Biol. Chem. 274(22): 15757-65.
[Abstract]. [PDF].

1998

Schumacher, A., O. Lichtarge, S. Schwartz and T. Magnuson (1998).
"The murine Polycomb-group gene eed and its human orthologue: functional implications of evolutionary conservation." Genomics 54(1): 79-88.
[Abstract]. [PDF].

1997

Lichtarge, O., K.R. Yamamoto and F.E. Cohen (1997).
"Identification of functional surfaces of the zinc binding domains of intracellular receptors." J. Mol. Biol. 274(3): 325-37.
[Abstract]. [PDF].

Onrust, R., P. Herzmark, P. Chi, P.D. Garcia, O. Lichtarge, C. Kingsley and H.R. Bourne (1997).
"Receptor and betagamma binding sites in the alpha subunit of the retinal G protein transducin." Science 275(5298): 381-4.
[Abstract]. [PDF].

Dunbrack, R.L., Jr., D.L. Gerloff, M. Bower, X. Chen, O. Lichtarge and F.E. Cohen (1997).
"Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996." Fold. Des. 2(2): R27-42.
[Abstract].

1996

Sheikh, S.P., T.A. Zvyaga, O. Lichtarge, T.P. Sakmar and H.R. Bourne (1996).
"Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F." Nature 383(6598): 347-50.
[Abstract].

Lichtarge, O., H.R. Bourne and F.E. Cohen (1996).
"Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex." Proc. Natl. Acad. Sci. U S A 93(15): 7507-11.
[Abstract]. [PDF].

Lichtarge, O., H.R. Bourne and F.E. Cohen (1996).
"An evolutionary trace method defines binding surfaces common to protein families." J. Mol. Biol. 257(2): 342-58.
[Abstract]. [PDF].