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Lichtarge Computational Biology Lab

Houston, Texas

Lichtarge Computational Biology Lab
Lichtarge Computational Biology Lab
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2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997 1996


Galaz-Montoya M, Wright SJ, Rodriguez GJ, Lichtarge O, Wensel TG.
"Beta-2-Adrenergic Receptor Activation Mobilizes Intracellular Calcium via a Non-Canonical cAMP-Independent Signaling Pathway."
J Biol Chem. In Press

Koire A, Kim YW, Wang J, Katsonis P, Jin H, Lichtarge O.
"Codon-level co-occurrences of germline variants and somatic mutations in cancer are rare but often lead to incorrect variant annotation and underestimated impact prediction."
PLoS ONE. 2017 Mar 28;12(3):e0174766. doi: 10.1371/journal.pone.0174766

Gallion J, Koire A, Katsonis P, Schoenegge A-M, Bouvier M, Lichtarge O.
"Predicting phenotype from genotype: improving accuracy through more robust experimental and computational modeling."
Human mutation. 2017 May;38(5):569-580. doi: 10.1002/humu.23193
[Abstract] [HTML]


Gallion J, Wilkins AD, Lichtarge O.
Pac Symp Biocomput. 2016;22:414-425.

Wilson SJ, Wilkins AD, Lin CH, Lua RC, Lichtarge O.
Pac Symp Biocomput. 2016;22:336-347.

Bocchini CE, Nahmod K, Katsonis P, Kim S, Kasembeli MM, Freeman A, Lichtarge O, Makedonas G, Tweardy DJ.
"Protein stabilization improves STAT3 function in autosomal dominant hyper-IgE syndrome."
Blood. 2016 Dec 29;128(26):3061-3072. doi: 10.1182/blood-2016-02-702373.

Li Z, Gonzalez CL, Wang B, Zhang Y, Mejia O, Katsonis P, Lichtarge O, Myers JN, El-Naggar AK, Caulin C.
"Cdkn2a suppresses metastasis in squamous cell carcinomas induced by the gain-of-function mutant p53(R172H)."
J Pathol. 2016 Oct;240(2):224-34. doi: 10.1002/path.4770.

Marciano DC, Lua RC, Herman C, Lichtarge O.
"Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness."
Phys Rev Lett. 2016 Jun 24;116(25):258104. doi: 10.1103/PhysRevLett.116.258104.

Yun-Min Sung, Angela D. Wilkins, Gustavo J. Rodriguez, Theodore G. Wensel, and Olivier Lichtarge
"Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation."
Proc. Natl. Acad. Sci. USA 2016 Mar 29;113(13):3539-44. doi: 10.1073/pnas.1516579113i

Lua RC, Wilson SJ, Konecki DM, Wilkins AD, Venner E, Morgan DH, Lichtarge O.
"UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures."
Nucleic Acids Res.. 2016 Jan 4;44(D1):D308-12. doi: 10.1093/nar/gkv1279. PMID: 26590254  

Koire A, Katsonis P, Lichtarge O.
Pac Symp Biocomput.. 2016;21:207-18. PMID: 26776187  

Regenbogen S, Wilkins AD, Lichtarge O.
Pac Symp Biocomput.. 2016;21:21-32. PMID: 26776170  


Mullany LK, Wong KK, Marciano DC, Katsonis P, King-Crane ER, Ren YA, Lichtarge O, Richards JS.
"Specific TP53 Mutants Overrepresented in Ovarian Cancer Impact CNV, TP53 Activity, Responses to Nutlin-3a, and Cell Survival."
Neoplasia.. 2015 Oct;17(10):789-803. doi: 10.1016/j.neo.2015.10.003 PMID: 26585234  

Meena Nagarajan, Angela D. Wilkins, Benjamin J. Bachman, Ilya B. Novikov, Sheng Hua Bao, Peter Haas, María E. Terrón-Díaz, Sumit Bhatia, Anbu K. Adikesaven, Jacques J. Labrie, Sam Regenbogen, Christie M. Buchovecky, Curtis R. Pickering, Linda Kato, Andreas Martin Lisewski, Ana Lelescu, Houyin Zhang, Stephen Boyer, Griff Weber, Ying Chen, Lawrence Donehower, Scott Spangler, Olivier Lichtarge
"Predicting Future Scientific Discoveries Based on a Networked Analysis of the Past Literature."
International Conference on Knowledge Discovery and Data Mining - 2015 
August 10-13, 2015, Sydney, Australia

Peterson SM, Pack TF, Wilkins AD, Urs NM, Urban DJ, Bass CE, Lichtarge O, Caron MG.
"Elucidation of G-protein and β-arrestin functional selectivity at the dopamine D2 receptor."
Proc Natl Acad Sci U S A. 2015 May 11. pii: 201502742. [Epub ahead of print]. PMID: 25964346 

Osman AA, Monroe MM, Ortega Alves MV, Patel AA, Katsonis P, Fitzgerald AL, Neskey DM, Frederick MJ, Woo SH, Caulin C, Hsu TK, McDonald TO, Kimmel M, Meyn RE, Lichtarge O, Myers JN.
"Wee-1 Kinase Inhibition Overcomes Cisplatin Resistance Associated with High-Risk TP53 Mutations in Head and Neck Cancer through Mitotic Arrest Followed by Senescence."
Mol Cancer Ther. 2015 Feb;14(2):608-19. doi: 10.1158/1535-7163.MCT-14-0735-T. Epub 2014 Dec 10. PMID: 25504633 

Kang HJ, Wilkins AD, Lichtarge O, Wensel TG.
"Determinants of Endogenous Ligand Specificity Divergence among Metabotropic Glutamate Receptors."
J Biol Chem. 2015 Jan 30;290(5):2870-8. doi: 10.1074/jbc.M114.622233. Epub 2014 Dec 17. PMID: 25519912

Neskey DM, Osman AA, Ow TJ, Katsonis P, McDonald T, Hicks SC, Hsu TK, Pickering CR, Ward A, Patel A, Yordy JS, Skinner HD, Giri U, Sano D, Story MD, Beadle BM, El-Naggar AK, Kies MS, William WN, Caulin C, Frederick M, Kimmel M, Myers JN, Lichtarge O.
"Evolutionary Action score of TP53 (EAp53) identifies high risk mutations associated with decreased survival and increased distant metastases in head and neck cancer."
Cancer Res. 2015 Jan 29. pii: canres.2735.2014. [Epub ahead of print]. PMID: 25634208 

Osman AA, Neskey DM, Katsonis P, Patel AA, Ward AM, Hsu TK, Hicks SC, McDonald TO, Ow TJ, Ortega Alves M, Pickering CR, Skinner HD,Zhao M, Sturgis EM, Kies MS, El-Naggar A, Perrone F, Licitra L, Bossi P, Kimmel M, Frederick MJ, Lichtarge O, Myers JN.
" Evolutionary Action Score of TP53 Coding Variants (EAp53) is Predictive of Platinum Response in Head and Neck Cancer Patients."s
Cancer Res. 2015 Feb 17. pii: canres.2729.2014. [Epub ahead of print] PMID: 25691460.



Genome Research

Katsonis P, Lichtarge O.
"A formal perturbation equation between genotype and phenotype determines the evolutionary action of protein coding variations on fitness."
Genome Res. 2014 Sep 12. pii: gr.176214.114. PMID: 25217195

Lisewski AM, Quiros JP, Ng CL, Adikesavan AK, Miura K, Putluri N, Eastman RT, Scanfeld D, Regenbogen SJ, Altenhofen L, Llinás M, Sreekumar A, Long C , Fidock DA and Lichtarge O.
"Supergenomic Network Compression and the Discovery of EXP1 as a Glutathione Transferase Inhibited by Artesunate."
Cell. (2014). Volume 158, Issue 4, Pages 916-928. DOI: 10.1016/j.cell.2014.07.011.

Scott Spangler, Angela D Wilkins, Benjamin J Bachman, Meena Nagarajan, Tajhal Dayaram, Peter Haas, Sam Regenbogen, Curtis R Pickering, Austin Comer, Jeffrey N Myers, Ioana Stanoi, Linda Kato, Ana Lelescu, Jacques J Labrie, Neha Parikh, Andreas Martin Lisewski, Lawrence Donehower, Ying Chen, Olivier Lichtarge
"Automated hypothesis generation based on mining scientific literature"
KDD. 2014. doi: 10.1145/2623330.2623667.

Kang HJ, Menlove K, Ma J, Wilkins A, Lichtarge O, Wensel TG
"Selectivity and evolutionary divergence of metabotropic glutamate receptors for endogenous ligands and G proteins coupled to phospholipase C or TRP channels."
J Biol Chem. 2014 Oct 24;289(43):29961-74. doi: 10.1074/jbc.M114.574483.

Katsonis P*, Koire A*, Wilson SJ*, Hsu TK, Lua RC, Wilkins AD, Lichtarge O.
"Single nucleotide variations: Biological impact and theoretical interpretation."
Protein Sci. 2014 Sep 18. doi: 10.1002/pro.2552. [Epub ahead of print]
*These authors contributed equally

Marciano DC, Lua RC, Katsonis P, Amin SR, Herman C, Lichtarge O.
"Negative Feedback in Genetic Circuits Confers Evolutionary Resilience and Capacitance."
Cell Rep. 2014 Jun 4. pii: S2211-1247(14)00393-3. doi: 0.1016/j.celrep.2014.05.018. PMID: 24910431.

Lua RC, Marciano DC, Katsonis P, Adikesavan AK, Wilkins AD, Lichtarge O.
"Prediction and redesign of protein-protein interactions."
Prog Biophys Mol Biol. 2014 May 27. pii: S0079-6107(14)00040-6. doi: 10.1016/j.pbiomolbio.2014.05.004. PMID: 24878423.

Homan EP, Lietman C, Grafe I, Lennington J, Morello R, Napierala D, Jiang MM, Munivez EM, Dawson B, Bertin TK, Chen Y, Lua R, Lichtarge O, Hicks J, Weis MA, Eyre D, Lee BH.
"Differential effects of collagen prolyl 3-hydroxylation on skeletal tissues."
PLoS Genet. (2014), 10(1):e1004121. PMID: 24465224.

Young E, Zheng ZY, Wilkins AD, Jeong HT, Li M, Lichtarge O, Chang EC.
"Regulation of Ras localization and cell transformation by evolutionarily conserved palmitoyltransferases."
Mol Cell Biol. 2014 Feb, 34(3):374-85. PMID: 24248599.


Zheng L, Sepulveda L, Lua R, Lichtarge O, Golding I, Sokac A.
"The Maternal-to-Zygotic Transition Targets Actin to Promote Robustness during Morphogenesis."
PLOS Genetics. November 2013, Volume 9 Issue 11.

Amin S, Erdin S, Ward M, Lua R, Lichtarge O.
"Prediction and experimental validation of enzyme substrate specificity in protein structures."
PNAS. 2013 Sep 24.

Wilkins AD, Venner E, Marciano DC, Erdin S, Atri B, Lua RC, Lichtarge O.
"Accounting for epistatic interactions improves the functional analysis of protein structures."
Bioinformatics. 2013 Sep 19. PMID: 24021383.

Rababa'h A, Craft JW Jr, Wijaya CS, Atrooz F, Fan Q, Singh S, Guillory AN, Katsonis P, Lichtarge O, McConnell BK.
"Protein Kinase A and Phosphodiesterase-4D3 Binding to Coding Polymorphisms of Cardiac Muscle Anchoring Protein (mAKAP)."
J Mol Biol. 2013 Sep 23;425(18):3277-88. doi: 10.1016/j.jmb.2013.06.014. Epub 2013 Jun 25. PMID: 23806656

Erdin S, Venner E, Lisewski AM, Lichtarge O.
"Function prediction from networks of local evolutionary similarity in protein structure."
BMC Bioinformatics. 2013;14 Suppl 3:S6. doi: 10.1186/1471-2105-14-S3-S6. Epub 2013 Feb 28. PMID: 23514548

Baker SA, Chen L, Wilkins AD, Yu P, Lichtarge O, Zoghbi HY.
"An AT-Hook Domain in MeCP2 Determines the Clinical Course of Rett Syndrome and Related Disorders."
Cell. Feb 28;152(5):984-96. doi: 10.1016/j.cell.2013.01.038.(2013).

Shoji-Kawata S, et al. and Levine B.
"Identification of a candidate therapeutic autophagy-inducing peptide."
Nature. 494, 201–206 (14 February 2013) doi:10.1038/nature11866.

Radivojac P, et al., Friedberg I.
"A large-scale evaluation of computational protein function prediction."
Nature Methods 10, 221–227 (2013) doi:10.1038/nmeth.2340.


Mamun AAMA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM.
"Identity and Function of a Large Gene Network Underlying Mutagenic Repair of DNA Breaks."
Science. 7 December 2012: Vol. 338 no. 6112 pp. 1344-1348 DOI: 10.1126/science.1226683 Accepted May 30 2012.
[Abstract]. [HTML].

Bachman BJ*, Venner E*, Lua RC, Erdin S, Lichtarge O.
"ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape."
Bioinformatics. Accepted May 30 2012.
*-These authors contributed equally to this work.

Wilkins AD, Bachman BJ, Erdin S, Lichtarge O.
"The use of evolutionary patterns in protein annotation."
Current Opinion in Structural Biology. Accepted May 24 2012.

Wilkins AD, Erdin S, Lua R, Lichtarge O.
"Evolutionary trace for prediction and redesign of protein functional sites."
Methods Mol Biol. 2012;819:29-42.


Adikesavan AK, Katsonis P, Marciano DC, Lua RC, Herman C, Lichtarge O.
"Separation of Recombination and SOS Response in E. coli RecA Suggests LexA Interaction Sites."
PLoS Genetics. 2011 Sept;7(9): e1002244. doi:10.1371/journal.pgen.1002244.

Schaaf CP, Koster J, Katsonis P, Kratz L, Shchelochkov OA, Scaglia F, Kelley RI, Lichtarge O, Waterham HR, Shinawi M.
"Desmosterolosis-phenotypic and molecular characterization of a third case and review of the literature."
Am J Med Genet A. 2011 Jul;155A(7):1597-604. doi: 10.1002/ajmg.a.34040. Epub 2011 Jun 10. PMID: 21671375

Erdin S, Lisewski AM and Lichtarge O.
"Protein function prediction: towards integration of similarity metrics."
Current Opinion in Structural Biology. Volume 21, Issue 2, April 2011, Pages 180-188. doi:10.1016/
[Abstract]. [PDF].

Haberle J, Shchelochkov OA, Wang J, Katsonis P, Hall L, Reiss S, Eeds A, Willis A, Yadav M, Summar S, and the Urea Cycle Disorders Consortium, Lichtarge L, Rubio V, Wong LJ.
"Molecular Defects in Human Carbamoyl Phosphate Synthetase I: Mutational Spectrum, Diagnostic and Protein Structure Considerations." Human Mutation. 2011 May 5; 32(6);579-589. DOI: 10.1002/humu.21406.
[Abstract]. [PDF]. [HTML].


Venner E, Lisewski AM, Erdin S, Ward RW, Amin S and Lichtarge O.
"Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities."
PLoS One 2010 Dec 13;5(12): e14286. doi:10.1371/journal.pone.0014286.
[Abstract]. [PDF]. [HTML].

Lua RC and Lichtarge O.
"PyETV: A PyMOL Evolutionary Trace viewer to analyze functional site predictions in protein complexes"
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq566
[Abstract]. [PDF]

Must Read!Rodriguez GJ, Yao R, Lichtarge O* and Wensel T*.
Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. PNAS. 2010 Apr 27;107(17):7787-92. Epub 2010 Apr 12.
[Abstract]. [PDF].

Wilkins AD, Lua R, Erdin S, Ward RM and Lichtarge O.
Sequence and Structure Continuity of Evolutionary Importance Improves Protein Functional Site Discovery and Annotation. Protein Science. 2010 Apr 27;19(7):1296-1311. [Epub 2010 Apr 27].
[Abstract]. [PDF][Supplementary Material].

Lisewski AM and Lichtarge O.
Untangling complex networks: risk minimization in financial markets through accessible spin glass ground states. Physica A. 2010 August 15;389(16):3250-3253.
[Abstract]. [PDF].

Lichtarge O and Wilkins AD.
Evolution: a guide to perturb protein function and networks. Current Opinion in Structural Biology. 2010 May 3. Epub 2010 May 3.
[Abstract]. [PDF].

Bonde MM, Yao R, Ma JN, Madabushi S, Haunso S, Burstein ES, Whistler JL, Sheikh SP, Lichtarge O, and Lerche-Hansen J.
An Angiotensin II Type 1 Receptor Activation Switch Patch Revealed through Evolutionary Trace Analysis. Biochemical Pharmacology. Biochem Pharmacol. 2010 Jul 1;80(1):86-94
[Abstract]. [PDF].

Erdin S, Ward RM, Venner E, and Lichtarge O.
Evolutionary Trace Annotation of Protein Function in the Structural Proteome. J Mol Biol. 2010 Mar 12;396(5):1451-1473.
[Abstract]. [PDF]. [Supplementary Material].

Baameur F, Morgan DH, Yao H, Tran TM, Hammitt RA, Sabui S, McMurray JS, Lichtarge O, and Clark RB.
Role for the RH Domain of GRK5 and 6 in {beta}2-Adrenergic Receptor and Rhodopsin Phosphorylation. Mol Pharmacol. 2010 Mar;77(3):405-15. Epub 2009 Dec 28
[Abstract]. [PDF].


Shaibani, A., O.A. Shchelochkov, S. Zhang, P. Katsonis, O. Lichtarge, L. Wong, M. Shinawi.
Mitochondrial Neurogastrointestinal Encephalopathy Due to Mutations in RRM2B. Arch Neurol. 2009 Aug;66(8):1028-32.
[Abstract]. [PDF].

Kobayashi, H., K. Ogawa, R. Yao, O. Lichtarge and M. Bouvier.
Functional Rescue of Beta1-adrenoceptor Dimerization and Trafficking by Pharmacological Chaperones. Traffic. 2009 Aug;10(8):1019-33. Epub 2009 Jun 9.
[Abstract]. [PDF].

Rajagopalan, L., F.A. Pereira, O. Lichtarge, W.E. Brownell.
Identification of Functionally Important Residues/Domains in Membrane Proteins Using an Evolutionary Approach Coupled with Systematic Mutational Analysis. Methods Mol Biol. 2009. 493:287-97
[Abstract]. [PDF].

Ward, R.M., E. Venner, B. Daines, S. Murray, S. Erdin, D.M. Kristensen, and O. Lichtarge.
Evolutionary Trace Annotation Server: Automated Enzyme Function Prediction in Protein Structures Using 3D Templates. Bioinformatics. 2009. doi: 10.1093/bioinformatics/btp160
[Abstract]. [PDF].


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

Highly AccessedKristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, and Lichtarge O.
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].

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


Shin H, Lisewski AM and Lichtarge O.
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 BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, and Kavraki LE.
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.

Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, and Kavraki LE.
Composite motifs integrating multiple protein structures increase sensitivity for function prediction. Comput Syst Bioinformatics Conf. 2007;6:343-55.

Mihalek I, Res I, and Lichtarge O.
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].

RecommendedRibes-Zamora A, Mihalek I, Lichtarge O, and Bertuch AA.
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 BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE.
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 CB, Mihalek I, Lichtarge O, Jalan A, Vodopiutz J, Muhl A, Bodamer OA.
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 AM and Lichtarge O.
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, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, and Kavraki LE.
Cavity-aware motifs reduce false positives in protein function prediction. Comput. Syst. Bioinformatics Conf. 2006;:311-23 PMID: 17369649
[Abstract]. [PDF].


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 DH, Kristensen DM, Mittleman D, and Lichtarge O.
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 HS, Mihalek I, and Lichtarge O.
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, Res I and Lichtarge O.
"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, He Q, Salicru EM, Smyth CL, and Lichtarge O.
"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 BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O and Kavraki LE.
"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.

Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, and Lichtarge O.
"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, Mihalek I, Ecker GF, Kopp S, and Lichtarge O.
"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.

Mihalek I, Res I, and Lichtarge O.
"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, Res I, and Lichtarge O.
"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].

RecommendedShenoy SK, Drake MT, Nelson CD, Houtz DA, Xiao K, Madabushi S, Reiter E, Premont RT, Lichtarge O, and Lefkowitz RJ.
"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].


Gu P, Morgan DH, Sattar M, Xu X, Wagner R, Ravisconi M, Lichtarge O, and Cooney AJ.
"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, Gu P, Sattar M, Cooney AJ, Lichtarge O. (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 Lichtarge O. (2005).
"Character and Evolution of Protein-Protein Interfaces" Phys. Bio. 2 : S36-S43.
[Abstract]. [PDF].

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

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


Cushman I, Bowman BR, Sowa ME, Lichtarge O, Quiocho FA, Moore M. (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].

Must Read!Quan XJ, Denayer T, Yan J, Jafar-Nejad H, Philippi A, Lichtarge O, Vleminckx K, Hassan BA. (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, Res I, Lichtarge O. (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, Gross AK, Philippi A, Meng EC, Wensel TG, Lichtarge O. (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].


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

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

Lin CY, Varma MG, Joubel A, Madabushi S, Lichtarge O and Barber DL. (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.

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


Yang M, Wang W, Zhong M, Philippi A, Lichtarge O and Sanborn BM (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, Li N, Sokal I, Sowa ME, Lichtarge O, Wensel TG, Saperstein DA, Baehr W and Palczewski K. (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 Sowa ME (2002).
"Evolutionary predictions of binding surfaces and interactions." Curr. Opin. Struct. Biol. 12(1): 21-7.
[Abstract]. [PDF].

ReommendedMadabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, Sowa ME and Lichtarge O. (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, Sowa ME and Philippi A (2002).
"Evolutionary traces of functional surfaces along G protein signaling pathway." Methods Enzymol. 344: 536-56.



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

Sowa ME, He W, Slep KC, Kercher MA, Lichtarge O and Wensel TG. (2001).
"Prediction and confirmation of a site critical for effector regulation of RGS domain activity." Nat. Struct. Biol. 8(3): 234-7.
[Abstract]. [PDF].



Geva A, Lassere TB, Lichtarge O, Pollitt SK and Baranski TJ. (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 RE, Van den Veyver IB, Schultz R, Malicki DM, Tran CQ, Dahle EJ, Philippi A, Timar L, Percy AK, Motil KJ, Lichtarge O, Smith EO, Glaze DG and Zoghbi HY. (2000).
"Influence of mutation type and X chromosome inactivation on Rett syndrome phenotypes." Ann. Neurol. 47(5): 670-9.
[Abstract]. [PDF].

Lloyd TE, Verstreken P, Ostrin EJ, Phillippi A, Lichtarge O and Bellen HJ. (2000).
"A genome-wide search for synaptic vesicle cycle proteins in Drosophila." Neuron 26(1): 45-50.

Sowa ME, He W, Wensel TG and Lichtarge O. (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].


Sheikh SP, Vilardarga JP, Baranski TJ, Lichtarge O, Iiri T, Meng EC, Nissenson RA and Bourne HR. (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 TJ, Herzmark P, Lichtarge O, Gerber BO, Trueheart J, Meng EC, Iiri T, Sheikh SP and Bourne HR (1999).
"C5a receptor activation. Genetic identification of critical residues in four transmembrane helices." J. Biol. Chem. 274(22): 15757-65.
[Abstract]. [PDF].


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


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

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

Dunbrack RL Jr, Gerloff DL, Bower M, Chen X, Lichtarge O and Cohen FE. (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.


Sheikh SP, Zvyaga TA, Lichtarge O, Sakmar TP and Bourne HR. (1996).
"Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F." Nature 383(6598): 347-50.

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