Publications


2017

Chun YS, Passot G, Yamashita S, Nusrat M, Katsonis P, Loree JM, Conrad C, Tzeng CD, Xiao L, Aloia TA, Eng C, Kopetz SE, Lichtarge O, Vauthey JN.
Deleterious Effect of RAS and Evolutionary High-risk TP53 Double Mutation in Colorectal Liver Metastases..
Ann Surg.. 2017 Aug; PMID: 28767562 DOI: 10.1097/SLA.0000000000002450

Abstract  Web Access

Galaz-Montoya M, Wright SJ, Rodriguez GJ, Lichtarge O, Wensel TG.
β2-Adrenergic receptor activation mobilizes intracellular calcium via a non-canonical cAMP-independent signaling pathway..
J Biol Chem. 2017 Jun; 292(24):9967-9974. PMID: 28442571 DOI: 10.1074/jbc.M117.787119

 Web Access

Cancer Genome Atlas Research Network. Electronic address: wheeler@bcm.edu; Cancer Genome Atlas Research Network..
Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma.
Cell. 2017 Jun; 169(7):1327-1341.e23. PMID: 28622513 DOI: 10.1016/j.cell.2017.05.046

 Web Access

Katsonis P, Lichtarge O.
Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI-blinded contests..
Human Mutation. 2017 May; PMID: 28544059 DOI: 10.1002/humu.23266

 Web Access

Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, Martelli PL, Niroula A, Pal LR, Repo S, Scaini MC, Vihinen M, Wei Q, Xu Q, Yang Y, Yin Y, Zaucha J, Zhao H, Zhou Y, Brenner SE, Moult J, Tosatto SCE.
Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI..
Hum Mutat. 2017 Apr; PMID: 28440912 DOI: 10.1002/humu.23235

 Web Access

Xu Q, Tang Q, Katsonis P, Lichtarge O, Jones D, Bovo S, Babbi G, Martelli PL, Casadio R, Lee GR, Seok C, Fenton AW, Dunbrack RL Jr.
Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4..
Hum Mutat. 2017 Mar; PMID: 28370845 DOI: 10.1002/humu.23222

 Web Access

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; 12(3):e0174766. DOI: 10.1371/journal.pone.0174766

 Web Access

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 Feb; 569-580. DOI: 10.1002/humu.23193

 Web Access

2016

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; 128(26):3061-3072. PMID: 27799162 DOI: 10.1182/blood-2016-02-702373

 Web Access

Gallion J, Wilkins AD, Lichtarge O.
HUMAN KINASES DISPLAY MUTATIONAL HOTSPOTS AT COGNATE POSITIONS WITHIN CANCER.
Pac Symp Biocomput. 2016 Nov; 22:414-425. PMID: 27896994

 Web Access

Wilson SJ, Wilkins AD, Lin CH, Lua RC, Lichtarge O.
DISCOVERY OF FUNCTIONAL AND DISEASE PATHWAYS BY COMMUNITY DETECTION IN PROTEIN-PROTEIN INTERACTION NETWORKS.
Pac Symp Biocomput. 2016 Nov; 22:336-347. PMID: 27896987

 Web Access

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. PMID: 27447534 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; 116(25):258104. PMID: 27391757 DOI: 0.1103/PhysRevLett.116.258104

 Web Access

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. 2016 May; 112(22):7097-102. PMID: 25964346 DOI: 10.1073/pnas.1502742112

 Web Access

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. 2016 Mar; 113(13):3539-44. PMID: 26979958 DOI: 10.1073/pnas.1516579113i

 Web Access

Koire A, Katsonis P, Lichtarge O.
REPURPOSING GERMLINE EXOMES OF THE CANCER GENOME ATLAS DEMANDS A CAUTIOUS APPROACH AND SAMPLE-SPECIFIC VARIANT FILTERING..
Pac Symp Biocomput. 2016 Jan; 21:207-18. PMID: 26776187

 Web Access

Regenbogen S, Wilkins AD, Lichtarge O.
COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS..
Pac Symp Biocomput. 2016 Jan; 21:21-32. PMID: 26776170

 Web Access

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; 44(D1):D308-12. PMID: 26590254 DOI: 10.1093/nar/gkv1279

 Web Access

2015

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. PMID: 26585234 DOI: 10.1016/j.neo.2015.10.003

 Web Access

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. 2015 Aug;

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..
Cancer Res. 2015 Feb; 75(7):1205-15. PMID: 25691460 DOI: 10.1158/0008-5472.CAN-14-2729

 Web Access

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. PMID: 25504633 DOI: 10.1158/1535-7163.MCT-14-0735-T

 Web Access

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

 Web Access

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; 75(7):1527-36. PMID: 25634208 DOI: 10.1158/0008-5472.CAN-14-2735

 Web Access

2014

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; 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; DOI: 10.1002/pro.2552

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; 24(12):8. PMID: 25217195 DOI: 10.1101/gr.176214.114

 Web Access

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 Aug; DOI: 10.1145/2623330.2623667

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 Aug; 158(4):916-928. DOI: 10.1016/j.cell.2014.07.011

 Web Access

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; 7(6): PMID: 24910431 DOI: 0.1016/j.celrep.2014.05.018

 Web Access

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; 116(2-3):194-202. PMID: 24878423 DOI: 10.1016/j.pbiomolbio.2014.05.004

 Web Access

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 DOI: 10.1128/MCB.01248-13

 Web Access

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 Jan; 10(1):e1004121. PMID: 24465224 DOI: 10.1371/journal.pgen.1004121

 Web Access

2013

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. 2013 Nov; 9(11): DOI: 10.1371/journal.pgen.1003901

 Web Access

Amin S, Erdin S, Ward M, Lua R, Lichtarge O.
Prediction and experimental validation of enzyme substrate specificity in protein structures..
PNAS. 2013 Sep; 110(45):E4195-E4202. DOI: 10.1073/pnas.1305162110

 Web Access

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; 425(18):3277-88. PMID: 23806656 DOI: 10.1016/j.jmb.2013.06.014

 Web Access

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; 29(21):2714-21. PMID: 24021383 DOI: 10.1093/bioinformatics/btt489

 Web Access

Radivojac P, et al., Friedberg I..
A large-scale evaluation of computational protein function prediction..
Nature Method. 2013 Mar; 10(3):221-7.

Abstract

Erdin S, Venner E, Lisewski AM, Lichtarge O.
Function prediction from networks of local evolutionary similarity in protein structure..
BMC Bioinformatics.. 2013 Mar; 14(S6): PMID: 23514548 DOI: 10.1186/1471-2105-14-S3-S6

 Web Access

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. 2013 Feb; 152(5):984-96. PMID: 23452848 DOI: 0.1016/j.cell.2013.01.038

Shoji-Kawata S, et al. and Levine B.
Identification of a candidate therapeutic autophagy-inducing peptide..
Nature. 2013 Feb; 494(201): DOI: 10.1038/nature11866

2012

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. 2012 Dec; 338(6112):1344-1348. DOI: 10.1126/science.1226683

 Web Access

Bachman BJ*, Venner E*, Lua RC, Erdin S, Lichtarge O.
ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape..
Bioinformatics. 2012 May;

Wilkins AD, Bachman BJ, Erdin S, Lichtarge O.
he use of evolutionary patterns in protein annotation..
Current Opinion in Structural Biology. 2012 May;

 Web Access

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

Abstract

2011

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 Sep; 7(9):e1002244. DOI: 10.1371/journal.pgen.1002244

 Web Access

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. PMID: 21671375 DOI: 10.1002/ajmg.a.34040

 Web Access

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; 32(6):579-589. DOI: 10.1002/humu.21406

Abstract

Erdin S, Lisewski AM and Lichtarge O.
Protein function prediction: towards integration of similarity metrics.
Current Opinion in Structural Biology. 2011 Apr; 21(2):180-188. DOI: 10.1016/j.sbi.2011.02.001

Abstract  Download

2010

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; 5(12):e14286. DOI: 10.1371/journal.pone.0014286

 Web Access

Lua RC and Lichtarge O.
PyETV: A PyMOL Evolutionary Trace viewer to analyze functional site predictions in protein complexes.
Bioinformatics. 2010 Oct; 26(23):2981-2982. DOI: 10.1093/bioinformatics/btq566

 Web Access

Lisewski AM and Lichtarge O.
Untangling complex networks: risk minimization in financial markets through accessible spin glass ground states..
Physica A. 2010 Aug; 389(16):3250-3253. DOI: 10.1016/j.physa.2010.04.005

Abstract

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. 2010 Jul; 80(1):86-94. PMID: 20227396 DOI: 10.1016/j.bcp.2010.03.006

Abstract

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; 107(17):7787-92.

Abstract  Download

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 Sci. 2010 Apr; 19(7):1296-1311.

Abstract  Web Access

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. PMID: 20038610 DOI: 10.1124/mol.109.058115

Abstract

Erdin S, Ward RM, Venner E, and Lichtarge O.
Evolutionary Trace Annotation of Protein Function in the Structural Proteome..
J Mol Biol. 2010 Mar; 396(5):1451-73. PMID: 20036248 DOI: 10.1016/j.jmb.2009.12.037

Abstract

Lichtarge O and Wilkins AD.
Evolution: a guide to perturb protein function and networks..
Current Opinion in Structural Biology. 2010 Mar; 20(3):351-9. PMID: 20444593 DOI: 10.1016/j.sbi.2010.04.002

Abstract

2009

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. PMID: 19667227 DOI: 10.1001/archneurol.2009.139

Abstract

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. PMID: 19515093 DOI: 10.1111/j.1600-0854.2009.00932.x

Abstract

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 Jun; 25(11):1426-7. PMID: 19307237 DOI: 10.1093/bioinformatics/btp160

Abstract

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 Apr; 493:287-97. PMID: 18839354 DOI: 10.1007/978-1-59745-523-7_17

Abstract

2008

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; 3(5):e2136. PMID: 18461181 DOI: 10.1371/journal.pone.0002136

Abstract

Kristensen 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; 9(1):17. PMID: 18190718 DOI: 10.1186/1471-2105-9-17

Abstract

2007

Mihalek I, Res I and Lichtarge O.
Background frequencies for residue variability estimates: BLOSUM revisited..
BMC Bioinformatics.. 2007 Dec; 8(488): PMID: 18162129

Abstract

Shin H, Lisewski AM and Lichtarge O.
Graph sharpening plus graph integration: a synergy that improves protein functional classification..
Bioinformatics. 2007 Dec; 23(23):3217-24. PMID: 17977886 DOI: 10.1093/bioinformatics/btm511

Abstract

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 Aug; 6:55. PMID: 17951837

Abstract

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; 14(6):791-816. PMID: 17691895 DOI: 10.1089/cmb.2007.R017

Abstract

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;

Abstract  Web Access

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; 369(2):584-95.

Abstract  Web Access

Ribes-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.

Abstract

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  Web Access

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; 22(16):2049-50.

Abstract

Lisewski AM and Lichtarge O..
Rapid detection of similarity in protein structure and function through contact metric distances..
Nucl. Acids Res.. 2006 Nov; 34(22):e152. PMID: 17130161 DOI: 10.1093/nar/gkl788

 Web Access

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; 65(1):111-23.

Abstract  Web Access

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; 64(4):1046-57.

Abstract

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 Aug; 5:311-23. PMID: 17369649

Abstract  Web Access

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; 22(16):2049-50.

Abstract

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 Sci. 2006 Jun; 15(6):1530-6.

Abstract

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

Abstract

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. 2006 Apr; 13(7):793-805.

Abstract

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..
Research in Computational Molecular Biology. 2006 Apr; 500-515.

Abstract

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; 22(2):149-56.

Abstract

Shenoy 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; 281(2):1261-73.

Abstract

2005

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. 2005 Sep; 280(36):31818-29. PMID: 15994320

Abstract

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

Abstract

Res I. and Lichtarge O.
Character and Evolution of Protein-Protein Interfaces.
Phys Bio. 2005 May; 2:S36-S43.

Abstract  Download

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

Abstract

Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE.
Algorithms for Structural Comparison and Statistical Analysis of 3-D Protein Motifs..
Pac Symp Biocomput. 2005 Mar; 334-45.

Abstract  Web Access

2004

Cushman I, Bowman BR, Sowa ME, Lichtarge O, Quiocho FA, Moore M.
Computational and Biochemical Identification of a Nuclear Pore Complex Binding Site on the Nuclear Transport Carrier NTF2.
J Mol Biol. 2004 Nov; 344(2):303-10. PMID: 15522285

Abstract

Mihalek I, Res I, Lichtarge O.
A Family of Evolution-Entropy Hybrid Methods for Ranking of Protein Residues by Importance.
J Mol Biol. 2004 May; 336(5):1265-82.

Abstract

Quan XJ, Denayer T, Yan J, Jafar-Nejad H, Philippi A, Lichtarge O, Vleminckx K, Hassan BA.
Evolution of neural precursor selection: functional divergence of proneural proteins.
Development. 2004 Apr; 131(8):1679-89.

Abstract

Madabushi S, Gross AK, Philippi A, Meng EC, Wensel TG, Lichtarge O.
Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions.
J Biol Chem. 2004 Feb; 279(9):8126-32.

Abstract

2003

Mihalek I, Yao H, Res I, Lichtarge O.
Combining inference from evolution and geometric probability in protein structure evaluation..
J Mol Biol. 2003 Aug; 331(1):263-79.

Abstract

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

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Lin CY, Varma MG, Joubel A, Madabushi S, Lichtarge O and Barber DL.
Conserved motifs in somatostatin, D2-dopamine, and Alpha2B-adrenergic receptors for inhibiting the Na-H exchanger NHE1..
J Biol Chem. 2003 Apr; 278(17):15128-35.

Abstract

Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, Kimmel M, Kavraki L and Lichtarge O.
An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures.
J Mol Biol. 2003 Feb; 326(1):255-61.

Abstract

2002

Lichtarge O, Sowa ME and Philippi A.
Evolutionary traces of functional surfaces along G protein signaling pathway..
Methods Enzymol. 2002 Jun; 344:536-56.

Abstract

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

Abstract

Lichtarge O and Sowa ME.
Evolutionary predictions of binding surfaces and interactions..
Current Opinion in Structural Biology. 2002 Feb; 12(1):21-7.

Abstract

Madabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, Sowa ME and Lichtarge O.
Structural clusters of evolutionary trace residues are statistically significant and common in proteins..
J Mol Biol. 2002 Feb; 316(1):139-54.

Abstract

manishi Y, Li N, Sokal I, Sowa ME, Lichtarge O, Wensel TG, Saperstein DA, Baehr W and Palczewski K.
Characterization of retinal guanylate cyclase-activating protein 3 (GCAP3) from zebrafish to man..
Eur J Neurosci. 2002 Jan; 15(1):63-78.

Abstract

2001

Lichtarge O.
Getting past appearances: the many-fold consequences of remote homology..
Nat. Struct. Biol. 2001 Nov; 8(11):918-20.

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

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2000

Geva A, Lassere TB, Lichtarge O, Pollitt SK and Baranski TJ..
Genetic mapping of the human C5a receptor. Identification of transmembrane amino acids critical for receptor function..
J Biol Chem. 2000 Nov; 275(45):35393-401.

Abstract

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.
Influence of mutation type and X chromosome inactivation on Rett syndrome phenotypes..
Ann. Neurol. 2000 May; 47(5):670-9.

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

Abstract

Sowa ME, He W, Wensel TG and Lichtarge O.
A regulator of G protein signaling interaction surface linked to effector specificity..
Proc Natl Acad Sci U S A. 2000 Feb; 97(4):1483-8.

Abstract

1999

Sheikh SP, Vilardarga JP, Baranski TJ, Lichtarge O, Iiri T, Meng EC, Nissenson RA and Bourne HR.
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. 1999 Jun; 274(24):17033-41.

Abstract

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

Abstract

1998

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

Abstract

1997

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

Abstract

Dunbrack RL Jr, Gerloff DL, Bower M, Chen X, Lichtarge O and Cohen FE.
Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996..
Fold. Des. 1997 Jun; 2(2):R27-42.

Abstract

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

Abstract

1996

Lichtarge O, Bourne HR and Cohen FE.
Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex..
Proc Natl Acad Sci U S A. 1996 Jul; 93(15):7505-11.

Abstract

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

Abstract

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

Abstract