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OLIVIER LICHTARGE

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
DivisionMolecular & Human Genetics
AddressOne Baylor Plaza
Houston TX 77030
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    Other Positions
    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Pharmacology and Chemical Biology
    DivisionPharmacology

    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Biochemistry & Molecular Biology
    DivisionBiochemistry & Molecular Biology


    Collapse Research 
    Collapse research activities and funding
    R01GM066099     (LICHTARGE, OLIVIER)Jul 1, 2002 - Feb 28, 2019
    NIH/NIGMS
    Functional Determinants in G Protein-Coupled Receptors
    Role: Principal Investigator

    R01GM079656     (LICHTARGE, OLIVIER)Apr 1, 2007 - Dec 31, 2019
    NIH/NIGMS
    Comparative genomics of protein structure and function
    Role: Principal Investigator

    U01DE025181     (MYERS, JEFFREY NICHOLAS)Jul 1, 2015 - Apr 30, 2019
    NIH/NIDCR
    Translating genomic alterations into novel therapeutic targets in head and neck cancer through computational and functional approaches
    Role: Co-Principal Investigator

    R01AG061105     (LICHTARGE, OLIVIER)Sep 30, 2018 - May 31, 2023
    NIH/NIA
    A knowledge map to find Alzheimer's disease drugs
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. 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. 2019 May; 269(5):917-923. PMID: 28767562.
      View in: PubMed
    2. Lin CH, Konecki DM, Liu M, Wilson SJ, Nassar H, Wilkins AD, Gleich DF, Lichtarge O. Multimodal Network Diffusion Predicts Future Disease-Gene-Chemical Associations. Bioinformatics. 2018 Oct 09. PMID: 30304494.
      View in: PubMed
    3. Choi BK, Dayaram T, Parikh N, Wilkins AD, Nagarajan M, Novikov IB, Bachman BJ, Jung SY, Haas PJ, Labrie JL, Pickering CR, Adikesavan AK, Regenbogen S, Kato L, Lelescu A, Buchovecky CM, Zhang H, Bao SH, Boyer S, Weber G, Scott KL, Chen Y, Spangler S, Donehower LA, Lichtarge O. Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2. Proc Natl Acad Sci U S A. 2018 10 16; 115(42):10666-10671. PMID: 30266789.
      View in: PubMed
    4. Clarke CN, Katsonis P, Hsu TK, Koire AM, Silva-Figueroa A, Christakis I, Williams MD, Kutahyalioglu M, Kwatampora L, Xi Y, Lee JE, Koptez ES, Busaidy NL, Perrier ND, Lichtarge O. Comprehensive Genomic Characterization of Parathyroid Cancer Identifies Novel Candidate Driver Mutations and Core Pathways. J Endocr Soc. 2019 Mar 01; 3(3):544-559. PMID: 30788456.
      View in: PubMed
    5. Karamitri A, Plouffe B, Bonnefond A, Chen M, Gallion J, Guillaume JL, Hegron A, Boissel M, Canouil M, Langenberg C, Wareham NJ, Le Gouill C, Lukasheva V, Lichtarge O, Froguel P, Bouvier M, Jockers R. Type 2 diabetes-associated variants of the MT2 melatonin receptor affect distinct modes of signaling. Sci Signal. 2018 Aug 28; 11(545). PMID: 30154102.
      View in: PubMed
    6. Almannai M, Wang J, Dai H, El-Hattab AW, Faqeih EA, Saleh MA, Al Asmari A, Alwadei AH, Aljadhai YI, AlHashem A, Tabarki B, Lines MA, Grange DK, Benini R, Alsaman AS, Mahmoud A, Katsonis P, Lichtarge O, Wong LC. FARS2 deficiency; new cases, review of clinical, biochemical, and molecular spectra, and variants interpretation based on structural, functional, and evolutionary significance. Mol Genet Metab. 2018 11; 125(3):281-291. PMID: 30177229.
      View in: PubMed
    7. Swings T, Marciano DC, Atri B, Bosserman RE, Wang C, Leysen M, Bonte C, Schalck T, Furey I, Van den Bergh B, Verstraeten N, Christie PJ, Herman C, Lichtarge O, Michiels J. CRISPR-FRT targets shared sites in a knock-out collection for off-the-shelf genome editing. Nat Commun. 2018 06 08; 9(1):2231. PMID: 29884781.
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    8. Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 04 05; 173(2):355-370.e14. PMID: 29625052.
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    9. Suryavanshi SV, Jadhav SM, Anderson KL, Katsonis P, Lichtarge O, McConnell BK. Human muscle-specific A-kinase anchoring protein polymorphisms modulate the susceptibility to cardiovascular diseases by altering cAMP/PKA signaling. Am J Physiol Heart Circ Physiol. 2018 Jul 01; 315(1):H109-H121. PMID: 29600899.
      View in: PubMed
    10. Nair A, Chung HC, Sun T, Tyagi S, Dobrolecki LE, Dominguez-Vidana R, Kurley SJ, Orellana M, Renwick A, Henke DM, Katsonis P, Schmitt E, Chan DW, Li H, Mao S, Petrovic I, Creighton CJ, Gutierrez C, Dubrulle J, Stossi F, Tyner JW, Lichtarge O, Lin CY, Zhang B, Scott KL, Hilsenbeck SG, Sun J, Yu X, Osborne CK, Schiff R, Christensen JG, Shields DJ, Rimawi MF, Ellis MJ, Shaw CA, Lewis MT, Westbrook TF. Combinatorial inhibition of PTPN12-regulated receptors leads to a broadly effective therapeutic strategy in triple-negative breast cancer. Nat Med. 2018 May; 24(4):505-511. PMID: 29578538.
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    11. Gennarino VA, Palmer EE, McDonell LM, Wang L, Adamski CJ, Koire A, See L, Chen CA, Schaaf CP, Rosenfeld JA, Panzer JA, Moog U, Hao S, Bye A, Kirk EP, Stankiewicz P, Breman AM, McBride A, Kandula T, Dubbs HA, Macintosh R, Cardamone M, Zhu Y, Ying K, Dias KR, Cho MT, Henderson LB, Baskin B, Morris P, Tao J, Cowley MJ, Dinger ME, Roscioli T, Caluseriu O, Suchowersky O, Sachdev RK, Lichtarge O, Tang J, Boycott KM, Holder JL, Zoghbi HY. A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures. Cell. 2018 02 22; 172(5):924-936.e11. PMID: 29474920.
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    12. Lisewski AM, Quiros JP, Mittal M, Putluri N, Sreekumar A, Haeggström JZ, Lichtarge O. Potential role of Plasmodium falciparum exported protein 1 in the chloroquine mode of action. Int J Parasitol Drugs Drug Resist. 2018 04; 8(1):31-35. PMID: 29324251.
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    13. Schönegge AM, Gallion J, Picard LP, Wilkins AD, Le Gouill C, Audet M, Stallaert W, Lohse MJ, Kimmel M, Lichtarge O, Bouvier M. Evolutionary action and structural basis of the allosteric switch controlling ß2AR functional selectivity. Nat Commun. 2017 12 18; 8(1):2169. PMID: 29255305.
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    14. Otaify GA, Whyte MP, Gottesman GS, McAlister WH, Eric Gordon J, Hollander A, Andrews MV, El-Mofty SK, Chen WS, Veis DV, Stolina M, Woo AS, Katsonis P, Lichtarge O, Zhang F, Shinawi M. Gnathodiaphyseal dysplasia: Severe atypical presentation with novel heterozygous mutation of the anoctamin gene (ANO5). Bone. 2018 02; 107:161-171. PMID: 29175271.
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    15. Katsonis P, Lichtarge O. Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI-blinded contests. Hum Mutat. 2017 09; 38(9):1072-1084. PMID: 28544059.
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    16. 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 09; 38(9):1042-1050. PMID: 28440912.
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    17. 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. Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Hum Mutat. 2017 09; 38(9):1123-1131. PMID: 28370845.
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    18. Galaz-Montoya M, Wright SJ, Rodriguez GJ, Lichtarge O, Wensel TG. ß2-Adrenergic receptor activation mobilizes intracellular calcium via a non-canonical cAMP-independent signaling pathway. J Biol Chem. 2017 06 16; 292(24):9967-9974. PMID: 28442571.
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    19. 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; 12(3):e0174766. PMID: 28350864.
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    20. Gallion J, Koire A, Katsonis P, Schoenegge AM, Bouvier M, Lichtarge O. Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling. Hum Mutat. 2017 05; 38(5):569-580. PMID: 28230923.
      View in: PubMed
    21. 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. 2017; 22:336-347. PMID: 27896987.
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    22. Gallion J, Wilkins AD, Lichtarge O. HUMAN KINASES DISPLAY MUTATIONAL HOTSPOTS AT COGNATE POSITIONS WITHIN CANCER. Pac Symp Biocomput. 2017; 22:414-425. PMID: 27896994.
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    23. 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 12 29; 128(26):3061-3072. PMID: 27799162.
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    24. 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 10; 240(2):224-34. PMID: 27447534.
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    25. 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. PMID: 27391757.
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    26. Sung YM, Wilkins AD, Rodriguez GJ, Wensel TG, Lichtarge O. Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation. Proc Natl Acad Sci U S A. 2016 Mar 29; 113(13):3539-44. PMID: 26979958.
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    27. Regenbogen S, Wilkins AD, Lichtarge O. COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS. Pac Symp Biocomput. 2016; 21:21-32. PMID: 26776170.
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    28. 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; 21:207-18. PMID: 26776187.
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    29. 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 04; 44(D1):D308-12. PMID: 26590254.
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    30. 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.
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    31. Peterson SM, Pack TF, Wilkins AD, Urs NM, Urban DJ, Bass CE, Lichtarge O, Caron MG. Elucidation of G-protein and ß-arrestin functional selectivity at the dopamine D2 receptor. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):7097-102. PMID: 25964346.
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    32. Osman AA, Neskey DM, Katsonis P, Patel AA, Ward AM, Hsu TK, Hicks SC, McDonald TO, Ow TJ, Alves MO, 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 Is Predictive of Platinum Response in Head and Neck Cancer Patients. Cancer Res. 2015 Apr 01; 75(7):1205-15. PMID: 25691460.
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    33. 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 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer. Cancer Res. 2015 Apr 01; 75(7):1527-36. PMID: 25634208.
      View in: PubMed
    34. 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. PMID: 25519912.
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    35. 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.
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    36. 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 Dec; 23(12):1650-66. PMID: 25234433.
      View in: PubMed
    37. 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 Dec; 24(12):2050-8. PMID: 25217195.
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    38. 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. PMID: 25193666.
      View in: PubMed
    39. 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, Lichtarge O. Supergenomic network compression and the discovery of EXP1 as a glutathione transferase inhibited by artesunate. Cell. 2014 Aug 14; 158(4):916-928. PMID: 25126794.
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    40. 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 26; 7(6):1789-95. PMID: 24910431.
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    41. Lua RC, Marciano DC, Katsonis P, Adikesavan AK, Wilkins AD, Lichtarge O. Prediction and redesign of protein-protein interactions. Prog Biophys Mol Biol. 2014 Nov-Dec; 116(2-3):194-202. PMID: 24878423.
      View in: PubMed
    42. 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.
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    43. 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.
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    44. Zheng L, Sepúlveda LA, Lua RC, Lichtarge O, Golding I, Sokac AM. The maternal-to-zygotic transition targets actin to promote robustness during morphogenesis. PLoS Genet. 2013 Nov; 9(11):e1003901. PMID: 24244181.
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    45. Amin SR, Erdin S, Ward RM, Lua RC, Lichtarge O. Prediction and experimental validation of enzyme substrate specificity in protein structures. Proc Natl Acad Sci U S A. 2013 Nov 05; 110(45):E4195-202. PMID: 24145433.
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    46. 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 Nov 01; 29(21):2714-21. PMID: 24021383.
      View in: PubMed
    47. Rababa'h A, Craft JW, 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. PMID: 23806656.
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    48. 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 28; 152(5):984-96. PMID: 23452848.
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    49. 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. PMID: 23514548.
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    50. Shoji-Kawata S, Sumpter R, Leveno M, Campbell GR, Zou Z, Kinch L, Wilkins AD, Sun Q, Pallauf K, MacDuff D, Huerta C, Virgin HW, Helms JB, Eerland R, Tooze SA, Xavier R, Lenschow DJ, Yamamoto A, King D, Lichtarge O, Grishin NV, Spector SA, Kaloyanova DV, Levine B. Identification of a candidate therapeutic autophagy-inducing peptide. Nature. 2013 Feb 14; 494(7436):201-6. PMID: 23364696.
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    51. Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013 Mar; 10(3):221-7. PMID: 23353650.
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    52. Al Mamun AA, 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 07; 338(6112):1344-8. PMID: 23224554.
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    53. Bachman BJ, Venner E, Lua RC, Erdin S, Lichtarge O. ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape. Bioinformatics. 2012 Aug 15; 28(16):2186-8. PMID: 22689386.
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    54. Wilkins AD, Bachman BJ, Erdin S, Lichtarge O. The use of evolutionary patterns in protein annotation. Curr Opin Struct Biol. 2012 Jun; 22(3):316-25. PMID: 22633559.
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    55. Wilkins A, Erdin S, Lua R, Lichtarge O. Evolutionary trace for prediction and redesign of protein functional sites. Methods Mol Biol. 2012; 819:29-42. PMID: 22183528.
      View in: PubMed
    56. Adikesavan AK, Katsonis P, Marciano DC, Lua R, Herman C, Lichtarge O. Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites. PLoS Genet. 2011 Sep; 7(9):e1002244. PMID: 21912525.
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    57. 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.
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    58. Häberle J, Shchelochkov OA, Wang J, Katsonis P, Hall L, Reiss S, Eeds A, Willis A, Yadav M, Summar S, Lichtarge O, Rubio V, Wong LJ, Summar M. Molecular defects in human carbamoy phosphate synthetase I: mutational spectrum, diagnostic and protein structure considerations. Hum Mutat. 2011 Jun; 32(6):579-89. PMID: 21120950.
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    59. Erdin S, Lisewski AM, Lichtarge O. Protein function prediction: towards integration of similarity metrics. Curr Opin Struct Biol. 2011 Apr; 21(2):180-8. PMID: 21353529.
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    60. Venner E, Lisewski AM, Erdin S, Ward RM, Amin SR, 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. PMID: 21179190.
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    61. Lua RC, Lichtarge O. PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes. Bioinformatics. 2010 Dec 01; 26(23):2981-2. PMID: 20929911.
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    62. Lisewski AM, Lichtarge O. Untangling complex networks: risk minimization in financial markets through accessible spin glass ground states. Physica A. 2010 Aug 15; 389(16):3250-3253. PMID: 20625477.
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    63. Wilkins AD, Lua R, Erdin S, Ward RM, Lichtarge O. Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation. Protein Sci. 2010 Jul; 19(7):1296-311. PMID: 20506260.
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    64. Lichtarge O, Wilkins A. Evolution: a guide to perturb protein function and networks. Curr Opin Struct Biol. 2010 Jun; 20(3):351-9. PMID: 20444593.
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    65. Rodriguez GJ, Yao R, Lichtarge O, Wensel TG. Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. Proc Natl Acad Sci U S A. 2010 Apr 27; 107(17):7787-92. PMID: 20385837.
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    66. Bonde MM, Yao R, Ma JN, Madabushi S, Haunsø S, Burstein ES, Whistler JL, Sheikh SP, Lichtarge O, Hansen JL. An angiotensin II type 1 receptor activation switch patch revealed through evolutionary trace analysis. Biochem Pharmacol. 2010 Jul 01; 80(1):86-94. PMID: 20227396.
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    67. Erdin S, Ward RM, Venner E, Lichtarge O. Evolutionary trace annotation of protein function in the structural proteome. J Mol Biol. 2010 Mar 12; 396(5):1451-73. PMID: 20036248.
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    68. Baameur F, Morgan DH, Yao H, Tran TM, Hammitt RA, Sabui S, McMurray JS, Lichtarge O, Clark RB. Role for the regulator of G-protein signaling homology domain of G protein-coupled receptor kinases 5 and 6 in beta 2-adrenergic receptor and rhodopsin phosphorylation. Mol Pharmacol. 2010 Mar; 77(3):405-15. PMID: 20038610.
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    69. Shaibani A, Shchelochkov OA, Zhang S, Katsonis P, Lichtarge O, Wong LJ, Shinawi M. Mitochondrial neurogastrointestinal encephalopathy due to mutations in RRM2B. Arch Neurol. 2009 Aug; 66(8):1028-32. PMID: 19667227.
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    70. Kobayashi H, Ogawa K, Yao R, Lichtarge O, Bouvier M. Functional rescue of beta-adrenoceptor dimerization and trafficking by pharmacological chaperones. Traffic. 2009 Aug; 10(8):1019-33. PMID: 19515093.
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    71. Ward RM, Venner E, Daines B, Murray S, Erdin S, Kristensen DM, Lichtarge O. Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. Bioinformatics. 2009 Jun 01; 25(11):1426-7. PMID: 19307237.
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    72. Rajagopalan L, Pereira FA, Lichtarge O, Brownell WE. 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. PMID: 18839354.
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    73. Ward RM, Erdin S, Tran TA, Kristensen DM, Lisewski AM, Lichtarge O. De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS One. 2008 May 07; 3(5):e2136. PMID: 18461181.
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    74. Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics. 2008 Jan 11; 9:17. PMID: 18190718.
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    75. Mihalek I, Res I, Lichtarge O. Background frequencies for residue variability estimates: BLOSUM revisited. BMC Bioinformatics. 2007 Dec 27; 8:488. PMID: 18162129.
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    76. Shin H, Lisewski AM, Lichtarge O. Graph sharpening plus graph integration: a synergy that improves protein functional classification. Bioinformatics. 2007 Dec 01; 23(23):3217-24. PMID: 17977886.
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    77. Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, 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. PMID: 17691895.
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    78. 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(2a):353-82. PMID: 17589966.
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    79. Mihalek I, Res I, Lichtarge O. On itinerant water molecules and detectability of protein-protein interfaces through comparative analysis of homologues. J Mol Biol. 2007 Jun 01; 369(2):584-95. PMID: 17434530.
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    80. Ribes-Zamora A, Mihalek I, Lichtarge O, Bertuch AA. Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions. Nat Struct Mol Biol. 2007 Apr; 14(4):301-7. PMID: 17351632.
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    81. Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE. Composite motifs integrating multiple protein structures increase sensitivity for function prediction. Comput Syst Bioinformatics Conf. 2007; 6:343-55. PMID: 17951837.
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    82. 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 06; 26(49):12727-34. PMID: 17151276.
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    83. Lisewski AM, Lichtarge O. Rapid detection of similarity in protein structure and function through contact metric distances. Nucleic Acids Res. 2006; 34(22):e152. PMID: 17130161.
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    84. Yao H, Mihalek I, Lichtarge O. Rank information: a structure-independent measure of evolutionary trace quality that improves identification of protein functional sites. Proteins. 2006 Oct 01; 65(1):111-23. PMID: 16894615.
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    85. Raviscioni M, He Q, Salicru EM, Smith CL, Lichtarge O. Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors. Proteins. 2006 Sep 01; 64(4):1046-57. PMID: 16835908.
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    86. Morgan DH, Kristensen DM, Mittelman D, Lichtarge O. ET viewer: an application for predicting and visualizing functional sites in protein structures. Bioinformatics. 2006 Aug 15; 22(16):2049-50. PMID: 16809388.
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    87. Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, 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. PMID: 16672239.
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    88. Mihalek I, Res I, Lichtarge O. Evolutionary trace report_maker: a new type of service for comparative analysis of proteins. Bioinformatics. 2006 Jul 01; 22(13):1656-7. PMID: 16644792.
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    89. Mihalek I, Res I, Lichtarge O. Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins. Proteins. 2006 Apr 01; 63(1):87-99. PMID: 16397893.
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    90. Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE. Cavity-aware motifs reduce false positives in protein function prediction. Comput Syst Bioinformatics Conf. 2006; 311-23. PMID: 17369649.
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    91. Chiba P, Mihalek I, Ecker GF, Kopp S, 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. Curr Med Chem. 2006; 13(7):793-805. PMID: 16611068.
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    92. Mihalek I, Res I, 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. PMID: 16303797.
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    93. Shenoy SK, Drake MT, Nelson CD, Houtz DA, Xiao K, Madabushi S, Reiter E, Premont RT, Lichtarge O, 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. PMID: 16280323.
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    94. 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 15; 350(3):402-15. PMID: 15946684.
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    95. Gu P, Morgan DH, Sattar M, Xu X, Wagner R, Raviscioni M, Lichtarge O, Cooney AJ. Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptors. J Biol Chem. 2005 Sep 09; 280(36):31818-29. PMID: 15994320.
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    96. Res I, Lichtarge O. Character and evolution of protein-protein interfaces. Phys Biol. 2005 Jun; 2(2):S36-43. PMID: 16204847.
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    97. Res I, Mihalek I, Lichtarge O. An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinformatics. 2005 May 15; 21(10):2496-501. PMID: 15728113.
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    98. Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE. Algorithms for structural comparison and statistical analysis of 3D protein motifs. Pac Symp Biocomput. 2005; 334-45. PMID: 15759639.
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    99. Cushman I, Bowman BR, Sowa ME, Lichtarge O, Quiocho FA, Moore MS. Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2. J Mol Biol. 2004 Nov 19; 344(2):303-10. PMID: 15522285.
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    100. 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. PMID: 15084454.
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    101. Mihalek I, Res I, Lichtarge O. A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol. 2004 Mar 05; 336(5):1265-82. PMID: 15037084.
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    102. 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 27; 279(9):8126-32. PMID: 14660595.
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    103. Mihalek I, Res I, Yao H, Lichtarge O. Combining inference from evolution and geometric probability in protein structure evaluation. J Mol Biol. 2003 Aug 01; 331(1):263-79. PMID: 12875851.
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    104. Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, Kimmel M, Kavraki L, Lichtarge O. An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol. 2003 Feb 07; 326(1):255-61. PMID: 12547207.
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    105. Lin CY, Varma MG, Joubel A, Madabushi S, Lichtarge O, Barber DL. Conserved motifs in somatostatin, D2-dopamine, and alpha 2B-adrenergic receptors for inhibiting the Na-H exchanger, NHE1. J Biol Chem. 2003 Apr 25; 278(17):15128-35. PMID: 12566440.
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    106. Lichtarge O, Yao H, Kristensen DM, Madabushi S, Mihalek I. Accurate and scalable identification of functional sites by evolutionary tracing. J Struct Funct Genomics. 2003; 4(2-3):159-66. PMID: 14649300.
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    107. Yang M, Wang W, Zhong M, Philippi A, Lichtarge O, 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. PMID: 11923477.
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    108. Madabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, Sowa ME, Lichtarge O. Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol. 2002 Feb 08; 316(1):139-54. PMID: 11829509.
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    109. Lichtarge O, Sowa ME. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol. 2002 Feb; 12(1):21-7. PMID: 11839485.
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    110. Lichtarge O, Sowa ME, Philippi A. Evolutionary traces of functional surfaces along G protein signaling pathway. Methods Enzymol. 2002; 344:536-56. PMID: 11771409.
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    111. Imanishi Y, Li N, Sokal I, Sowa ME, Lichtarge O, Wensel TG, Saperstein DA, Baehr W, Palczewski K. Characterization of retinal guanylate cyclase-activating protein 3 (GCAP3) from zebrafish to man. Eur J Neurosci. 2002 Jan; 15(1):63-78. PMID: 11860507.
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    112. Lichtarge O. Getting past appearances: the many-fold consequences of remote homology. Nat Struct Biol. 2001 Nov; 8(11):918-20. PMID: 11685232.
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    113. Sowa ME, He W, Slep KC, Kercher MA, Lichtarge O, 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. PMID: 11224568.
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    114. Geva A, Lassere TB, Lichtarge O, Pollitt SK, Baranski TJ. Genetic mapping of the human C5a receptor. Identification of transmembrane amino acids critical for receptor function. J Biol Chem. 2000 Nov 10; 275(45):35393-401. PMID: 10952985.
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    115. 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, Zoghbi HY. Influence of mutation type and X chromosome inactivation on Rett syndrome phenotypes. Ann Neurol. 2000 May; 47(5):670-9. PMID: 10805343.
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    116. Lloyd TE, Verstreken P, Ostrin EJ, Phillippi A, Lichtarge O, Bellen HJ. A genome-wide search for synaptic vesicle cycle proteins in Drosophila. Neuron. 2000 Apr; 26(1):45-50. PMID: 10798391.
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    117. Sowa ME, He W, Wensel TG, Lichtarge O. A regulator of G protein signaling interaction surface linked to effector specificity. Proc Natl Acad Sci U S A. 2000 Feb 15; 97(4):1483-8. PMID: 10677488.
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    118. Sheikh SP, Vilardarga JP, Baranski TJ, Lichtarge O, Iiri T, Meng EC, Nissenson RA, 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 11; 274(24):17033-41. PMID: 10358054.
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    119. Baranski TJ, Herzmark P, Lichtarge O, Gerber BO, Trueheart J, Meng EC, Iiri T, Sheikh SP, Bourne HR. C5a receptor activation. Genetic identification of critical residues in four transmembrane helices. J Biol Chem. 1999 May 28; 274(22):15757-65. PMID: 10336477.
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    120. Schumacher A, Lichtarge O, Schwartz S, Magnuson T. The murine Polycomb-group gene eed and its human orthologue: functional implications of evolutionary conservation. Genomics. 1998 Nov 15; 54(1):79-88. PMID: 9806832.
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    121. Lichtarge O, Yamamoto KR, Cohen FE. Identification of functional surfaces of the zinc binding domains of intracellular receptors. J Mol Biol. 1997 Dec 05; 274(3):325-37. PMID: 9405143.
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    122. Onrust R, Herzmark P, Chi P, Garcia PD, Lichtarge O, Kingsley C, Bourne HR. Receptor and betagamma binding sites in the alpha subunit of the retinal G protein transducin. Science. 1997 Jan 17; 275(5298):381-4. PMID: 8994033.
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    123. Dunbrack RL, Gerloff DL, Bower M, Chen X, Lichtarge O, 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; 2(2):R27-42. PMID: 9135979.
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    124. Sheikh SP, Zvyaga TA, Lichtarge O, Sakmar TP, Bourne HR. Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F. Nature. 1996 Sep 26; 383(6598):347-50. PMID: 8848049.
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    125. Lichtarge O, Bourne HR, 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 23; 93(15):7507-11. PMID: 8755504.
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    126. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol. 1996 Mar 29; 257(2):342-58. PMID: 8609628.
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    127. Jardetzky O, Lichtarge O, Brinkley J, Madrid M. The structure of proteins and their binding sites: NMR and artificial intelligence. Prog Clin Biol Res. 1989; 289:145-56. PMID: 2726796.
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    128. Lichtarge O, Jardetzky O, Li CH. Secondary structure determination of human beta-endorphin by 1H NMR spectroscopy. Biochemistry. 1987 Sep 08; 26(18):5916-25. PMID: 2960378.
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    129. Lichtarge O, Cornelius CW, Buchanan BG, Jardetzky O. Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data. Proteins. 1987; 2(4):340-58. PMID: 3448608.
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    130. Goldsmith HL, Lichtarge O, Tessier-Lavigne M, Spain S. Some model experiments in hemodynamics: VI. Two-body collisions between blood cells. Biorheology. 1981; 18(3-6):531-55. PMID: 7326392.
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