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OLIVIER LICHTARGE

TitleProfessor
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular & Human Genetics
AddressOne Baylor Plaza
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    Other Positions
    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Biochemistry and Molecular Pharmacology
    DivisionBiochemistry & Mol Pharmacology

    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Medicine
    DivisionMedicine-Endocrinology


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    R01AG074009     (LICHTARGE, OLIVIER)Sep 15, 2021 - Jun 30, 2026
    NIH
    Decoding the impact of sex differences on Alzheimer's disease risk
    Role: Principal Investigator
    U01AG068214     (LICHTARGE, OLIVIER)Jul 1, 2021 - Jun 30, 2026
    NIH
    Cognitive Computing of Alzheimer's Disease Genes and Risk
    Role: Principal Investigator
    R01AG061105     (LICHTARGE, OLIVIER)Sep 30, 2018 - May 31, 2024
    NIH
    A knowledge map to find Alzheimer's disease drugs
    Role: Principal Investigator
    U01DE025181     (MYERS, JEFFREY NICHOLAS)Jul 1, 2015 - Apr 30, 2021
    NIH
    Translating genomic alterations into novel therapeutic targets in head and neck cancer through computational and functional approaches
    Role: Co-Principal Investigator
    R01GM079656     (LICHTARGE, OLIVIER)Apr 1, 2007 - Dec 31, 2020
    NIH
    Comparative genomics of protein structure and function
    Role: Principal Investigator
    R01GM066099     (LICHTARGE, OLIVIER)Jul 1, 2002 - Aug 31, 2023
    NIH
    Functional Determinants in G-Protein-Coupled Receptors
    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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Meena JK, Wang JH, Neill NJ, Keough D, Putluri N, Katsonis P, Koire AM, Lee H, Bowling EA, Tyagi S, Orellana M, Dominguez-Vida?a R, Li H, Eagle K, Danan C, Chung HC, Yang AD, Wu W, Kurley SJ, Ho BM, Zoeller JR, Olson CM, Meerbrey KL, Lichtarge O, Sreekumar A, Dacso CC, Guddat LW, Rejman D, Hockov? D, Janeba Z, Simon LM, Lin CY, Pillon MC, Westbrook TF. MYC Induces Oncogenic Stress through RNA Decay and Ribonucleotide Catabolism in Breast Cancer. Cancer Discov. 2024 Sep 04; 14(9):1699-1716. PMID: 39193992; PMCID: PMC11372365.
      Citations:    Fields:    Translation:HumansAnimalsCells
    2. Zhang J, Kinch L, Katsonis P, Lichtarge O, Jagota M, Song YS, Sun Y, Shen Y, Kuru N, Dereli O, Adebali O, Alladin MA, Pal D, Capriotti E, Turina MP, Savojardo C, Martelli PL, Babbi G, Casadio R, Pucci F, Rooman M, Cia G, Tsishyn M, Strokach A, Hu Z, van Loggerenberg W, Roth FP, Radivojac P, Brenner SE, Cong Q, Grishin NV. Assessing predictions on fitness effects of missense variants in HMBS in CAGI6. Hum Genet. 2024 Aug 07. PMID: 39110250.
      Citations:    Fields:    
    3. Chen Y, Lee K, Woo J, Kim DW, Keum C, Babbi G, Casadio R, Martelli PL, Savojardo C, Manfredi M, Shen Y, Sun Y, Katsonis P, Lichtarge O, Pejaver V, Seward DJ, Kamandula A, Bakolitsa C, Brenner SE, Radivojac P, O'Donnell-Luria AH, Mooney S, Jain S, Chen Y, Lee K, Woo J, Kim DW, Keum C, Babbi G, Casadio R, Martelli PL, Savojardo C, Manfredi M, Shen Y, Sun Y, Katsonis P, Lichtarge O, Pejaver V, Seward DJ, Kamandula A, Bakolitsa C, Brenner SE, Radivojac P, O'Donnell-Luria A, Mooney SD, Jain S. Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers. Res Sq. 2024 Jul 02. PMID: 39011112; PMCID: PMC11247923.
      Citations:    
    4. Kaur A, Rojek AE, Symes E, Nawas MT, Patel AA, Patel JL, Sojitra P, Aqil B, Sukhanova M, McNerney ME, Wu LP, Akmatbekov A, Segal J, Tjota MY, Gurbuxani S, Cheng JX, Yeon SY, Ravisankar HV, Fitzpatrick C, Lager A, Drazer MW, Saygin C, Wanjari P, Katsonis P, Lichtarge O, Churpek JE, Ghosh SB, Patel AB, Menon MP, Arber DA, Wang P, Venkataraman G. Real world predictors of response and 24-month survival in high-grade TP53-mutated myeloid neoplasms. Blood Cancer J. 2024 06 18; 14(1):99. PMID: 38890297; PMCID: PMC11189545.
      Citations:    Fields:    Translation:Humans
    5. Jain S, Trinidad M, Nguyen TB, Jones K, Neto SD, Ge F, Glagovsky A, Jones C, Moran G, Wang B, Rahimi K, ?alici SZ, Cedillo LR, Berardelli S, ?zden B, Chen K, Katsonis P, Williams A, Lichtarge O, Rana S, Pradhan S, Srinivasan R, Sajeed R, Joshi D, Faraggi E, Jernigan R, Kloczkowski A, Xu J, Song Z, ?zkan S, Padilla N, de la Cruz X, Acuna-Hidalgo R, Grafm?ller A, Jim?nez Barr?n LT, Manfredi M, Savojardo C, Babbi G, Martelli PL, Casadio R, Sun Y, Zhu S, Shen Y, Pucci F, Rooman M, Cia G, Raimondi D, Hermans P, Kwee S, Chen E, Astore C, Kamandula A, Pejaver V, Ramola R, Velyunskiy M, Zeiberg D, Mishra R, Sterling T, Goldstein JL, Lugo-Martinez J, Kazi S, Li S, Long K, Brenner SE, Bakolitsa C, Radivojac P, Suhr D, Suhr T, Clark WT, Jain S, Trinidad M, Nguyen TB, Jones K, Neto SD, Ge F, Glagovsky A, Jones C, Moran G, Wang B, Rahimi K, ?alici SZ, Cedillo LR, Berardelli S, ?zden B, Chen K, Katsonis P, Williams A, Lichtarge O, Rana S, Pradhan S, Srinivasan R, Sajeed R, Joshi D, Faraggi E, Jernigan R, Kloczkowski A, Xu J, Song Z, ?zkan S, Padilla N, de la Cruz X, Acuna-Hidalgo R, Grafm?ller A, Jim?nez Barr?n LT, Manfredi M, Savojardo C, Babbi G, Martelli PL, Casadio R, Sun Y, Zhu S, Shen Y, Pucci F, Rooman M, Cia G, Raimondi D, Hermans P, Kwee S, Chen E, Astore C, Kamandula A, Pejaver V, Ramola R, Velyunskiy M, Zeiberg D, Mishra R, Sterling T, Goldstein JL, Lugo-Martinez J, Kazi S, Li S, Long K, Brenner SE, Bakolitsa C, Radivojac P, Suhr D, Suhr T, Clark WT. Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A. bioRxiv. 2024 Jun 17. PMID: 38798479; PMCID: PMC11118473.
      Citations:    
    6. Chinnam NB, Thapar R, Arvai AS, Sarker AH, Soll JM, Paul T, Syed A, Rosenberg DJ, Hammel M, Bacolla A, Katsonis P, Asthana A, Tsai MS, Ivanov I, Lichtarge O, Silverman RH, Mosammaparast N, Tsutakawa SE, Tainer JA. ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase. J Biol Chem. 2024 Jun; 300(6):107368. PMID: 38750793; PMCID: PMC11214414.
      Citations:    Fields:    Translation:HumansCells
    7. Stenton SL, O'Leary MC, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson MW, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A. Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project. Hum Genomics. 2024 04 29; 18(1):44. PMID: 38685113; PMCID: PMC11057178.
      Citations: 3     Fields:    Translation:Humans
    8. Bradley CC, Wang C, Gordon AJE, Wen AX, Luna PN, Cooke MB, Kohrn BF, Kennedy SR, Avadhanula V, Piedra PA, Lichtarge O, Shaw CA, Ronca SE, Herman C. Targeted accurate RNA consensus sequencing (tARC-seq) reveals mechanisms of replication error affecting SARS-CoV-2 divergence. Nat Microbiol. 2024 May; 9(5):1382-1392. PMID: 38649410; PMCID: PMC11384275.
      Citations: 3     Fields:    Translation:HumansCells
    9. Shepherdson JL, Hutchison K, Don DW, McGillivray G, Choi TI, Allan CA, Amor DJ, Banka S, Basel DG, Buch LD, Carere DA, Carroll R, Clayton-Smith J, Crawford A, Dun? M, Faivre L, Gilfillan CP, Gold NB, Gripp KW, Hobson E, Holtz AM, Innes AM, Isidor B, Jackson A, Katsonis P, Amel Riazat Kesh L, Genomics England Research Consortium, K?ry S, Lecoquierre F, Lockhart P, Maraval J, Matsumoto N, McCarrier J, McCarthy J, Miyake N, Moey LH, N?meth AH, ?stergaard E, Patel R, Pope K, Posey JE, Schnur RE, Shaw M, Stolerman E, Taylor JP, Wadman E, Wakeling E, White SM, Wong LC, Lupski JR, Lichtarge O, Corbett MA, Gecz J, Nicolet CM, Farnham PJ, Kim CH, Shinawi M. Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt. Am J Hum Genet. 2024 03 07; 111(3):487-508. PMID: 38325380; PMCID: PMC10940019.
      Citations: 3     Fields:    Translation:HumansAnimals
    10. Lord J, Oquendo CJ, Wai HA, Douglas AGL, Bunyan DJ, Wang Y, Hu Z, Zeng Z, Danis D, Katsonis P, Williams A, Lichtarge O, Chang Y, Bagnall RD, Mount SM, Matthiasardottir B, Lin C, Hansen TVO, Leman R, Martins A, Houdayer C, Krieger S, Bakolitsa C, Peng Y, Kamandula A, Radivojac P, Baralle D. Predicting the impact of rare variants on RNA splicing in CAGI6. Hum Genet. 2024 Jan 03. PMID: 38170232.
      Citations: 2     Fields:    
    11. Gao W, Liu L, Huh E, Gbahou F, Cecon E, Oshima M, Houz? L, Katsonis P, Hegron A, Fan Z, Hou G, Charpentier G, Boissel M, Derhourhi M, Marre M, Balkau B, Froguel P, Scharfmann R, Lichtarge O, Dam J, Bonnefond A, Liu J, Jockers R. Human GLP1R variants affecting GLP1R cell surface expression are associated with impaired glucose control and increased adiposity. Nat Metab. 2023 Oct; 5(10):1673-1684. PMID: 37709961; PMCID: PMC11610247.
      Citations:    Fields:    Translation:Humans
    12. Shapiro D, Lee K, Asmussen J, Bourquard T, Lichtarge O. Evolutionary Action-Machine Learning Model Identifies Candidate Genes Associated With Early-Onset Coronary Artery Disease. J Am Heart Assoc. 2023 09 05; 12(17):e029103. PMID: 37642027; PMCID: PMC10547338.
      Citations:    Fields:    Translation:Animals
    13. Stenton SL, O'Leary M, Lemire G, VanNoy GE, DiTroia S, Ganesh VS, Groopman E, O'Heir E, Mangilog B, Osei-Owusu I, Pais LS, Serrano J, Singer-Berk M, Weisburd B, Wilson M, Austin-Tse C, Abdelhakim M, Althagafi A, Babbi G, Bellazzi R, Bovo S, Carta MG, Casadio R, Coenen PJ, De Paoli F, Floris M, Gajapathy M, Hoehndorf R, Jacobsen JOB, Joseph T, Kamandula A, Katsonis P, Kint C, Lichtarge O, Limongelli I, Lu Y, Magni P, Mamidi TKK, Martelli PL, Mulargia M, Nicora G, Nykamp K, Pejaver V, Peng Y, Pham THC, Podda MS, Rao A, Rizzo E, Saipradeep VG, Savojardo C, Schols P, Shen Y, Sivadasan N, Smedley D, Soru D, Srinivasan R, Sun Y, Sunderam U, Tan W, Tiwari N, Wang X, Wang Y, Williams A, Worthey EA, Yin R, You Y, Zeiberg D, Zucca S, Bakolitsa C, Brenner SE, Fullerton SM, Radivojac P, Rehm HL, O'Donnell-Luria A. Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project. medRxiv. 2023 Aug 04. PMID: 37577678; PMCID: PMC10418577.
      Citations:    
    14. Aspromonte MC, Conte AD, Zhu S, Tan W, Shen Y, Zhang Y, Li Q, Wang MH, Babbi G, Bovo S, Martelli PL, Casadio R, Althagafi A, Toonsi S, Kulmanov M, Hoehndorf R, Katsonis P, Williams A, Lichtarge O, Xian S, Surento W, Pejaver V, Mooney SD, Sunderam U, Srinivasan R, Murgia A, Piovesan D, Tosatto SCE, Leonardi E. CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs). Res Sq. 2023 Aug 02. PMID: 37577579; PMCID: PMC10418555.
      Citations:    
    15. Wang C, Govindarajan H, Katsonis P, Lichtarge O. ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis. Bioinformatics. 2023 08 01; 39(8). PMID: 37522889; PMCID: PMC10412404.
      Citations:    Fields:    Translation:Cells
    16. Konecki DM, Hamrick S, Wang C, Agosto MA, Wensel TG, Lichtarge O. CovET: A covariation-evolutionary trace method that identifies protein structure-function modules. J Biol Chem. 2023 07; 299(7):104896. PMID: 37290531; PMCID: PMC10338321.
      Citations:    Fields:    Translation:Cells
    17. Bourquard T, Lee K, Al-Ramahi I, Pham M, Shapiro D, Lagisetty Y, Soleimani S, Mota S, Wilhelm K, Samieinasab M, Kim YW, Huh E, Asmussen J, Katsonis P, Botas J, Lichtarge O. Functional variants identify sex-specific genes and pathways in Alzheimer's Disease. Nat Commun. 2023 05 13; 14(1):2765. PMID: 37179358; PMCID: PMC10183026.
      Citations: 4     Fields:    Translation:Humans
    18. Yu W, Chen Y, Putluri N, Osman A, Coarfa C, Putluri V, Kamal AHM, Asmussen JK, Katsonis P, Myers JN, Lai SY, Lu W, Stephan CC, Powell RT, Johnson FM, Skinner HD, Kazi J, Ahmed KM, Hu L, Threet A, Meyer MD, Bankson JA, Wang T, Davis J, Parker KR, Harris MA, Baek ML, Echeverria GV, Qi X, Wang J, Frederick AI, Walsh AJ, Lichtarge O, Frederick MJ, Sandulache VC. Evolution of cisplatin resistance through coordinated metabolic reprogramming of the cellular reductive state. Br J Cancer. 2023 06; 128(11):2013-2024. PMID: 37012319; PMCID: PMC10205814.
      Citations: 1     Fields:    Translation:HumansCells
    19. Huh E, Agosto MA, Wensel TG, Lichtarge O. Coevolutionary signals in metabotropic glutamate receptors capture residue contacts and long-range functional interactions. J Biol Chem. 2023 04; 299(4):103030. PMID: 36806686; PMCID: PMC10060750.
      Citations:    Fields:    Translation:Cells
    20. Lagisetty Y, Bourquard T, Al-Ramahi I, Mangleburg CG, Mota S, Soleimani S, Shulman JM, Botas J, Lee K, Lichtarge O. Identification of risk genes for Alzheimer's disease by gene embedding. Cell Genom. 2022 Sep 14; 2(9). PMID: 36268052; PMCID: PMC9581494.
      Citations: 2     
    21. Parvandeh S, Donehower LA, Panagiotis K, Hsu TK, Asmussen JK, Lee K, Lichtarge O. EPIMUTESTR: a nearest neighbor machine learning approach to predict cancer driver genes from the evolutionary action of coding variants. Nucleic Acids Res. 2022 07 08; 50(12):e70. PMID: 35412634; PMCID: PMC9262594.
      Citations: 1     Fields:    Translation:Humans
    22. Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O. Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. Nat Commun. 2022 06 09; 13(1):3189. PMID: 35680894; PMCID: PMC9184624.
      Citations: 1     Fields:    Translation:Cells
    23. Bradley CC, Gordon AJE, Wang C, Cooke MB, Kohrn BF, Kennedy SR, Lichtarge O, Ronca SE, Herman C. RNA polymerase inaccuracy underlies SARS-CoV-2 variants and vaccine heterogeneity. Res Sq. 2022 Jun 02. PMID: 35677076; PMCID: PMC9176646.
      Citations:    
    24. Michikawa C, Torres-Saavedra PA, Silver NL, Harari PM, Kies MS, Rosenthal DI, Le QT, Jordan RC, Duose DY, Mallampati S, Trivedi S, Luthra R, Wistuba II, Osman AA, Lichtarge O, Foote RL, Parvathaneni U, Hayes DN, Pickering CR, Myers JN. Evolutionary Action Score of TP53 Analysis in Pathologically High-Risk Human Papillomavirus-Negative Head and Neck Cancer From a Phase 2 Clinical Trial: NRG Oncology Radiation Therapy Oncology Group 0234. Adv Radiat Oncol. 2022 Nov-Dec; 7(6):100989. PMID: 36420184; PMCID: PMC9677209.
      Citations: 2     
    25. Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet. 2022 Oct; 141(10):1549-1577. PMID: 35488922; PMCID: PMC9055222.
      Citations:    Fields:    
    26. Hsu TK, Asmussen J, Koire A, Choi BK, Gadhikar MA, Huh E, Lin CH, Konecki DM, Kim YW, Pickering CR, Kimmel M, Donehower LA, Frederick MJ, Myers JN, Katsonis P, Lichtarge O. A general calculus of fitness landscapes finds genes under selection in cancers. Genome Res. 2022 05; 32(5):916-929. PMID: 35301263; PMCID: PMC9104707.
      Citations: 2     Fields:    Translation:Humans
    27. Flock T, Gallion JM, Houston S, Daly CA, Lichtarge O, Deupi X, Plouffe B, Karamitri A, Bonnefond A, Guillaume JL, Le Gouill C, Froguel P, Jockers R, Bouvier M. Structural Elements Directing G Proteins and ?-Arrestin Interactions with the Human Melatonin Type 2 Receptor Revealed by Natural Variants. ACS Pharmacol Transl Sci. 2022 Feb 11; 5(2):89-101. PMID: 35846981; PMCID: PMC9281605.
      Citations:    
    28. Huh E, Gallion J, Agosto MA, Wright SJ, Wensel TG, Lichtarge O. Recurrent high-impact mutations at cognate structural positions in class A G protein-coupled receptors expressed in tumors. Proc Natl Acad Sci U S A. 2021 12 21; 118(51). PMID: 34916293; PMCID: PMC8713800.
      Citations: 1     Fields:    Translation:HumansCells
    29. Tsutakawa SE, Bacolla A, Katsonis P, Bralic A, Hamdan SM, Lichtarge O, Tainer JA, Tsai CL. Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication. Front Mol Biosci. 2021; 8:791792. PMID: 34966786; PMCID: PMC8710748.
      Citations:    
    30. Wang C, Konecki DM, Marciano DC, Govindarajan H, Williams AM, Wastuwidyaningtyas B, Bourquard T, Katsonis P, Lichtarge O. Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family. Bioinformatics. 2021 11 18; 37(22):4033-4040. PMID: 34043002; PMCID: PMC8243408.
      Citations: 3     Fields:    
    31. Moiani D, Link TM, Brosey CA, Katsonis P, Lichtarge O, Kim Y, Joachimiak A, Ma Z, Kim IK, Ahmed Z, Jones DE, Tsutakawa SE, Tainer JA. An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2. Methods Enzymol. 2021; 661:407-431. PMID: 34776222; PMCID: PMC8474023.
      Citations: 2     Fields:    Translation:HumansCells
    32. Lin CH, Lichtarge O. Using interpretable deep learning to model cancer dependencies. Bioinformatics. 2021 Sep 09; 37(17):2675-2681. PMID: 34042953; PMCID: PMC8428607.
      Citations:    Fields:    
    33. Huh E, Deupi X, Le Gouill C, Boissel M, Balkau B, Froguel P, Lichtarge O, Hegron A, Sokrat B, Gao W, Canouil M, Charpentier G, Roussel R, Plouffe B, Bonnefond A, Jockers R, Bouvier M. Identification of Key Regions Mediating Human Melatonin Type 1 Receptor Functional Selectivity Revealed by Natural Variants. ACS Pharmacol Transl Sci. 2021 Oct 08; 4(5):1614-1627. PMID: 34661078; PMCID: PMC8507577.
      Citations:    
    34. Sharma A, Tobar-Tosse F, Chand Dakal T, Liu H, Biswas A, Menon A, Paruchuri A, Katsonis P, Lichtarge O, Gromiha MM, Ludwig M, Schmidt-Wolf IGH, Holz FG, Loeffler KU, Herwig-Carl MC. PPAR-Responsive Elements Enriched with Alu Repeats May Contribute to Distinctive PPAR?-DNMT1 Interactions in the Genome. Cancers (Basel). 2021 Aug 07; 13(16). PMID: 34439147; PMCID: PMC8391462.
      Citations:    
    35. Koire A, Katsonis P, Kim YW, Buchovecky C, Wilson SJ, Lichtarge O. A method to delineate de novo missense variants across pathways prioritizes genes linked to autism. Sci Transl Med. 2021 05 19; 13(594). PMID: 34011629; PMCID: PMC8916821.
      Citations: 6     Fields:    Translation:Humans
    36. Cea-Rama I, Katsonis P, Bargiela R, Golyshin PN, Lichtarge O, Ferrer M, Sanz-Aparicio J, Coscol?n C. Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase. Comput Struct Biotechnol J. 2021; 19:2307-2317. PMID: 33995922; PMCID: PMC8105184.
      Citations: 3     
    37. Marbach F, Stoyanov G, Erger F, Stratakis CA, Settas N, London E, Rosenfeld JA, Torti E, Haldeman-Englert C, Sklirou E, Kessler E, Ceulemans S, Nelson SF, Martinez-Agosto JA, Palmer CGS, Signer RH, Undiagnosed Diseases Network, Andrews MV, Grange DK, Willaert R, Person R, Telegrafi A, Sievers A, Laugsch M, Cheng Y, Lichtarge O, Katsonis P, Stocco A, Schaaf CP, Thei? S. Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain. Genet Med. 2021 08; 23(8):1465-1473. PMID: 33833410; PMCID: PMC8354857.
      Citations: 1     Fields:    Translation:Humans
    38. Kanagal-Shamanna R, Montalban-Bravo G, Katsonis P, Sasaki K, Class CA, Jabbour E, Sallman D, Hunter AM, Benton C, Chien KS, Luthra R, Bueso-Ramos CE, Kadia T, Andreeff M, Komrokji RS, Al Ali NH, Short N, Daver N, Routbort MJ, Khoury JD, Patel K, Ganan-Gomez I, Wei Y, Borthakur G, Ravandi F, Do KA, Soltysiak KA, Lichtarge O, Medeiros LJ, Kantarjian H, Garcia-Manero G. Evolutionary action score identifies a subset of TP53 mutated myelodysplastic syndrome with favorable prognosis. Blood Cancer J. 2021 03 06; 11(3):52. PMID: 33677472; PMCID: PMC7936977.
      Citations: 2     Fields:    Translation:Humans
    39. Brosey CA, Houl JH, Katsonis P, Balapiti-Modarage LPF, Bommagani S, Arvai A, Moiani D, Bacolla A, Link T, Warden LS, Lichtarge O, Jones DE, Ahmed Z, Tainer JA. Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors. Prog Biophys Mol Biol. 2021 08; 163:171-186. PMID: 33636189; PMCID: PMC7901392.
      Citations: 16     Fields:    Translation:HumansCells
    40. Wang C, Konecki DM, Marciano DC, Govindarajan H, Williams AM, Wastuwidyaningtyas B, Bourquard T, Katsonis P, Lichtarge O. Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and the greater coronavirus family. Res Sq. 2021 Feb 15. PMID: 33106800; PMCID: PMC7587783.
      Citations:    
    41. Kim YW, Al-Ramahi I, Koire A, Wilson SJ, Konecki DM, Mota S, Soleimani S, Botas J, Lichtarge O. Harnessing the paradoxical phenotypes of APOE ?2 and APOE ?4 to identify genetic modifiers in Alzheimer's disease. Alzheimers Dement. 2021 05; 17(5):831-846. PMID: 33576571; PMCID: PMC8247413.
      Citations: 7     Fields:    Translation:HumansAnimals
    42. Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. Prog Biophys Mol Biol. 2021 08; 163:87-108. PMID: 33035590; PMCID: PMC8021618.
      Citations: 18     Fields:    Translation:HumansCells
    43. Pham M, Wilson S, Govindarajan H, Lin CH, Lichtarge O. Discovery of disease- and drug-specific pathways through community structures of a literature network. Bioinformatics. 2020 06 01; 36(11):3623. PMID: 32259836; PMCID: PMC7267819.
      Citations:    Fields:    
    44. Gallion J, Pelletier D, Cawkill D, Nagi K, Gosink M, Jenkinson S, Ren Y, Somps C, Lichtarge O, Schmidt A, Benredjem B, Dallaire P, Charbonneau J, Lukasheva V, Murat B, Van Der Westhuizen E, Le Gouill C, Bouvier M, Pineyro G. Author Correction: Exploring use of unsupervised clustering to associate signaling profiles of GPCR ligands to clinical response. Nat Commun. 2020 Apr 16; 11(1):1929. PMID: 32300106; PMCID: PMC7162847.
      Citations:    Fields:    
    45. Novikov IB, Wilkins AD, Lichtarge O. An Evolutionary Trace method defines functionally important bases and sites common to RNA families. PLoS Comput Biol. 2020 03; 16(3):e1007583. PMID: 32208421; PMCID: PMC7092961.
      Citations:    Fields:    Translation:HumansAnimalsCells
    46. Pham M, Wilson S, Govindarajan H, Lin CH, Lichtarge O. Discovery of disease- and drug-specific pathways through community structures of a literature network. Bioinformatics. 2020 03 01; 36(6):1881-1888. PMID: 31738408; PMCID: PMC7103064.
      Citations: 1     Fields:    
    47. Pham M, Lichtarge O. Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks. Pac Symp Biocomput. 2020; 25:439-450. PMID: 31797617; PMCID: PMC7043368.
      Citations: 2     Fields:    Translation:Humans
    48. Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkiran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Gemovic B, Perovic VR, Davidovic RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijevic V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I, Fern?ndez JM, Renaux A, T?r?nen P, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Bj?rne J, ?muc T. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019 11 19; 20(1):244. PMID: 31744546; PMCID: PMC6864930.
      Citations: 83     Fields:    Translation:HumansAnimalsCells
    49. Wright SJ, Agosto MA, Lichtarge O, Wensel TG, Terr?n-D?az ME. Residues and residue pairs of evolutionary importance differentially direct signaling bias of D2 dopamine receptors. J Biol Chem. 2019 12 13; 294(50):19279-19291. PMID: 31676688; PMCID: PMC6916503.
      Citations:    Fields:    Translation:HumansCells
    50. Sharma A, Biswas A, Liu H, Sen S, Paruchuri A, Katsonis P, Lichtarge O, Chand Dakal T, Maulik U, Gromiha MM, Bandyopadhyay S, Ludwig M, Holz FG, Loeffler KU, Herwig-Carl MC. Mutational Landscape of the BAP1 Locus Reveals an Intrinsic Control to Regulate the miRNA Network and the Binding of Protein Complexes in Uveal Melanoma. Cancers (Basel). 2019 Oct 19; 11(10). PMID: 31635116; PMCID: PMC6826957.
      Citations: 15     
    51. Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep. 2019 Sep 10; 28(11):3010. PMID: 31509758.
      Citations: 24     Fields:    
    52. Gallion J, Pelletier D, Cawkill D, Nagi K, Gosink M, Jenkinson S, Ren Y, Somps C, Lichtarge O, Schmidt A, Benredjem B, Dallaire P, Charbonneau J, Lukasheva V, Murat B, Van Der Westhuizen E, Le Gouill C, Bouvier M, Pineyro G. Exploring use of unsupervised clustering to associate signaling profiles of GPCR ligands to clinical response. Nat Commun. 2019 09 09; 10(1):4075. PMID: 31501422; PMCID: PMC6733853.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    53. Kasak L, Hunter JM, Udani R, Bakolitsa C, Hu Z, Adhikari AN, Babbi G, Casadio R, Gough J, Guerrero RF, Jiang Y, Joseph T, Katsonis P, Kotte S, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Moult J, Pal LR, Poitras J, Radivojac P, Rao A, Sivadasan N, Sunderam U, Saipradeep VG, Yin Y, Zaucha J, Brenner SE, Meyn MS. CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases. Hum Mutat. 2019 09; 40(9):1373-1391. PMID: 31322791; PMCID: PMC7318886.
      Citations: 5     Fields:    Translation:Humans
    54. Zhang J, Kinch LN, Cong Q, Katsonis P, Lichtarge O, Savojardo C, Babbi G, Martelli PL, Capriotti E, Casadio R, Garg A, Pal D, Weile J, Sun S, Verby M, Roth FP, Grishin NV. Assessing predictions on fitness effects of missense variants in calmodulin. Hum Mutat. 2019 09; 40(9):1463-1473. PMID: 31283071; PMCID: PMC6744288.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    55. Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Radivojac P, Rousseau F, Pal LR, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Repo S, Moult J, Brenner SE, Friedberg I, V?liaho J. Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Hum Mutat. 2019 09; 40(9):1530-1545. PMID: 31301157; PMCID: PMC7325732.
      Citations: 4     Fields:    Translation:Humans
    56. Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Nodzak C, Pal LR, Radivojac P, Savojardo C, Shi X, Zhou Y, Uppal A, Xu Q, Yin Y, Pejaver V, Wang M, Wei L, Moult J, Yu GK, Brenner SE, LeBowitz JH. Assessment of predicted enzymatic activity of a-N-acetylglucosaminidase variants of unknown significance for CAGI 2016. Hum Mutat. 2019 09; 40(9):1519-1529. PMID: 31342580; PMCID: PMC7156275.
      Citations: 4     Fields:    Translation:Humans
    57. Cline MS, Babbi G, Bonache S, Cao Y, Casadio R, Katsonis P, Lai C, Lichtarge O, Martelli PL, Mishne G, Mooney SD, O'Conner R, Pagel KA, Pejaver V, Radivojac P, Savojardo C, Shen Y, Sun Y, Topper S, Parsons MT, Spurdle AB, Goldgar DE, ENIGMA Consortium, de la Cruz X, D?ez O, Guti?rrez-Enr?quez S, Moles-Fern?ndez A, Montalban G, Ootes L, ?zkan S, Padilla N, Riera C. Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants. Hum Mutat. 2019 09; 40(9):1546-1556. PMID: 31294896; PMCID: PMC6744348.
      Citations: 9     Fields:    Translation:Humans
    58. Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner SE, Kann MG. Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Hum Mutat. 2019 09; 40(9):1612-1622. PMID: 31241222; PMCID: PMC6744287.
      Citations: 4     Fields:    Translation:Humans
    59. Monzon AM, Carraro M, Chiricosta L, Reggiani F, Han J, Ozturk K, Wang Y, Miller M, Bromberg Y, Capriotti E, Savojardo C, Babbi G, Martelli PL, Casadio R, Katsonis P, Lichtarge O, Carter H, Kousi M, Katsanis N, Andreoletti G, Moult J, Brenner SE, Ferrari C, Leonardi E, Tosatto SCE. Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5. Hum Mutat. 2019 09; 40(9):1474-1485. PMID: 31260570; PMCID: PMC7354699.
      Citations: 5     Fields:    Translation:Humans
    60. Katsonis P, Lichtarge O. CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation. Hum Mutat. 2019 09; 40(9):1436-1454. PMID: 31317604; PMCID: PMC6900054.
      Citations: 15     Fields:    Translation:Humans
    61. Donehower LA, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA, Soussi T. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep. 2019 07 30; 28(5):1370-1384.e5. PMID: 31365877; PMCID: PMC7546539.
      Citations: 123     Fields:    Translation:Humans
    62. Savojardo C, Petrosino M, Babbi G, Bovo S, Corbi-Verge C, Casadio R, Fariselli P, Folkman L, Garg A, Karimi M, Katsonis P, Kim PM, Lichtarge O, Martelli PL, Pasquo A, Pal D, Shen Y, Strokach AV, Turina P, Zhou Y, Andreoletti G, Brenner SE, Chiaraluce R, Consalvi V, Capriotti E. Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge. Hum Mutat. 2019 09; 40(9):1392-1399. PMID: 31209948; PMCID: PMC6744327.
      Citations: 8     Fields:    Translation:HumansCells
    63. Carraro M, Monzon AM, Chiricosta L, Reggiani F, Aspromonte MC, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, Pal LR, Yin Y, Limongelli I, Andreoletti G, Moult J, Wilson SJ, Katsonis P, Lichtarge O, Chen J, Wang Y, Hu Z, Brenner SE, Ferrari C, Murgia A, Tosatto SCE, Leonardi E. Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Hum Mutat. 2019 09; 40(9):1330-1345. PMID: 31144778; PMCID: PMC7341177.
      Citations: 3     Fields:    Translation:Humans
    64. Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, Pal LR, Savojardo C, Yin Y, Zhou Y, Radivojac P, Bromberg Y. Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Hum Mutat. 2019 09; 40(9):1495-1506. PMID: 31184403; PMCID: PMC6744362.
      Citations: 8     Fields:    Translation:Humans
    65. McInnes G, Daneshjou R, Katsonis P, Lichtarge O, Srinivasan R, Rana S, Radivojac P, Mooney SD, Pagel KA, Stamboulian M, Jiang Y, Capriotti E, Wang Y, Bromberg Y, Bovo S, Savojardo C, Martelli PL, Casadio R, Pal LR, Moult J, Brenner SE, Altman R. Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum Mutat. 2019 09; 40(9):1314-1320. PMID: 31140652; PMCID: PMC7047641.
      Citations: 4     Fields:    Translation:Humans
    66. 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. 2019 05 01; 35(9):1536-1543. PMID: 30304494; PMCID: PMC6499233.
      Citations: 5     Fields:    Translation:HumansCells
    67. 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 05; 269(5):917-923. PMID: 28767562; PMCID: PMC7462436.
      Citations: 52     Fields:    Translation:Humans
    68. 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; PMCID: PMC6196525.
      Citations: 13     Fields:    Translation:HumansCells
    69. 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; PMCID: PMC6372985.
      Citations: 17     
    70. Karamitri A, Chen M, Gallion J, Guillaume JL, Hegron A, Langenberg C, Wareham NJ, Lichtarge O, Jockers R, Plouffe B, Bonnefond A, Boissel M, Canouil M, Le Gouill C, Lukasheva V, Froguel P, Bouvier M. Type 2 diabetes-associated variants of the MT2 melatonin receptor affect distinct modes of signaling. Sci Signal. 2018 08 28; 11(545). PMID: 30154102.
      Citations: 17     Fields:    Translation:HumansCells
    71. 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.
      Citations: 8     Fields:    Translation:HumansCells
    72. 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 Jun 08; 9(1):2231. PMID: 29884781; PMCID: PMC5993718.
      Citations: 2     Fields:    Translation:Cells
    73. 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, Cancer Genome Atlas Research Network, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L, Reimand J. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 04 05; 173(2):355-370.e14. PMID: 29625052; PMCID: PMC5949147.
      Citations: 239     Fields:    Translation:HumansCells
    74. 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 07 01; 315(1):H109-H121. PMID: 29600899; PMCID: PMC6087776.
      Citations: 6     Fields:    Translation:HumansCells
    75. 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 05; 24(4):505-511. PMID: 29578538; PMCID: PMC6675908.
      Citations: 21     Fields:    Translation:HumansAnimalsCells
    76. 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; PMCID: PMC5832058.
      Citations: 48     Fields:    Translation:HumansAnimalsCells
    77. Lisewski AM, Quiros JP, Mittal M, Putluri N, Sreekumar A, Lichtarge O, Haeggstr?m JZ. 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; PMCID: PMC5963095.
      Citations: 4     Fields:    Translation:HumansAnimals
    78. Gallion J, Wilkins AD, Kimmel M, Lichtarge O, Sch?negge AM, Picard LP, Le Gouill C, Audet M, Stallaert W, Lohse MJ, Bouvier M. Evolutionary action and structural basis of the allosteric switch controlling ?2AR functional selectivity. Nat Commun. 2017 12 18; 8(1):2169. PMID: 29255305; PMCID: PMC5735088.
      Citations: 26     Fields:    Translation:HumansCells
    79. 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; PMCID: PMC5987759.
      Citations: 8     Fields:    Translation:Humans
    80. 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; PMCID: PMC5600169.
      Citations: 16     Fields:    Translation:Humans
    81. Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, 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, Fariselli P. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Hum Mutat. 2017 09; 38(9):1042-1050. PMID: 28440912; PMCID: PMC5561474.
      Citations: 6     Fields:    Translation:HumansCells
    82. Xu Q, Tang Q, Katsonis P, Lichtarge O, Jones D, Lee GR, Seok C, Fenton AW, Dunbrack RL, Bovo S, Babbi G, Martelli PL, Casadio R. Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4. Hum Mutat. 2017 09; 38(9):1123-1131. PMID: 28370845; PMCID: PMC5561472.
      Citations: 6     Fields:    Translation:HumansCells
    83. Galaz-Montoya M, Wright SJ, Rodriguez GJ, Lichtarge O, Wensel TG. ?2-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; PMCID: PMC5473248.
      Citations: 12     Fields:    Translation:HumansCells
    84. 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; PMCID: PMC5370158.
      Citations:    Fields:    Translation:HumansCells
    85. Gallion J, Koire A, Katsonis P, Lichtarge O, Schoenegge AM, Bouvier M. Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling. Hum Mutat. 2017 05; 38(5):569-580. PMID: 28230923; PMCID: PMC5516182.
      Citations: 16     Fields:    Translation:HumansCells
    86. 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; PMCID: PMC5140035.
      Citations: 4     Fields:    Translation:Humans
    87. Wilkins AD, Lichtarge O, Gallion J. HUMAN KINASES DISPLAY MUTATIONAL HOTSPOTS AT COGNATE POSITIONS WITHIN CANCER. Pac Symp Biocomput. 2017; 22:414-425. PMID: 27896994; PMCID: PMC5157159.
      Citations: 1     Fields:    Translation:HumansCells
    88. 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; PMCID: PMC5201093.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    89. 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; PMCID: PMC8570672.
      Citations: 17     Fields:    Translation:HumansAnimals
    90. 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; PMCID: PMC5152588.
      Citations: 2     Fields:    Translation:Cells
    91. 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; PMCID: PMC4822589.
      Citations: 21     Fields:    Translation:HumansCells
    92. 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; PMCID: PMC4722962.
      Citations: 2     Fields:    Translation:Humans
    93. Katsonis P, Lichtarge O, Koire A. 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; PMCID: PMC4720392.
      Citations: 13     Fields:    Translation:Humans
    94. 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; PMCID: PMC4702906.
      Citations: 9     Fields:    Translation:Cells
    95. 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; PMCID: PMC4656807.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    96. Peterson SM, Pack TF, Wilkins AD, Urs NM, Urban DJ, Bass CE, Lichtarge O, Caron MG. Elucidation of G-protein and ?-arrestin functional selectivity at the dopamine D2 receptor. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):7097-102. PMID: 25964346; PMCID: PMC4460444.
      Citations: 39     Fields:    Translation:HumansAnimalsCells
    97. 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; PMCID: PMC4615655.
      Citations: 41     Fields:    Translation:HumansAnimalsCells
    98. 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; PMCID: PMC4383697.
      Citations: 80     Fields:    Translation:HumansCells
    99. 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; PMCID: PMC4317032.
      Citations: 11     Fields:    Translation:HumansCells
    100. 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; PMCID: PMC4557970.
      Citations: 58     Fields:    Translation:HumansAnimalsCells
    101. 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; PMCID: PMC4253807.
      Citations: 37     Fields:    Translation:Humans
    102. 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; PMCID: PMC4248321.
      Citations: 74     Fields:    Translation:Humans
    103. 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; PMCID: PMC4208005.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    104. Lisewski AM, Quiros JP, Ng CL, Adikesavan AK, Putluri N, Scanfeld D, Regenbogen SJ, Sreekumar A, Fidock DA, Lichtarge O, Miura K, Eastman RT, Altenhofen L, Llin?s M, Long C. 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; PMCID: PMC4167585.
      Citations: 53     Fields:    Translation:AnimalsCells
    105. 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; PMCID: PMC4103627.
      Citations: 11     Fields:    
    106. 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; PMCID: PMC4246023.
      Citations: 10     Fields:    Translation:Humans
    107. 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; PMCID: PMC3900401.
      Citations: 18     Fields:    Translation:AnimalsCells
    108. 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; PMCID: PMC3911504.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    109. Zheng L, Lua RC, Lichtarge O, Golding I, Sokac AM, Sep?lveda LA. The maternal-to-zygotic transition targets actin to promote robustness during morphogenesis. PLoS Genet. 2013 Nov; 9(11):e1003901. PMID: 24244181; PMCID: PMC3820746.
      Citations: 8     Fields:    Translation:AnimalsCells
    110. 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; PMCID: PMC3831482.
      Citations: 16     Fields:    
    111. 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; PMCID: PMC3799481.
      Citations: 18     Fields:    Translation:Cells
    112. 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; PMCID: PMC3808176.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    113. 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; PMCID: PMC3641682.
      Citations: 102     Fields:    Translation:AnimalsCells
    114. 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; PMCID: PMC3584919.
      Citations: 5     Fields:    Translation:Cells
    115. 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; PMCID: PMC3788641.
      Citations: 356     Fields:    Translation:HumansAnimalsCells
    116. 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, 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, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Supek F, Panov P, 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, T?r?nen P, Ka?ner R, H?nigschmid P, Bj?rne J, ?kunca N, Bo?njak M, D?eroski S, ?muc T. A large-scale evaluation of computational protein function prediction. Nat Methods. 2013 Mar; 10(3):221-7. PMID: 23353650; PMCID: PMC3584181.
      Citations: 350     Fields:    Translation:HumansAnimals
    117. 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; PMCID: PMC3782309.
      Citations: 100     Fields:    Translation:Cells
    118. 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; PMCID: PMC3413384.
      Citations: 5     Fields:    
    119. 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; PMCID: PMC3439137.
      Citations: 19     Fields:    
    120. 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; PMCID: PMC4892863.
      Citations: 36     Fields:    Translation:Cells
    121. 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; PMCID: PMC3164682.
      Citations: 40     Fields:    Translation:Cells
    122. 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; PMCID: PMC4995031.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    123. Shchelochkov OA, Wang J, Katsonis P, Hall L, Reiss S, Eeds A, Willis A, Yadav M, Summar S, Urea Cycle Disorders Consortium, Lichtarge O, Rubio V, Wong LJ, Summar M, H?berle J. 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; PMCID: PMC4861085.
      Citations: 25     Fields:    Translation:HumansCells
    124. 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; PMCID: PMC3120633.
      Citations: 20     Fields:    
    125. 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; PMCID: PMC3001439.
      Citations: 13     Fields:    Translation:Cells
    126. 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; PMCID: PMC2982157.
      Citations: 22     Fields:    Translation:Cells
    127. 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; PMCID: PMC2899695.
      Citations: 2     
    128. 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; PMCID: PMC2974822.
      Citations: 14     Fields:    Translation:Cells
    129. 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; PMCID: PMC2916956.
      Citations: 19     Fields:    Translation:HumansCells
    130. 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; PMCID: PMC2867884.
      Citations: 59     Fields:    Translation:HumansCells
    131. Bonde MM, Yao R, Ma JN, Madabushi S, Burstein ES, Whistler JL, Lichtarge O, Hansen JL, Hauns? S, Sheikh SP. 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; PMCID: PMC2864232.
      Citations: 6     Fields:    Translation:AnimalsCells
    132. 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; PMCID: PMC2831211.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    133. 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; PMCID: PMC2835418.
      Citations: 35     Fields:    Translation:HumansCells
    134. 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; PMCID: PMC2747647.
      Citations: 34     Fields:    Translation:Humans
    135. Ogawa K, Yao R, Lichtarge O, Bouvier M, Kobayashi H. Functional rescue of beta-adrenoceptor dimerization and trafficking by pharmacological chaperones. Traffic. 2009 Aug; 10(8):1019-33. PMID: 19515093; PMCID: PMC2755524.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    136. 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; PMCID: PMC2682511.
      Citations: 18     Fields:    Translation:Cells
    137. 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; PMCID: PMC2673147.
      Citations: 5     Fields:    Translation:Cells
    138. 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; PMCID: PMC2362850.
      Citations: 20     Fields:    
    139. 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; PMCID: PMC2219985.
      Citations: 41     Fields:    Translation:Cells
    140. Mihalek I, Res I, Lichtarge O. Background frequencies for residue variability estimates: BLOSUM revisited. BMC Bioinformatics. 2007 Dec 27; 8:488. PMID: 18162129; PMCID: PMC2267808.
      Citations: 4     Fields:    Translation:Cells
    141. 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.
      Citations: 22     Fields:    Translation:Cells
    142. 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.
      Citations: 14     Fields:    Translation:Cells
    143. 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.
      Citations: 6     Fields:    Translation:Cells
    144. 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.
      Citations: 4     Fields:    Translation:Cells
    145. 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.
      Citations: 65     Fields:    Translation:HumansAnimalsCells
    146. 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.
      Citations: 2     Fields:    Translation:Cells
    147. 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; PMCID: PMC2675645.
      Citations: 33     Fields:    Translation:HumansAnimalsCells
    148. 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; PMCID: PMC1702494.
      Citations: 18     Fields:    Translation:Cells
    149. 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.
      Citations: 12     Fields:    Translation:Cells
    150. 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.
      Citations: 10     Fields:    Translation:HumansCells
    151. 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.
      Citations: 43     Fields:    Translation:Cells
    152. 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; PMCID: PMC2242527.
      Citations: 17     Fields:    
    153. 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.
      Citations: 39     Fields:    Translation:HumansAnimals
    154. 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.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    155. 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.
      Citations: 4     Fields:    Translation:AnimalsCells
    156. 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.
      Citations: 8     Fields:    Translation:Cells
    157. 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.
      Citations: 11     Fields:    Translation:Cells
    158. 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.
      Citations: 344     Fields:    Translation:HumansAnimalsCells
    159. 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.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    160. 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.
      Citations: 12     Fields:    Translation:Cells
    161. Res I, Lichtarge O. Character and evolution of protein-protein interfaces. Phys Biol. 2005 Jun; 2(2):S36-43. PMID: 16204847.
      Citations: 10     Fields:    Translation:Cells
    162. 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.
      Citations: 40     Fields:    Translation:Cells
    163. 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.
      Citations: 12     Fields:    Translation:Cells
    164. 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.
      Citations: 11     Fields:    Translation:HumansCells
    165. 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.
      Citations: 27     Fields:    Translation:AnimalsCells
    166. 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.
      Citations: 162     Fields:    Translation:HumansAnimalsCells
    167. 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.
      Citations: 76     Fields:    Translation:AnimalsCells
    168. 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.
      Citations: 22     Fields:    Translation:Cells
    169. 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.
      Citations: 71     Fields:    Translation:Cells
    170. 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.
      Citations: 6     Fields:    Translation:AnimalsCells
    171. 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.
      Citations: 17     Fields:    Translation:Cells
    172. 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.
      Citations: 5     Fields:    Translation:AnimalsCells
    173. 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.
      Citations: 84     Fields:    Translation:Cells
    174. Lichtarge O, Sowa ME. Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol. 2002 Feb; 12(1):21-7. PMID: 11839485.
      Citations: 87     Fields:    Translation:HumansCells
    175. Lichtarge O, Sowa ME, Philippi A. Evolutionary traces of functional surfaces along G protein signaling pathway. Methods Enzymol. 2002; 344:536-56. PMID: 11771409.
      Citations: 11     Fields:    Translation:AnimalsCells
    176. 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; PMCID: PMC1363676.
      Citations: 63     Translation:HumansAnimalsCells
    177. Lichtarge O. Getting past appearances: the many-fold consequences of remote homology. Nat Struct Biol. 2001 Nov; 8(11):918-20. PMID: 11685232.
      Citations: 5     Fields:    Translation:Cells
    178. 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.
      Citations: 44     Fields:    Translation:Cells
    179. 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.
      Citations: 11     Fields:    Translation:HumansCells
    180. 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.
      Citations: 80     Fields:    Translation:HumansCells
    181. 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.
      Citations: 47     Fields:    Translation:AnimalsCells
    182. 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; PMCID: PMC26460.
      Citations: 28     Fields:    Translation:HumansAnimalsCells
    183. 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.
      Citations: 44     Fields:    Translation:HumansAnimalsCells
    184. 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.
      Citations: 29     Fields:    Translation:HumansAnimalsCells
    185. 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.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    186. 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.
      Citations: 36     Fields:    Translation:Cells
    187. 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.
      Citations: 65     Fields:    Translation:AnimalsCells
    188. 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.
      Citations: 11     Fields:    Translation:Cells
    189. 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.
      Citations: 92     Fields:    Translation:AnimalsCells
    190. 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; PMCID: PMC38775.
      Citations: 47     Fields:    Translation:Cells
    191. 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.
      Citations: 475     Fields:    Translation:HumansAnimalsCells
    192. 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.
      Citations: 1     Fields:    Translation:Cells
    193. 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.
      Citations: 4     Fields:    Translation:HumansCells
    194. 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.
      Citations:    Fields:    Translation:Cells
    195. 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.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
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