Publications

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, Dunø 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; Küry S, Lecoquierre F, Lockhart P, Maraval J, Matsumoto N, McCarrier J, McCarthy J, Miyake N, Moey LH, Németh AH, Østergaard 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 Feb; PMID: 38325380 DOI: 10.1016/j.ajhg.2024.01.007

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; PMID: 38170232 DOI: 10.1007/s00439-023-02624-3

Gao W, Liu L, Huh E, Gbahou F, Cecon E, Oshima M, Houzé 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 Sep; PMID: 37709961 DOI: 10.1038/s42255-023-00889-6

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 Sep; 12(17): PMID: 37642027 DOI: 10.1161/JAHA.122.029103

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; PMID: 37577678 DOI: 10.1101/2023.08.02.23293212

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, Sriniva 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; PMID: 37577579 DOI: 10.21203/rs.3.rs-3209168/v1

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 Aug; 39(8): PMID: 10.1093/bioinfor DOI: 10.1093/bioinformatics/btad467

Konecki DM, Hamrick S, Wang C, Agosto MA, Wensel TG, Lichtarge O..
CovET: A covariation-evolutionary trace method that identifies protein structure-function modules..
Res Sq. 2023 Jul; 299(7): PMID: 37290531 DOI: 10.1016/j.jbc.2023.104896

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 Jun; PMID: 37012319 DOI: 10.1038/s41416-023-02253-7

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 May; PMID: 37179358 DOI: 10.1038/s41467-023-38374-z

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 Apr; PMID: 36806686 DOI: 10.1016/j.jbc.2023.103030

Katsonis P, Wilhelm K, Williams A, Lichtarge O.
Genome interpretation using in silico predictors of variant impact.
Human Genetics. 2022 Oct; 1549-1577. PMID: 35488922 DOI: 10.1007/s00439-022-02457-6

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 Genomics. 2022 Sep; 2(9): PMID: 36268052 DOI: 10.1016/j.xgen.2022.100162

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 Jul; PMID: 35412634 DOI: 10.1093/nar/gkac215

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.
Nature Communications. 2022 Jun; PMID: 35680894 DOI: 10.1038/s41467-022-30889-1

Herman C, Bradley C, Gordon A, Wang C, Cooke M, Kohrn B, Kennedy S, Lichtarge O, Ronca S.
RNA polymerase inaccuracy underlies SARS-CoV-2 variants and vaccine heterogeneity.
Researchsquare. 2022 Jun; PMID: 35677076 DOI: 10.21203/rs.3.rs-1690086/v1

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 May; PMID: 36420184 DOI: 10.1016/j.adro.2022.100989

Hsu TK, Asmussen JK, Koire AM, Choi BK, Gadhikar MA, Huh E, Lin CH, Konecki DM, Kim YW, Pickering C, 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 Research. 2022 Mar; PMID: 35301263 DOI: 10.1101/gr.275811.121

Plouffe B, Karamitri A, Flock T, Gallion JM, Houston S, Daly CA, Bonnefond A, Guillaume JL, Le Gouill C, Froguel P, Lichtarge O, Deupi X, Jockers R, Bouvier M.
Structural Elements Directing G Proteins and β-Arrestin Interactions with the Human Melatonin Type 2 Receptor Revealed by Natural Variants.
ACS Pharmacol Transl Sci. 2022 Jan; PMID: 35846981 DOI: 10.1021/acsptsci.1c00239

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 Dec; PMID: 34916293 DOI: 10.1073/pnas.2113373118

Tsutakawa SE, Bacolla A, Katsonis P, Bralić 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.
Frontiers in Molecular Biosciences. 2021 Dec; PMID: 34966786 DOI: 10.3389/fmolb.2021.791792

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 Sep; 407-431. PMID: 34776222 DOI: 10.1016/bs.mie.2021.09.003

Hegron A, Huh E, Deupi X, Sokrat B, Gao W, Le Gouill C, Canouil M, Boissel M, Charpentier G, Roussel R, Balkau B, Froguel P, Plouffe B, Bonnefond A, Lichtarge O, 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 Sep; PMID: 34661078 DOI: 10.1021/acsptsci.1c00157

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 PPARγ-DNMT1 Interactions in the Genome.
Cancers (Basel). 2021 Aug; PMID: 34439147 DOI: 10.3390/cancers13163993

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.
Progress in Biophysics and Molecular Biology. 2021 Aug; 163:171-186. PMID: 33636189 DOI: 10.1016/j.pbiomolbio.2021.02.002

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, Theiß S, Cheng Y, Lichtarge O, Katsonis P, Stocco A, Schaaf CP.
Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain.
Genet Med. 2021 Aug; 1465-1473. PMID: 33833410 DOI: 10.1038/s41436-021-01152-7

Lin CH, Lichtarge O..
Using Interpretable Deep Learning to Model Cancer Dependencies.
Bioinformatics. 2021 May; 2675-2681. PMID: 34042953 DOI: 10.1093/bioinformatics/btab137

Chen Wang, Daniel M Konecki, David C Marciano, Harikumar Govindarajan, Amanda M Williams, Brigitta Wastuwidyaningtyas, Thomas Bourquard, Panagiotis Katsonis, Olivier Lichtarge.
Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family.
Bioinformatics. 2021 May; 4033-4040. PMID: 34043002 DOI: 10.1093/bioinformatics/btab406

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.
Science Translational Medicine. 2021 May; 13(594): PMID: 34011629 DOI: 10.1126/scitranslmed.abc1739

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 ɛ2 and APOE ɛ4 to identify genetic modifiers in Alzheimer's disease..
Alzheimers Dement. 2021 May; PMID: 33576571 DOI: 10.1002/alz.12240

Cea-Rama I, Coscolín C, Katsonis P, Bargiela R, Golyshin PN, Lichtarge O, Ferrer M, Sanz-Aparicio J..
Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase.
Computational and Structural Biotechnology Journal. 2021 Apr; PMID: 33995922 DOI: 10.1016/j.csbj.2021.04.041

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, Theiß S, Cheng Y, Lichtarge O, Katsonis P, Stocco A, Schaaf CP..
Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain.
Genetics in Medicine. 2021 Apr; PMID: 33833410 DOI: 10.1038/s41436-021-01152-7

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 journal. 2021 Mar; PMID: 33677472 DOI: 10.1038/s41408-021-00446-y

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.
Progress in Biophysics and Molecular Biology. 2021 Feb; 2307-2317. PMID: 33636189 DOI: 10.1016/j.pbiomolbio.2021.02.002

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.
Progress in Biophysics and Molecular Biology. 2020 Oct; PMID: 33035590 DOI: 10.1016/j.pbiomolbio.2020.09.010

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 Jun; 36(11):3623. PMID: 31738408 DOI: 10.1093/bioinformatics/btaa114

Pham M, Lichtarge O.
Exploring use of unsupervised clustering to associate signaling profiles of GPCR ligands to clinical response.
Pacific Symposium on Biocomputing. 2020 Jun; 25:439-450. PMID: 31797617 DOI: 10.1142/9789811215636_0039

Benredjem B, Gallion J, Pelletier D, Dallaire P, Charbonneau J, Cawkill D, Nagi K, Gosink M, Lukasheva V, Jenkinson S, Ren Y, Somps C, Murat B, Van Der Westhuizen E, Le Gouill C,Lichtarge O, Schmidt A, Bouvier M, Pineyro G..
Author Correction: Exploring use of unsupervised clustering to associate signaling profiles of GPCR ligands to clinical response.
Nature Communications. 2020 Apr; 11(1):1929. PMID: 32300106 DOI: 10.1038/s41467-020-15945-y

Novikov IB, Wilkins AD, Lichtarge O.
An Evolutionary Trace method defines functionally important bases and sites common to RNA families.
PLOS Computational Biology. 2020 Mar; 16(3): PMID: 32208421 DOI: 10.1371/journal.pcbi.1007583

Terrón-Díaz ME, Wright SJ, Agosto MA, Lichtarge O, Wensel TG..
Residues and residue pairs of evolutionary importance differentially direct signaling bias of D2 dopamine receptors..
Journal of Biological chemistry. 2019 Dec; 294(50):19279-19291. PMID: 31676688 DOI: 10.1074/jbc.RA119.008068

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, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović 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, Renaux A, 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, Törönen P, 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, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević 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, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, 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..
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens..
Genome Biology volume. 2019 Nov; 20: PMID: 31744546 DOI: 10.1186/s13059-019-1835-8

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. 2019 Oct; 11(10):1600. PMID: 31635116 DOI: 10.3390/cancers11101600

Besma Benredjem, Jonathan Gallion, Dennis Pelletier, Paul Dallaire, Johanie Charbonneau, Darren Cawkill, Karim Nagi, Mark Gosink, Viktoryia Lukasheva, Stephen Jenkinson, Yong Ren, Christopher Somps, Brigitte Murat, Emma Van Der Westhuizen, Christian Le Gouill, Olivier Lichtarge, Anne Schmidt, Michel Bouvier, Graciela Pineyro.
Exploring use of unsupervised clustering to associate signaling profiles of GPCR ligands to clinical response.
Nature communications. 2019 Sep; 10(1):4075. PMID: 31501422 DOI: 10.1038/s41467-019-11875-6

Donehower LA1,Soussi T2,Korkut A3,Liu Y3,Schultz A3,Cardenas M4,Li X3,Babur O5,Hsu TK6,Lichtarge O7,Weinstein JN3,Akbani R3;Cancer Genome Atlas Network,Wheeler DA4..
Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas..
Cell Reports. 2019 Sep; 28(11): PMID: 31509758 DOI: 10.1016/j.celrep.2019.08.061

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 alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016..
Human mutation. 2019 Sep; 40(9):1519-1529. PMID: 31342580 DOI: 10.1002/humu.23875

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..
Human mutation. 2019 Sep; 40(9):1373-1391. PMID: 31322791 DOI: 10.1002/humu.23874

Katsonis P,Lichtarge O..
CAGI5: Objective performance assessments of predictions based on the Evolutionary Action equation..
Human mutation. 2019 Sep; 40(9):1436-1454. PMID: 31317604 DOI: 10.1002/humu.23873

Cline MS,Babbi G,Bonache S,Cao Y,Casadio R,de la Cruz X,Dez O,Gutirrez-Enrquez S,Katsonis P,Lai C,Lichtarge O,Martelli PL,Mishne G,Moles-Fernndez A,Montalban G,Mooney SD,O'Conner R,Ootes L,zkan S,Padilla N,Pagel KA,Pejaver V,Radivojac P,Riera C,Savojardo C,Shen Y,Sun Y,Topper S,Parsons MT,Spurdle AB,Goldgar DE..
Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants..
Human mutation. 2019 Sep; 40(9):1546-1556. PMID: 31294896 DOI: 10.1002/humu.23861

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..
Human mutation. 2019 Sep; PMID: 31283071 DOI: 10.1002/humu.23857

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..
Human mutation. 2019 Sep; 40(9):1392-1399. PMID: 31209948 DOI: 10.1002/humu.23843

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..
Human mutation. 2019 Sep; 40(9):1495-1506. PMID: 31184403 DOI: 10.1002/humu.23838

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..
Human mutation. 2019 Sep; 40(9):1330-1345. PMID: 31144778 DOI: 10.1002/humu.23823

McInnes G,Daneshjou R,Katsonis P,Lichtarge O,Srinivasan RG,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 S,Altman R..
Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges..
Human mutation. 2019 Sep; 40(9):1314-1320. PMID: 31140652 DOI: 10.1002/humu.23825

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, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I..
Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants..
Human mutation. 2019 Sep; 40(9):1530-1545. PMID: 31301157 DOI: 10.1002/humu.23868

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..
Human mutation. 2019 Sep; 40(9):1612-1622. PMID: 31241222 DOI: 10.1002/humu.23849

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.
Human mutation. 2019 Sep; 40(9):1474-1485. PMID: 31260570 DOI: 10.1002/humu.23856

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..
Human mutation. 2019 Jul; PMID: 31260570 DOI: 10.1002/humu.23856

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 S,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..
Human mutation. 2019 Jun; PMID: 31241222 DOI: 10.1002/humu.23849

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..
Annals of Surgery. 2019 May; 269(5):917-923. PMID: 28767562 DOI: 10.1097/SLA.0000000000002450

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 May; 35(9):1536-1543. PMID: 30304494 DOI: 10.1093/bioinformatics/bty858

Choi BK, Dayaram T, Parikh N, Wilkins A, Nagarajan M, Novikov I, Bachman B, 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.
PNAS. 2018 Oct; 115(42):10666-10671. PMID: 30266789 DOI: 10.1073/pnas.1806643115

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 & core pathways.
Journal of the Endocrine Society. In Publication

Karamitri A, Plouffe B, Bonnefond A, Chen M, Gallion J, Guillaume J-L, Hegron A, Boissel M, Canouil M, Langenberg C, Wareham N, 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.
Science Signaling. 2018 Aug; 11(545): DOI: 10.1126/scisignal.aan6622

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 Jul; PMID: 30177229 DOI: 10.1016/j.ymgme.2018.07.014

Swings T, Marciano D, Atri B, Bosserman R, Wang C, Leysen M, Bonte C, Schalck T, Furey I, Van den Bergh B, Verstraeten N, Christie P, Herman C, Lichtarge O, Michiels J..
CRISPR-FRT targets shared sites in a knock-out collection for off-the-shelf genome editing.
Nature Communications. 2018 Jun; 9(1):2231. PMID: 29884781 DOI: 10.1038/s41467-018-04651-5

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 Apr; PMID: 29324251 DOI: 10.1016/j.ijpddr.2017.12.003

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, 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 Apr; 173(2):355-370. PMID: 29625052 DOI: 10.1016/j.cell.2018.03.039

Suryavanshi SV, Jadhav SM, Anderson KL, Katsonis P, Lichtarge O, McConnell BK.
Human muscle-specific A-kinase anchoring protein (mAKAP) polymorphisms modulate the susceptibility to cardiovascular diseases by altering cAMP/ PKA signaling.
Am J Physiol Heart Circ Physiol.. 2018 Mar; PMID: 29600899 DOI: 10.1152/ajpheart.00034.2018

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 Mar; PMID: 29578538 DOI: 10.1038/nm.4507

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 Jr., Zoghbi HY..
A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures..
Cell. 2018 Feb; 172(5):924-936.e11. PMID: 29474920 DOI: 10.1016/j.cell.2018.02.006

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 Feb; 161-171. PMID: 29175271 DOI: 10.1016/j.bone.2017.11.012

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 β2AR functional selectivity..
Nat Commun.. 2017 Dec; 8(1):2169. PMID: 29255305 DOI: 10.1038/s41467-017-02257-x

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

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

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

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

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

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

Gallion J, Koire A, Katsonis P, Schoenegge A-M, Bouvier M, Lichtarge O.
Predicting phenotype from genotype: improving accuracy through more robust experimental and computational modeling.
Human mutation. 2017 Feb; 569-580. DOI: 10.1002/humu.23193

Bocchini CE, Nahmod K, Katsonis P, Kim S, Kasembeli MM, Freeman A, Lichtarge O, Makedonas G, Tweardy DJ.
Protein stabilization improves STAT3 function in autosomal dominant hyper-IgE syndrome.
Blood. 2016 Dec; 128(26):3061-3072. PMID: 27799162 DOI: 10.1182/blood-2016-02-702373

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

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

Li Z, Gonzalez CL, Wang B, Zhang Y, Mejia O, Katsonis P, Lichtarge O, Myers JN, El-Naggar AK, Caulin C.
Cdkn2a suppresses metastasis in squamous cell carcinomas induced by the gain-of-function mutant p53(R172H)..
J Pathol. 2016 Oct; 240(2):224-34. PMID: 27447534 DOI: 10.1002/path.4770

Marciano DC, Lua RC, Herman C, Lichtarge O.
Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness..
Phys Rev Lett. 2016 Jun; 116(25):258104. PMID: 27391757 DOI: 0.1103/PhysRevLett.116.258104

Peterson SM, Pack TF, Wilkins AD, Urs NM, Urban DJ, Bass CE, Lichtarge O, Caron MG..
Elucidation of G-protein and β-arrestin functional selectivity at the dopamine D2 receptor..
Proc Natl Acad Sci U S A. 2016 May; 112(22):7097-102. PMID: 25964346 DOI: 10.1073/pnas.1502742112

Yun-Min Sung, Angela D. Wilkins, Gustavo J. Rodriguez, Theodore G. Wensel, and Olivier Lichtarge.
Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation..
Proc. Natl. Acad. Sci. 2016 Mar; 113(13):3539-44. PMID: 26979958 DOI: 10.1073/pnas.1516579113i

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

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

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

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

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

Osman AA, Neskey DM, Katsonis P, Patel AA, Ward AM, Hsu TK, Hicks SC, McDonald TO, Ow TJ, Ortega Alves M, Pickering CR, Skinner HD,Zhao M, Sturgis EM, Kies MS, El-Naggar A, Perrone F, Licitra L, Bossi P, Kimmel M, Frederick MJ, Lichtarge O, Myers JN.
Evolutionary Action Score of TP53 Coding Variants (EAp53) is Predictive of Platinum Response in Head and Neck Cancer Patients..
Cancer Res. 2015 Feb; 75(7):1205-15. PMID: 25691460 DOI: 10.1158/0008-5472.CAN-14-2729

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

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

Neskey DM, Osman AA, Ow TJ, Katsonis P, McDonald T, Hicks SC, Hsu TK, Pickering CR, Ward A, Patel A, Yordy JS, Skinner HD, Giri U, Sano D, Story MD, Beadle BM, El-Naggar AK, Kies MS, William WN, Caulin C, Frederick M, Kimmel M, Myers JN, Lichtarge O.
Evolutionary Action score of TP53 (EAp53) identifies high risk mutations associated with decreased survival and increased distant metastases in head and neck cancer..
Cancer Res. 2015 Jan; 75(7):1527-36. PMID: 25634208 DOI: 10.1158/0008-5472.CAN-14-2735

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

Katsonis P*, Koire A*, Wilson SJ*, Hsu TK, Lua RC, Wilkins AD, Lichtarge O.
Single nucleotide variations: Biological impact and theoretical interpretation..
Protein Sci. 2014 Sep; DOI: 10.1002/pro.2552

Katsonis P, Lichtarge O.
A formal perturbation equation between genotype and phenotype determines the evolutionary action of protein coding variations on fitness..
Genome Res. 2014 Sep; 24(12):8. PMID: 25217195 DOI: 10.1101/gr.176214.114

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

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

Marciano DC, Lua RC, Katsonis P, Amin SR, Herman C, Lichtarge O.
Negative Feedback in Genetic Circuits Confers Evolutionary Resilience and Capacitance..
Cell Rep. 2014 Jun; 7(6): PMID: 24910431 DOI: 0.1016/j.celrep.2014.05.018

Lua RC, Marciano DC, Katsonis P, Adikesavan AK, Wilkins AD, Lichtarge O.
Prediction and redesign of protein-protein interactions..
Prog Biophys Mol Biol. 2014 May; 116(2-3):194-202. PMID: 24878423 DOI: 10.1016/j.pbiomolbio.2014.05.004

Young E, Zheng ZY, Wilkins AD, Jeong HT, Li M, Lichtarge O, Chang EC.
Regulation of Ras localization and cell transformation by evolutionarily conserved palmitoyltransferases..
Mol Cell Biol. 2014 Feb; 34(3):374-85. PMID: 24248599 DOI: 10.1128/MCB.01248-13

Homan EP, Lietman C, Grafe I, Lennington J, Morello R, Napierala D, Jiang MM, Munivez EM, Dawson B, Bertin TK, Chen Y, Lua R, Lichtarge O, Hicks J, Weis MA, Eyre D, Lee BH.
Differential effects of collagen prolyl 3-hydroxylation on skeletal tissues..
PLoS Genet. 2014 Jan; 10(1):e1004121. PMID: 24465224 DOI: 10.1371/journal.pgen.1004121

Zheng L, Sepulveda L, Lua R, Lichtarge O, Golding I, Sokac A.
The Maternal-to-Zygotic Transition Targets Actin to Promote Robustness during Morphogenesis.
PLOS Genetics. 2013 Nov; 9(11): DOI: 10.1371/journal.pgen.1003901

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

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

Wilkins AD, Venner E, Marciano DC, Erdin S, Atri B, Lua RC, Lichtarge O.
Accounting for epistatic interactions improves the functional analysis of protein structures..
Bioinformatics. 2013 Sep; 29(21):2714-21. PMID: 24021383 DOI: 10.1093/bioinformatics/btt489

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

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

Baker SA, Chen L, Wilkins AD, Yu P, Lichtarge O, Zoghbi HY.
An AT-Hook Domain in MeCP2 Determines the Clinical Course of Rett Syndrome and Related Disorders..
Cell. 2013 Feb; 152(5):984-96. PMID: 23452848 DOI: 0.1016/j.cell.2013.01.038

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

Mamun AAMA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM.
Identity and Function of a Large Gene Network Underlying Mutagenic Repair of DNA Breaks..
Science. 2012 Dec; 338(6112):1344-1348. DOI: 10.1126/science.1226683

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

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

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

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

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

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

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

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

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

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

Bonde MM, Yao R, Ma JN, Madabushi S, Haunso S, Burstein ES, Whistler JL, Sheikh SP, Lichtarge O, and Lerche-Hansen J.
An Angiotensin II Type 1 Receptor Activation Switch Patch Revealed through Evolutionary Trace Analysis..
Biochemical Pharmacology. 2010 Jul; 80(1):86-94. PMID: 20227396 DOI: 10.1016/j.bcp.2010.03.006

Rodriguez GJ, Yao R, Lichtarge O* and Wensel T*.
Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors..
PNAS. 2010 Apr; 107(17):7787-92.

Wilkins AD, Lua R, Erdin S, Ward RM and Lichtarge O.
Sequence and Structure Continuity of Evolutionary Importance Improves Protein Functional Site Discovery and Annotation..
Protein Sci. 2010 Apr; 19(7):1296-1311.

Baameur F, Morgan DH, Yao H, Tran TM, Hammitt RA, Sabui S, McMurray JS, Lichtarge O, and Clark RB.
Role for the RH Domain of GRK5 and 6 in {beta}2-Adrenergic Receptor and Rhodopsin Phosphorylation..
Mol Pharmacol. 2010 Mar; 77(3):405-15. PMID: 20038610 DOI: 10.1124/mol.109.058115

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

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

Shaibani, A., O.A. Shchelochkov, S. Zhang, P. Katsonis, O. Lichtarge, L. Wong, M. Shinawi.
Mitochondrial Neurogastrointestinal Encephalopathy Due to Mutations in RRM2B.
Arch Neurol. 2009 Aug; 66(8):1028-32. PMID: 19667227 DOI: 10.1001/archneurol.2009.139

Kobayashi, H., K. Ogawa, R. Yao, O. Lichtarge and M. Bouvier.
Functional Rescue of Beta1-adrenoceptor Dimerization and Trafficking by Pharmacological Chaperones..
Traffic. 2009 Aug; 10(8):1019-33. PMID: 19515093 DOI: 10.1111/j.1600-0854.2009.00932.x

Ward, R.M., E. Venner, B. Daines, S. Murray, S. Erdin, D.M. Kristensen, and O. Lichtarge.
Evolutionary Trace Annotation Server: Automated Enzyme Function Prediction in Protein Structures Using 3D Templates..
Bioinformatics. 2009 Jun; 25(11):1426-7. PMID: 19307237 DOI: 10.1093/bioinformatics/btp160

Rajagopalan, L., F.A. Pereira, O. Lichtarge, W.E. Brownell..
Identification of Functionally Important Residues/Domains in Membrane Proteins Using an Evolutionary Approach Coupled with Systematic Mutational Analysis..
Methods Mol Biol. 2009 Apr; 493:287-97. PMID: 18839354 DOI: 10.1007/978-1-59745-523-7_17

Ward RM, Erdin S, Tran TA, Kristensen DM, Lisewski AM, and Lichtarge O.
De-Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features..
PLoS ONE. 2008 May; 3(5):e2136. PMID: 18461181 DOI: 10.1371/journal.pone.0002136

Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, and Lichtarge O.
Prediction of Enzyme Function Based on 3D Templates of Evolutionarily Important Amino Acids..
BMC Bioinformatics.. 2008 Jan; 9(1):17. PMID: 18190718 DOI: 10.1186/1471-2105-9-17

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

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

Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, and Kavraki LE.
Composite motifs integrating multiple protein structures increase sensitivity for function prediction..
Comput Syst Bioinformatics Conf.. 2007 Aug; 6:55. PMID: 17951837

Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, and Kavraki LE.
The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs..
J Comput Biol. 2007 Jul; 14(6):791-816. PMID: 17691895 DOI: 10.1089/cmb.2007.R017

Item CB, Mihalek I, Lichtarge O, Jalan A, Vodopiutz J, Muhl A, Bodamer OA.
Manifestation of hawkinsinuria in a patient compound heterozygous for hawkinsinuria and tyrosinemia III..
Mol Genet Metab. 2007 Jun;

Mihalek I, Res I, and Lichtarge O.
On itinerant waters and detectability of protein-protein interfaces through comparative analysis of homologues..
J Mol Biol. 2007 Jun; 369(2):584-95.

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

Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE.
Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction..
J Bioinform Comput Biol. 2007 Apr; 5(2):353-82.

Rajagopalan L, Patel N, Madabushi S, Goddard JA, Anjan V, Lin F, Shope C, Farrell B, Lichtarge O, Davidson AL, Brownell WE, Pereira FA.
Essential Helix Interactions in the Anion Transporter Domain of Prestin Revealed by Evolutionary Trace Analysis..
J Neurosci. 2006 Dec; 22(16):2049-50.

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

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

Raviscioni M, He Q, Salicru EM, Smyth CL, and Lichtarge O.
Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors..
Proteins. 2006 Sep; 64(4):1046-57.

Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, and Kavraki LE.
Cavity-aware motifs reduce false positives in protein function prediction..
Comput Syst Bioinformatics Conf.. 2006 Aug; 5:311-23. PMID: 17369649

Morgan DH, Kristensen DM, Mittleman D, and Lichtarge O.
ET Viewer: An Application for Predicting and Visualizing Functional Sites in Protein Structures..
Bioinformatics. 2006 Aug; 22(16):2049-50.

Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, and Lichtarge O.
Recurrent Use of Evolutionary Importance for Functional Annotation of Proteins Based on Local Structural Similarity..
Protein Sci. 2006 Jun; 15(6):1530-6.

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

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

Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O and Kavraki LE.
Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction..
Research in Computational Molecular Biology. 2006 Apr; 500-515.

Mihalek I, Res I, and Lichtarge O.
A structure and evolution guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins..
Bioinformatics. 2006 Jan; 22(2):149-56.

Shenoy SK, Drake MT, Nelson CD, Houtz DA, Xiao K, Madabushi S, Reiter E, Premont RT, Lichtarge O, and Lefkowitz RJ.
beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor..
J Biol Chem. 2006 Jan; 281(2):1261-73.

Gu P, Morgan DH, Sattar M, Xu X, Wagner R, Ravisconi M, Lichtarge O, and Cooney AJ.
Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptors..
J Biol Chem. 2005 Sep; 280(36):31818-29. PMID: 15994320

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

Amir RE, Van den Veyver IB, Schultz R, Malicki DM, Tran CQ, Dahle EJ, Philippi A, Timar L, Percy AK, Motil KJ, Lichtarge O, Smith EO, Glaze DG and Zoghbi HY.
Influence of mutation type and X chromosome inactivation on Rett syndrome phenotypes..
Ann. Neurol. 2000 May; 47(5):670-9.

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

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

Sheikh SP, Vilardarga JP, Baranski TJ, Lichtarge O, Iiri T, Meng EC, Nissenson RA and Bourne HR.
Similar structures and shared switch mechanisms of the beta2-adrenoceptor and the parathyroid hormone receptor. Zn(II) bridges between helices III and VI block activation..
J Biol Chem. 1999 Jun; 274(24):17033-41.

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

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

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

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

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

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

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

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