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Augustin Luna, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi J, Rodchenkov I, Babur Ö, Bachman JA, Gyori BM, Demir E, Bader GD, Sander C. Author-sourced capture of pathway knowledge in computable form using Biofactoid. Elife. 2021 12 03; 10. PMID: 34860157.
    Citations:    Fields:    
  2. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff-Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Willighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Dec; 17(12):e10851. PMID: 34939300.
    Citations:    Fields:    
  3. Luna A, Siper MC, Korkut A, Durupinar F, Dogrusoz U, Aslan JE, Sander C, Demir E, Babur O. Analyzing causal relationships in proteomic profiles using CausalPath. STAR Protoc. 2021 12 17; 2(4):100955. PMID: 34877547.
    Citations:    Fields:    
  4. Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D'Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 10; 17(10):e10387. PMID: 34664389.
    Citations: 7     Fields:    Translation:HumansCells
  5. Babur Ö, Luna A, Korkut A, Durupinar F, Siper MC, Dogrusoz U, Vaca Jacome AS, Peckner R, Christianson KE, Jaffe JD, Spellman PT, Aslan JE, Sander C, Demir E. Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns (N Y). 2021 Jun 11; 2(6):100257. PMID: 34179843.
    Citations: 10     
  6. Luna A, Elloumi F, Varma S, Wang Y, Rajapakse VN, Aladjem MI, Robert J, Sander C, Pommier Y, Reinhold WC. CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics. Nucleic Acids Res. 2021 01 08; 49(D1):D1083-D1093. PMID: 33196823.
    Citations: 14     Fields:    Translation:HumansCells
  7. Yuan B, Shen C, Luna A, Korkut A, Marks DS, Ingraham J, Sander C. CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy. Cell Syst. 2021 02 17; 12(2):128-140.e4. PMID: 33373583.
    Citations: 12     Fields:    Translation:Humans
  8. Liu EM, Luna A, Dong G, Sander C. netboxr: Automated discovery of biological process modules by network analysis in R. PLoS One. 2020; 15(11):e0234669. PMID: 33137091.
    Citations: 1     Fields:    Translation:Humans
  9. Tlemsani C, Pongor L, Elloumi F, Girard L, Huffman KE, Roper N, Varma S, Luna A, Rajapakse VN, Sebastian R, Kohn KW, Krushkal J, Aladjem MI, Teicher BA, Meltzer PS, Reinhold WC, Minna JD, Thomas A, Pommier Y. SCLC-CellMiner: A Resource for Small Cell Lung Cancer Cell Line Genomics and Pharmacology Based on Genomic Signatures. Cell Rep. 2020 10 20; 33(3):108296. PMID: 33086069.
    Citations: 15     Fields:    Translation:HumansCells
  10. Bergmann FT, Czauderna T, Dogrusoz U, Rougny A, Dräger A, Touré V, Mazein A, Blinov ML, Luna A. Systems biology graphical notation markup language (SBGNML) version 0.3. J Integr Bioinform. 2020 Jun 22; 17(2-3). PMID: 32568733.
    Citations: 5     Fields:    
  11. Reguant R, Antipin Y, Sheridan R, Dallago C, Diamantoukos D, Luna A, Sander C, Gauthier NP. AlignmentViewer: Sequence Analysis of Large Protein Families. F1000Res. 2020; 9. PMID: 33123346.
    Citations: 3     Fields:    Translation:Humans
  12. Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O'Callaghan C, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 2020 01 08; 48(D1):D489-D497. PMID: 31647099.
    Citations: 56     Fields:    Translation:Humans
  13. Guo T, Luna A, Rajapakse VN, Koh CC, Wu Z, Liu W, Sun Y, Gao H, Menden MP, Xu C, Calzone L, Martignetti L, Auwerx C, Buljan M, Banaei-Esfahani A, Ori A, Iskar M, Gillet L, Bi R, Zhang J, Zhang H, Yu C, Zhong Q, Varma S, Schmitt U, Qiu P, Zhang Q, Zhu Y, Wild PJ, Garnett MJ, Bork P, Beck M, Liu K, Saez-Rodriguez J, Elloumi F, Reinhold WC, Sander C, Pommier Y, Aebersold R. Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines. iScience. 2019 Nov 22; 21:664-680. PMID: 31733513.
    Citations: 11     
  14. Rougny A, Touré V, Moodie S, Balaur I, Czauderna T, Borlinghaus H, Dogrusoz U, Mazein A, Dräger A, Blinov ML, Villéger A, Haw R, Demir E, Mi H, Sorokin A, Schreiber F, Luna A. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J Integr Bioinform. 2019 Jun 13; 16(2). PMID: 31199769.
    Citations: 15     Fields:    Translation:Cells
  15. Saito Y, Li L, Coyaud E, Luna A, Sander C, Raught B, Asara JM, Brown M, Muthuswamy SK. LLGL2 rescues nutrient stress by promoting leucine uptake in ER+ breast cancer. Nature. 2019 05; 569(7755):275-279. PMID: 30996345.
    Citations: 41     Fields:    Translation:HumansAnimalsCells
  16. Rajapakse VN, Luna A, Yamade M, Loman L, Varma S, Sunshine M, Iorio F, Sousa FG, Elloumi F, Aladjem MI, Thomas A, Sander C, Kohn KW, Benes CH, Garnett M, Reinhold WC, Pommier Y. CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines. iScience. 2018 Dec 21; 10:247-264. PMID: 30553813.
    Citations: 54     
  17. Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 04 05; 173(2):321-337.e10. PMID: 29625050.
    Citations: 707     Fields:    Translation:HumansCells
  18. Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep. 2018 04 03; 23(1):172-180.e3. PMID: 29617658.
    Citations: 39     Fields:    Translation:HumansCells
  19. Reznik E, Luna A, Aksoy BA, Liu EM, La K, Ostrovnaya I, Creighton CJ, Hakimi AA, Sander C. A Landscape of Metabolic Variation across Tumor Types. Cell Syst. 2018 Mar 28; 6(3):301-313.e3. PMID: 29396322.
    Citations: 49     Fields:    Translation:Humans
  20. Senbabaoglu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA. Erratum to: Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2017 03 01; 18(1):46. PMID: 28249590.
    Citations: 2     Fields:    
  21. Reinhold WC, Varma S, Sunshine M, Rajapakse V, Luna A, Kohn KW, Stevenson H, Wang Y, Heyn H, Nogales V, Moran S, Goldstein DJ, Doroshow JH, Meltzer PS, Esteller M, Pommier Y. The NCI-60 Methylome and Its Integration into CellMiner. Cancer Res. 2017 02 01; 77(3):601-612. PMID: 27923837.
    Citations: 24     Fields:    Translation:HumansCells
  22. Senbabaoglu Y, Gejman RS, Winer AG, Liu M, Van Allen EM, de Velasco G, Miao D, Ostrovnaya I, Drill E, Luna A, Weinhold N, Lee W, Manley BJ, Khalil DN, Kaffenberger SD, Chen Y, Danilova L, Voss MH, Coleman JA, Russo P, Reuter VE, Chan TA, Cheng EH, Scheinberg DA, Li MO, Choueiri TK, Hsieh JJ, Sander C, Hakimi AA. Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures. Genome Biol. 2016 11 17; 17(1):231. PMID: 27855702.
    Citations: 287     Fields:    Translation:HumansCells
  23. Hakimi AA, Reznik E, Lee CH, Creighton CJ, Brannon AR, Luna A, Aksoy BA, Liu EM, Shen R, Lee W, Chen Y, Stirdivant SM, Russo P, Chen YB, Tickoo SK, Reuter VE, Cheng EH, Sander C, Hsieh JJ. An Integrated Metabolic Atlas of Clear Cell Renal Cell Carcinoma. Cancer Cell. 2016 Jan 11; 29(1):104-116. PMID: 26766592.
    Citations: 170     Fields:    Translation:Humans
  24. Luna A, Babur Ö, Aksoy BA, Demir E, Sander C. PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinformatics. 2016 04 15; 32(8):1262-4. PMID: 26685306.
    Citations: 10     Fields:    
  25. Luna A, Rajapakse VN, Sousa FG, Gao J, Schultz N, Varma S, Reinhold W, Sander C, Pommier Y. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. Bioinformatics. 2016 04 15; 32(8):1272-4. PMID: 26635141.
    Citations: 18     Fields:    Translation:Cells
  26. Mi H, Schreiber F, Moodie S, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger A. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. J Integr Bioinform. 2015 Sep 04; 12(2):265. PMID: 26528563.
    Citations: 12     Fields:    Translation:HumansAnimalsCells
  27. Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie S, Schreiber F, Villéger A. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. J Integr Bioinform. 2015 Sep 04; 12(2):264. PMID: 26528562.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  28. Luna A, McFadden GB, Aladjem MI, Kohn KW. Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. PLoS Comput Biol. 2015 May; 11(5):e1004144. PMID: 26020938.
    Citations: 7     Fields:    Translation:HumansAnimals
  29. Sousa FG, Matuo R, Tang SW, Rajapakse VN, Luna A, Sander C, Varma S, Simon PH, Doroshow JH, Reinhold WC, Pommier Y. Alterations of DNA repair genes in the NCI-60 cell lines and their predictive value for anticancer drug activity. DNA Repair (Amst). 2015 Apr; 28:107-15. PMID: 25758781.
    Citations: 28     Fields:    Translation:HumansCells
  30. Reinhold WC, Varma S, Rajapakse VN, Luna A, Sousa FG, Kohn KW, Pommier YG. Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer. Hum Genet. 2015 Jan; 134(1):3-11. PMID: 25213708.
    Citations: 10     Fields:    Translation:Humans
  31. Luna A, Aladjem MI, Kohn KW. SIRT1/PARP1 crosstalk: connecting DNA damage and metabolism. Genome Integr. 2013 Dec 20; 4(1):6. PMID: 24360018.
    Citations: 40     
  32. Fried JY, van Iersel MP, Aladjem MI, Kohn KW, Luna A. PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. Bioinformatics. 2013 Jun 01; 29(11):1465-6. PMID: 23547033.
    Citations: 3     Fields:    Translation:Humans
  33. van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics. 2012 Aug 01; 28(15):2016-21. PMID: 22581176.
    Citations: 35     Fields:    
  34. Kohn KW, Zeeberg BR, Reinhold WC, Sunshine M, Luna A, Pommier Y. Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes. PLoS One. 2012; 7(5):e35716. PMID: 22570691.
    Citations: 19     Fields:    Translation:HumansCells
  35. Chandan K, van Iersel MP, Aladjem MI, Kohn KW, Luna A. PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. Bioinformatics. 2012 Mar 15; 28(6):889-90. PMID: 22199389.
    Citations: 4     Fields:    
  36. Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW. PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics. 2011 Aug 01; 27(15):2165-6. PMID: 21636591.
    Citations: 10     Fields:    
  37. Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics. 2011 May 17; 12:167. PMID: 21586134.
    Citations: 11     Fields:    Translation:AnimalsCells
  38. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42. PMID: 20829833.
    Citations: 300     Fields:    Translation:Cells
  39. Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug; 27(8):735-41. PMID: 19668183.
    Citations: 344     Fields:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.