2017

Berg JS, Agrawal PB, Bailey DB Jr, Beggs AH, Brenner SE, Brower AM, Cakici JA, Ceyhan-Birsoy O, Chan K, Chen F, Currier RJ, Dukhovny D, Green RC, Harris-Wai J, Holm IA, Iglesias B, Joseph G, Kingsmore SF, Koenig BA, Kwok PY, Lantos J, Leeder SJ, Lewis MA, McGuire AL, Milko LV, Mooney SD, Parad RB, Pereira S, Petrikin J, Powell BC, Powell CM, Puck JM, Rehm HL, Risch N, Roche M, Shieh JT, Veeraraghavan N, Watson MS, Willig L, Yu TW, Urv T, Wise AL. “Newborn Sequencing in Genomic Medicine and Public Health.”Pediatrics. 2017 Feb;139(2). pii: e20162252. Link

Oetting WS, Béroud C, Brenner SE, Greenblatt M, Karchin R, Mooney SD, Sunyaev S. “Non-Coding Variation: The 2016 Annual Scientific Meeting of the Human Genome Variation Society.“ Hum Mutat. 2017 Jan 5. Link

2016

Khanna A, Kumar J, Vargas MA, Barrett L, Katewa S, Li P, McCloskey T, Sharma A, Naudé N, Nelson C, Brem R, Killilea DW, Mooney SD, Gill M, Kapahi P. “A genome-wide screen of bacterial mutants that enhance dauer formation in C. elegans.” Sci Rep. 2016 Dec 13;6:38764. Link

Morgan AA, Crawford DC, Denny JC, Mooney SD, Aronow BJ, Brenner SE. “PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY.” Pac Symp Biocomput. 2016;22:348-355. Link

Jiang Y, Oron TR, Clark WT, Bankapur AR, D’Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O’Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. “An expanded evaluation of protein function prediction methods shows an improvement in accuracy.”Genome Biol. 2016 Sep 7;17(1):184. Link

Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P. “The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease.“ PLoS Comput Biol. 2016 Aug 26;12(8):e1005091. Link

Peterson TA, Mort M, Cooper DN, Radivojac P, Kann MG, Mooney SD. “Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.” Hum Mutat. 2016 Nov;37(11):1137-1143. Link

Green RC, Goddard KA, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, Garrett JR, Gray SW, Henderson GE, Hindorff LA, Holm IA, Lewis MH, Hutter CM, Janne PA, Joffe S, Kaufman D, Knoppers BM, Koenig BA, Krantz ID, Manolio TA, McCullough L, McEwen J, McGuire A, Muzny D, Myers RM, Nickerson DA, Ou J, Parsons DW, Petersen GM, Plon SE, Rehm HL, Roberts JS, Robinson D, Salama JS, Scollon S, Sharp RR, Shirts B, Spinner NB, Tabor HK, Tarczy-Hornoch P, Veenstra DL, Wagle N, Weck K, Wilfond BS, Wilhelmsen K, Wolf SM, Wynn J, Yu JH; CSER Consortium.. “Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.” Am J Hum Genet. 2016 Jul 7;99(1):246. Link

Momcilovic O, Sivapatham R, Oron TR, Meyer M, Mooney S, Rao MS, Zeng X. “Derivation, Characterization, and Neural Differentiation of Integration-Free Induced Pluripotent Stem Cell Lines from Parkinson’s Disease Patients Carrying SNCA, LRRK2, PARK2, and GBA Mutations.” PLoS One. 2016 May 18;11(5):e0154890. Link

Green RC, Goddard KA, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, Garrett JR, Gray SW, Henderson GE, Hindorff LA, Holm IA, Lewis MH, Hutter CM, Janne PA, Joffe S, Kaufman D, Knoppers BM, Koenig BA, Krantz ID, Manolio TA, McCullough L, McEwen J, McGuire A, Muzny D, Myers RM, Nickerson DA, Ou J, Parsons DW, Petersen GM, Plon SE, Rehm HL, Roberts JS, Robinson D, Salama JS, Scollon S, Sharp RR, Shirts B, Spinner NB, Tabor HK, Tarczy-Hornoch P, Veenstra DL, Wagle N, Weck K, Wilfond BS, Wilhelmsen K, Wolf SM, Wynn J, Yu JH; CSER Consortium.. “Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.“Am J Hum Genet. 2016 Jun 2;98(6):1051-66. Link

Morgan AA, Mooney SD, Aronow BJ, Brenner SE. “PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY.” Pac Symp Biocomput. 2016;21:243-8. Link

Brenner SE, Kingsmore S, Mooney SD, Nussbaum R, Puck J. “USE OF GENOME DATA IN NEWBORNS AS A STARTING POINT FOR LIFE-LONG PRECISION MEDICINE.” Pac Symp Biocomput. 2016;21:568-75. Link

Mather CA, Mooney SD, Salipante SJ, Scroggins S, Wu D, Pritchard CC, Shirts BH. “CADD score has limited clinical validity for the identification of pathogenic variants in noncoding regions in a hereditary cancer panel.” Genet Med. 2016 May 5. doi: 10.1038/gim.2016.44. Link

Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C. “High-performance web services for querying gene and variant annotation.” Genome Biol. 2016 May 6;17(1):91. Link

2015

Katzman SM, Strotmeyer ES, Nalls MA, Zhao Y, Mooney S, Schork N, Newman AB, Harris TB, Yaffe K, Cummings SR, Liu Y, Tranah GJ; “Health, Aging, and Body Composition Study. Mitochondrial DNA Sequence Variation Associated With Peripheral Nerve Function in the Elderly.” J Gerontol A Biol Sci Med Sci. 2015 Nov;70(11):1400-8. Link

Caciotti A, Tonin R, Rigoldi M, Ferri L, Catarzi S, Cavicchi C, Procopio E, Donati MA, Ficcadenti A, Fiumara A, Barone R, Garavelli L, Rocco MD, Filocamo M, Antuzzi D, Scarpa M, Mooney SD, Li B, Skouma A, Bianca S, Concolino D, Casalone R, Monti E, Pantaleo M, Giglio S, Guerrini R, Parini R, Morrone A. “Optimizing the molecular diagnosis of GALNS: novel methods to define and characterize Morquio-A syndrome-associated mutations”. Hum Mutat. 2015 Mar;36(3):357-68. Link

Oetting WS, Greenblatt MS, Brookes AJ, Karchin R, Mooney SD. “Germline & somatic mosaicism: the 2014 annual scientific meeting of the Human Genome Variation Society.” Hum Mutat. 2015 Mar;36(3):390-3. Link

Friedberg I, Wass MN, Mooney SD, Radivojac P. “Ten simple rules for a community computational challenge.” PLoS Comput Biol. 2015 Apr 23;11(4):e1004150. Link

Ring KL, An MC, Zhang N, O’Brien RN, Ramos EM, Gao F, Atwood R, Bailus BJ, Melov S, Mooney SD, Coppola G, Ellerby LM. “Genomic Analysis Reveals Disruption of Striatal Neuronal Development and Therapeutic Targets in Human Huntington’s Disease Neural Stem Cells.” Stem Cell Reports. 2015 Dec 8;5(6):1023-38. Link

Mooney, Sean. “Progress towards the Integration of Pharmacogenomics in Practice.” Human Genetics 134.5 (2015): 459-65. Link

Tonin, Rodolfo, Anna Caciotti, Silvia Funghini, Giancarlo La Marca, Elisabetta Pasquini, Erica Cayton, Sean D. Mooney, Renzo Guerrini, and Amelia Morrone. “Biotinidase Deficiency Due to a De Novo Mutation or Gonadal Mosaicism in a First Child.” Clinica Chimica Acta 445 (2015): 70-72. Link

Friedberg, Iddo, Mark N. Wass, Sean D. Mooney, and Predrag Radivojac. “Ten Simple Rules for a Community Computational Challenge.” PLOS Computational Biology PLoS Comput Biol 11.4 (2015): e1004150 1-5. Link

Oetting, W. S., Greenblatt, M. S., Brookes, A. J., Karchin, R. and Mooney, S. D. , Germline & Somatic Mosaicism: The 2014 Annual Scientific Meeting of the Human Genome Variation Society. Hum. Mutat., 36 (2015): 390–393. Link

Caciotti, A., Tonin, R., Rigoldi, M., Ferri, L., Catarzi, S., Cavicchi, C., Procopio, E., Donati, M. A., Ficcadenti, A., Fiumara, A., Barone, R., Garavelli, L., Rocco, M. D., Filocamo, M., Antuzzi, D., Scarpa, M., Mooney, S. D., Li, B., Skouma, A., Bianca, S., Concolino, D., Casalone, R., Monti, E., Pantaleo, M., Giglio, S., Guerrini, R., Parini, R. and Morrone, A. , Optimizing the Molecular Diagnosis of GALNS: Novel Methods to Define and Characterize Morquio—A Syndrome-Associated Mutations. Hum. Mutat., 36 (2015): 357–368. Link

An, M., N. Zhang, K. Ring, R. N. O’Brien, F. Gao, R. Atwood, S. Melov, G. Mooney, L. M. Coppola, and M. Ellerby. “Presidential Symposium: Gene Network Analysis Reveals Modules Driving Neural Stem Cell Phenotypes in Huntington’s Disease.” Cell Transplantation 24.4 (2015): 752. Link

2014

James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Nicholas J Wang, Mukesh Bansal, Muhammad Ammad-Ud-Din, Petteri Hintsanen, Suleiman A Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, James J Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W Gray, and Gustavo Stolovitzky. “A Community Effort to Assess and Improve Drug Sensitivity Prediction Algorithms.” Nature Biotechnology (2014): Nature Biotechnology, 2014. Link

Tranah, Gregory J., Michael A. Nalls, Shana M. Katzman, Jennifer S. Yokoyama, Ernest T. Lam, Yiqiang Zhao, Sean Mooney, Fridtjof Thomas, Anne B. Newman, Yongmei Liu, Steven R. Cummings, Tamara B. Harris, and Kristine Yaffe. “Mitochondrial DNA Sequence Variation Associated with Dementia and Cognitive Function in the Elderly.” Journal Of Alzheimers Disease 32.2 (2014): 357-72. Link

Morrone, Amelia, Anna Caciotti, Robert Atwood, Kathryn Davidson, Chaoyi Du, Patricia Francis‐Lyon, Paul Harmatz, Matthew Mealiffe, Sean Mooney, Tal Ronnen Oron, April Ryles, Karl A. Zawadzki, and Nicole Miller. “Morquio A Syndrome‐Associated Mutations: A Review of Alterations in the GALNS Gene and a New Locus‐Specific Database.” Human Mutation 35.11 (2014): 1271-279. Link

Chen, Yun-Ching, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace Yeo, Violeta Beleva-Guthrie, Hannah Carter, Peter D. Stenson, David N. Cooper, Biao Li, Sean Mooney, and Rachel Karchin. “A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing.” Plos Computational Biology 10.9 (2014): Plos Computational Biology, 2014 Sep, Vol.10(9). Link

Cavicchi, Catia, Maria Alice Donati, Rossella Parini, Miriam Rigoldi, Mauro Bernardi, Francesca Orfei, Nicolo Gentiloni Silveri, Aniello Colasante, Silvia Funghini, Serena Catarzi, Elisabetta Pasquini, Giancarlo La Marca, Sean David Mooney, Renzo Guerrini, and Amelia Morrone. “Sudden Unexpected Fatal Encephalopathy in Adults with OTC Gene Mutations-Clues for Early Diagnosis and Timely Treatment.” Orphanet Journal Of Rare Diseases 9 (2014): Orphanet Journal Of Rare Diseases, 2014 Jul 16, Vol.9. Link

Li, Zhiyu, Jonathan M. Dilger, Vikas Pejaver, David Smiley, Randy J. Arnold, Sean D. Mooney, Suchetana Mukhopadhyay, Predrag Radivojac, and David E. Clemmer. “Intrinsic Size Parameters for Palmitoylated and Carboxyamidomethylated Peptides.” International Journal Of Mass Spectrometry 368 (2014): 6-14. Link

Morrone, A., K. L. Tylee, M. Al-Sayed, A. C. Brusius-Facchin, H. J. Caciotti, M. J. Church, K. Coll, L. Davidson, F. Fietz, S. Gort, I. Hegde, R. Y. Kubaski, N. Lacerda, A. Laranjeira, Kl Leistner-Segal, M. Mooney, Ac Pajares, Hj Pollard, Mj Ribeiro, K. Wang, and L. Miller. “Molecular Testing of 163 Patients with Morquio A (Mucopolysaccharidosis IVA) Identifies 39 Novel GALNS Mutations.” Molecular Genetics And Metabolism 112.2 (2014): 160-70. Link

Li, Biao, Chet Seligman, Janita Thusberg, Jackson Miller, Jim Auer, Michelle Whirl-Carrillo, Emidio Capriotti, Teri Klein, and Sean Mooney. “In Silico Comparative Characterization of Pharmacogenomic Missense Variants.” BMC Genomics 15 (2014): BMC Genomics, 2014, Vol.15. Link

Zykovich, Artem, Alan Hubbard, James M. Flynn, Mark Tarnopolsky, Mario F. Fraga, Chad Kerksick, Dan Ogborn, Lauren MacNeil, Sean D. Mooney, and Simon Melov. “Genome‐wide DNA Methylation Changes with Age in Disease‐free Human Skeletal Muscle.” Aging Cell 13.2 (2014): 360-66. Link

Tourette, Cendrine, Biao Li, Russell Bell, Shannon O’Hare, Linda S Kaltenbach, Sean D Mooney, and Robert E Hughes. “A Large Scale Huntingtin Protein Interaction Network Implicates Rho GTPase Signaling Pathways in Huntington Disease.” The Journal of Biological Chemistry 289.10 (2014): 6709-26. Link

Wass, Mark N., Sean D. Mooney, Michal Linial, Predrag Radivojac, and Iddo Friedberg. “The Automated Function Prediction SIG Looks Back at 2013 and Prepares for 2014.” Bioinformatics 30.14 (2014): 2091-092. Link

Mort, Matthew, Timothy Sterne-Weiler, Biao Li, Edward V. Ball, David N. Cooper, Predrag Radivojac, Jeremy R. Sanford, and Sean D. Mooney. “MutPred Splice: Machine Learning-based Prediction of Exonic Variants That Disrupt Splicing.” Genome Biology 15.1 (2014): Genome Biology, 2014, Vol.15(1). Link

Morrone, A., Tylee, K.L., Al-Sayed, M., Brusius-Facchin, A.C., Caciotti, A., Church, H.J., Coll, M.J., Davidson, K., Fietz, M.J., Gort, L., Hegde, M., Kubaski, F., Lacerda, L., Laranjeira, F., Leistner-Segal, S., Mooney, S., Pajares, S., Pollard, L., Ribeiro, I., Wang, R.Y., and Miller, N. “Corrigendum to “Molecular Testing of 163 Patients with Morquio A (Mucopolysaccharidosis IVA) Identifies 39 Novel GALNS Mutations” [Mol. Genet. Metab. 112 (2014) 160–170].” Molecular Genetics and Metabolism 113.3 (2014): 237. Link

An, Mahru, Zhang, Ningzhe, Ring, Karen, O’Brien, Robert, Melov, Simon, Mooney, Sean, Coppola, Giovanni, and Ellerby, Lisa M. “UNDERSTANDING THE PATHWAYS THAT LEAD TO NERVE CELL DEATH IN HUNTINGTON’S DISEASE.” Free Radical Biology and Medicine 76 (2014): S3. Link

Kolker, Eugene, Vural Özdemir, Lennart Martens, William Hancock, Gordon Anderson, Nathaniel Anderson, Sukru Aynacioglu, Ancha Baranova, Shawn R. Campagna, Rui Chen, John Choiniere, Stephen P. Dearth, Wu-Chun Feng, Lynnette Ferguson, Geoffrey Fox, Dmitrij Frishman, Robert Grossman, Allison Heath, Roger Higdon, Mara H. Hutz, Imre Janko, Lihua Jiang, Sanjay Joshi, Alexander Kel, Joseph W. Kemnitz, Isaac S. Kohane, Natali Kolker, Doron Lancet, Elaine Lee, Weizhong Li, Andrey Lisitsa, Adrian Llerena, Courtney Macnealy-Koch, Jean-Claude Marshall, Paola Masuzzo, Amanda May, George Mias, Matthew Monroe, Elizabeth Montague, Sean Mooney, Alexey Nesvizhskii, Santosh Noronha, Gilbert Omenn, Harsha Rajasimha, Preveen Ramamoorthy, Jerry Sheehan, Larry Smarr, Charles V. Smith, Todd Smith, Michael Snyder, Srikanth Rapole, Sanjeeva Srivastava, Larissa Stanberry, Elizabeth Stewart, Stefano Toppo, Peter Uetz, Kenneth Verheggen, Brynn H. Voy, Louise Warnich, Steven W. Wilhelm, and Gregory Yandl. “Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications.” Big Data 1.4 (2014): 196-201. Link

Ryles, April B., Chaoyi Du, Tal Oron, Robert Atwood, Sean D. Mooney, and Patricia Francis-Lyon. “Morquio Syndrome Type A Locus-specific Database: A Framework for a Curated Database to Identify and Characterize Pathogenic Variants in the GALNS Gene.” Molecular Genetics And Metabolism 111.2 (2014): S92. Link

2013

Bagchi, Angshuman, Mort, Matthew, Li, Biao, Xin, Fuxiao, Carlise, Carson, Oron, Tal, Powell, Corey, Youn, Eunseog, Radivojac, Predrag, Cooper, David N., and Mooney, Sean D. “Analysis of Features from Protein-protein Hetero-complex Structures to Predict Protein Interaction Interfaces Using Machine Learning.” Procedia Technology 10 (2013): 62-66. Link

Catarzi, Serena, Anna Caciotti, Janita Thusberg, Rodolfo Tonin, Sabrina Malvagia, Giancarlo La Marca, Elisabetta Pasquini, Catia Cavicchi, Lorenzo Ferri, Maria A. Donati, Federico Baronio, Renzo Guerrini, Sean D. Mooney, and Amelia Morrone. “Medium-Chain Acyl-CoA Deficiency: Outlines from Newborn Screening, In Silico Predictions, and Molecular Studies.” Scientific World Journal (2013): Scientific World Journal, 2013. Link

Flynn, James M., Monique N. O’Leary, Christopher A. Zambataro, Emmeline C. Academia, Michael P. Presley, Brittany J. Garrett, Artem Zykovich, Sean D. Mooney, Randy Strong, Clifford J. Rosen, Pankaj Kapahi, Michael D. Nelson, Brian K. Kennedy, and Simon Melov. “Late‐life Rapamycin Treatment Reverses Age‐related Heart Dysfunction.” Aging Cell 12.5 (2013): 851-62. Link

Rardin, Matthew J., John C. Newman, Jason M. Held, Michael P. Cusack, Dylan J. Sorensen, Biao Li, Birgit Schilling, Sean D. Mooney, C. Ronald Kahn, Eric Verdin, and Bradford W. Gibson. “Label-free Quantitative Proteomics of the Lysine Acetylome in Mitochondria Identifies Substrates of SIRT3 in Metabolic Pathways.” Proceedings Of The National Academy Of Sciences Of The United States Of Ame 110.16 (2013): 6601-606. Link

Mooney, Sean. “From Phenotype to Genotype: A New Twist on Identifying Genes Responsible for Inherited Hearing Loss.” Human Mutation 34.4 (2013): V. Link

Radivojac, Predrag, et al. “A Large-Scale Evaluation Of Computational Protein Function Prediction.” Nature Methods 10.3 (2013): 221-227. Link

Wittkop, Tobias, Emily Teravest, Uday S. Evani, K. Mathew Fleisch, Ari E. Berman, Corey Powell, Nigam H. Shah, and Sean D. Mooney. “STOP Using Just GO: A Multi-ontology Hypothesis Generation Tool for High Throughput Experimentation.” Bmc Bioinformatics 14 (2013): Bmc Bioinformatics, 2013 Feb 14, Vol.14. Link

Thompson, Bryony A., Marc S. Greenblatt, Maxime P. Vallee, Johanna C. Herkert, Chloe Tessereau, Erin L. Young, Ivan A. Adzhubey, Biao Li, Russell Bell, Bingjian Feng, Sean D. Mooney, Predrag Radivojac, Shamil R. Sunyaev, Thierry Frebourg, Robert M. W. Hofstra, Rolf H. Sijmons, Ken Boucher, Alun Thomas, David E. Goldgar, Amanda B. Spurdle, and Sean V. Tavtigian. “Calibration of Multiple In Silico Tools for Predicting Pathogenicity of Mismatch Repair Gene Missense Substitutions.” Human Mutation 34.1 (2013): 255-65. Link

2012

Peters, Theodore W., Matthew J. Rardin, Gregg Czerwieniec, Uday S. Evani, Pedro Reis-Rodrigues, Gordon J. Lithgow, Sean D. Mooney, Bradford W. Gibson, and Robert E. Hughes. “Tor1 Regulates Protein Solubility in Saccharomyces Cerevisiae.” Molecular Biology Of The Cell 23.24 (2012): 4679-688. Link

Miller, John P., Bridget E. Yates, Ismael Al-Ramahi, Ari E. Berman, Mario Sanhueza, Eugene Kim, Maria De Haro, Francesco DeGiacomo, Cameron Torcassi, Jennifer Holcomb, Juliette Gafni, Sean D. Mooney, Juan Botas, Lisa M. Ellerby, Robert E. Hughes, and Bingwei Lu. “A Genome-Scale RNA–Interference Screen Identifies RRAS Signaling as a Pathologic Feature of Huntington’s Disease (RRAS Pathway in Huntington’s Disease).” 8.11 (2012): E1003042. Link

Ackerman, Locke, Feingold, Reshey, Espana, Thusberg, Mooney, Bean, Dooley, Cua, Reeves, Sherman, and Maslen. “An Excess of Deleterious Variants in VEGF-A Pathway Genes in Down-Syndrome-Associated Atrioventricular Septal Defects.” The American Journal of Human Genetics 91.4 (2012): 646-59. Link

Koboldt, Daniel C., et al. “Comprehensive Molecular Portraits Of Human Breast Tumours.” Nature 490.7418 (2012): 61-70. Link

Haines, Bryan A., Darcy A. Davis, Artem Zykovich, Botao Peng, Rammohan Rao, Sean D. Mooney, Kunlin Jin, and David A. Greenberg. “Comparative Protein Interactomics of Neuroglobin and Myoglobin.” Journal of Neurochemistry 123.1 (2012): 192-98. Link

Tranah, Gregory J., Ernest T. Lam, Shana M. Katzman, Michael A. Nalls, Yiqiang Zhao, Daniel S. Evans, Jennifer S. Yokoyama, Ludmila Pawlikowska, Pui-Yan Kwok, Sean Mooney, Stephen Kritchevsky, Bret H. Goodpaster, Anne B. Newman, Tamara B. Harris, Todd M. Manini, and Steven R. Cummings. “Mitochondrial DNA Sequence Variation Is Associated with Free-living Activity Energy Expenditure in the Elderly.” Biochimica Et Biophysica Acta-Bioenergetics 1817.9 (2012): 1691-700. Link

Berman Ari E, Barnett William K, and Mooney Sean D. “Collaborative Software for Traditional and Translational Research.” Human Genomics 6.1 (2012): 21. Link

An, Mahru C., Ningzhe Zhang, Gary Scott, Daniel Montoro, Tobias Wittkop, Sean Mooney, Simon Melov, and Lisa M. Ellerby. “Genetic Correction of Huntington’s Disease Phenotypes in Induced Pluripotent Stem Cells.” Cell Stem Cell 11.2 (2012): 253-63. Link

Zhao, Yiqiang, and Sean D. Mooney. “Functional Organization and Its Implication in Evolution of the Human Protein-protein Interaction Network.” Bmc Genomics 13 (2012): Bmc Genomics, 2012 Apr 24, Vol.13. Link

Sam Ng, Janita Thusberg, Stephen Benz, Charles Vaske, Kyle Ellrott, Jing Zhu, Christina Yau, Eric Collisson, Sean Mooney, Christopher Benz, David Haussler, Joshua Stuart. “Predicting the impact of mutations in cancer using an integrated pathway approach.” The Journal of Cancer Research, AACR 103rd Annual Meeting (2012). Link

Funghini, S., Thusberg, J., Spada, M., Gasperini, S., Parini, R., Ventura, L., Meli, C., De Cosmo, L., Sibilio, M., Mooney, S.D., Guerrini, R., Donati, M.A., and Morrone, A. “Carbamoyl Phosphate Synthetase 1 Deficiency in Italy: Clinical and Genetic Findings in a Heterogeneous Cohort.” Gene: Gene (2012). Link

Biao Li, Predrag Radivojac, Sean Mooney. “Bioinformatics Approaches to the Functional Profiling of Genetic Variants.” Mutations in human genetic disease (2012). Link

Tranah, Gregory J., Michael A. Nalls, Shana M. Katzman, Jennifer S. Yokoyama, Ernest T. Lam, Yiqiang Zhao, Sean Mooney, Fridtjof Thomas, Anne B. Newman, Yongmei Liu, Steven R. Cummings, Tamara B. Harris, and Kristine Yaffe. “Mitochondrial DNA Sequence Variation Associated with Dementia and Cognitive Function in the Elderly.” Journal Of Alzheimers Disease 32.2 (2012): 357-72. Link

Wittkop, Tobias, Ari E. Berman, K. Mathew Fleisch, and Sean D. Mooney. “DEFOG: Discrete Enrichment of Functionally Organized Genes.” Integrative Biology 4.7 (2012): 795-804. Link

Reis‐Rodrigues, Pedro, Gregg Czerwieniec, Theodore W. Peters, Uday S. Evani, Silvestre Alavez, Emily A. Gaman, Maithili Vantipalli, Sean D. Mooney, Bradford W. Gibson, Gordon J. Lithgow, and Robert E. Hughes. “Proteomic Analysis of Age‐dependent Changes in Protein Solubility Identifies Genes That Modulate Lifespan.” Aging Cell 11.1 (2012): 120-27. Link

2011

Zhao, Yiqiang, Wyatt T. Clark, Matthew Mort, David N. Cooper, Predrag Radivojac, and Sean D. Mooney. “Prediction of Functional Regulatory SNPs in Monogenic and Complex Disease.” Human Mutation 32.10 (2011): 1183-190. Link

Wittkop, Tobias, and Sean D. Mooney. “INTRODUCTION: ADVANCES IN COMPUTATIONAL SYSTEMS BIOINFORMATICS.” Journal of Bioinformatics and Computational Biology 09.02 (2011): V-Vi. Link

Hawkins, Troy B., Jessica Dantzer, Brandon Peters, Mary Dinauer, Keithanne Mockaitis, Sean Mooney, and Kenneth Cornetta. “Identifying Viral Integration Sites Using SeqMap 2.0.” Bioinformatics 27.5 (2011): 720-22. Link

Liu, Jing-Yuan Y., and Sean D. D. Mooney. “Characterization of Ligand Type of Estrogen Receptor by MD Simulation and Mm-PBSA Free Energy Analysis.” International Journal of Biochemistry and Molecular Biology 2.2 (2011): 190-98. Link

2010

Xin, Fuxiao, Steven Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, and Predrag Radivojac. “Structure-based Kernels for the Prediction of Catalytic Residues and Their Involvement in Human Inherited Disease.” Bioinformatics 26.16 (2010): 1975-982. Link

Mort, Matthew, Uday S. Evani, Vidhya G. Krishnan, Kishore K. Kamati, Peter H. Baenziger, Angshuman Bagchi, Brandon J. Peters, Rakesh Sathyesh, Biao Li, Yanan Sun, Bin Xue, Nigam H. Shah, Maricel G. Kann, David N. Cooper, Predrag Radivojac, and Sean D. Mooney. “In Silico Functional Profiling of Human Disease‐associated and Polymorphic Amino Acid Substitutions.” Human Mutation 31.3 (2010): 335-46. Link

Li, Shuyan, Lilia M Iakoucheva, Sean D Mooney, and Predrag Radivojac. “Loss of Post-translational Modification Sites in Disease.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2010): 337-47. Link

Tirrell, Rob et al. “An Ontology-Neutral Framework for Enrichment Analysis.” AMIA Annual Symposium Proceedings 2010 (2010): 797–801. Link

Mooney, Sean D, Vidhya G Krishnan, and Uday S Evani. “Bioinformatic Tools for Identifying Disease Gene and SNP Candidates.” Methods in Molecular Biology (Clifton, N.J.) 628 (2010): 307-19. Link

2009

Li, Biao, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, and Predrag Radivojac. “Automated Inference of Molecular Mechanisms of Disease from Amino Acid Substitutions.” Bioinformatics 25.21 (2009): 2744-750. Link

Sadat, M. A., S. Dirscherl, L. Sastry, J. Dantzer, N. Pech, T. Griffin, Y. Hawkins, C. N. Zhao, A. Barese, C. Cross, W. S. Orazi, M. C. An, X. Goebel, M. Yoder, K. Li, S. D. Grez, MA Cornetta, S. Mooney, and L. Dinauer. “Retroviral Vector Integration in Post-transplant Hematopoiesis in Mice Conditioned with Either Submyeloablative or Ablative Irradiation.” Gene Therapy 16.12 (2009): 1452-464. Link

Hawkins, Troy B., Mohammed A. Sadat, Jessica Dantzer, Ken Cornetta, Sean D. Mooney, and Mary C. Dinauer. “Functional Analysis of Retroviral Vector Integration Sites in the Treatment of Murine X-Linked Chronic Granulomatous Disease Using Gene Ontology.” Molecular Therapy 17 (2009): S35. Link

Sanford, Jeremy R., Xin Wang, Matthew Mort, Natalia Vanduyn, David N. Cooper, Sean D. Mooney, Howard J. Edenberg, and Yunlong Liu. “Splicing Factor SFRS1 Recognizes a Functionally Diverse Landscape of RNA Transcripts.” Genome Research 19.3 (2009): 381-94. Link

Chen, Jake Y Y., Eunseog D. Youn, and Sean D Mooney. “Connecting Protein Interaction Data, Mutations, and Disease Using Bioinformatics.” Methods in Molecular Biology (Clifton, N.J.) 541 (2009): 449-61. Link

2008

Sinthuwiwat, Thivaratana, Phanasit Poowasanpetch, Angsana Wongngamrungroj, Somying Promso, Chirayu Auewarakul, Sean Mooney, and Chintana Tocharoentanaphol. “High-resolution Melting Curve Analysis for Genotyping of Common SNP in MTHFR Gene Using Fixed-cell Suspension.” Molecular And Cellular Probes 22.5-6 (2008): 329-32. Link

Si, Yue, Anna C Pulliam, Yvonne Linka, Samantha Ciccone, Cordula Leurs, Jin Yuan, Olaf Eckermann, Stefan Fruehauf, Sean Mooney, Helmut Hanenberg, and D Wade Clapp. “Overnight Transduction with Foamyviral Vectors Restores the Long-term Repopulating Activity of Fancc-/- Stem Cells.” Blood 112.12 (2008): 4458-65. Link

Radivojac Predrag, Peng Kang, Clark Wyatt, Peters Brandon, Mohan Amrita, Boyle Sean, and Mooney Sean. “Predicting Protein-Disease Relationships Using Sequence, Physicochemical Properties, and Molecular Function Information.” (2008). Link

Radivojac, Predrag, Peter H. Baenziger, Maricel G. Kann, Matthew E. Mort, Matthew W. Hahn, and Sean D. Mooney. “Gain and Loss of Phosphorylation Sites in Human Cancer.” Bioinformatics 24.16 (2008): I241-247. Link

Radivojac, Predrag, Kang Peng, Wyatt T. Clark, Brandon J. Peters, Amrita Mohan, Sean M. Boyle, and Sean D. Mooney. “An Integrated Approach to Inferring Gene–disease Associations in Humans.” Proteins: Structure, Function, and Bioinformatics 72.3 (2008): 1030-037. Link

B Peters, S Dirscherl, J Dantzer, J Nowacki, S Cross, X Li, K Cornetta, M C Dinauer, and S D Mooney. “Automated Analysis of Viral Integration Sites in Gene Therapy Research Using the SeqMap Web Resource.” Gene Therapy 15.18 (2008): 1294. Link

Firpi, Eunseog Youn, and Mooney. “Comparative Study of Particle Swarm Approaches for the Prediction of Functionally Important Residues in Protein Structures.” Advanced Information Networking and Applications – Workshops, 2008. AINAW 2008. 22nd International Conference on (2008): 714-19. Link

Wang, X, Wang, Gh, Shen, Cy, Li, L, Wang, Xg, Mooney, SD, Edenberg, Hj, Sanford, Jr, and Liu, Yl. “Using RNase Sequence Specificity to Refine the Identification of RNA-protein Binding Regions.” Bmc Genomics 9 (2008). Link

Chintana Tocharoentanaphol, Somying Promso, Dianna Zelenika, Tassanee Lowhnoo, Sissades Tongsima, Thanyachai Sura, Wasun Chantratita, Fumihiko Matsuda, Sean Mooney, and Anavaj Sakuntabhai. “Evaluation of Resequencing on Number of Tag SNPs of 13 Atherosclerosis-related Genes in Thai Population.” Journal of Human Genetics 53.1 (2008): 74. Link

Singh, Arti, Adebayo Olowoyeye, Peter H. Baenziger, Jessica Dantzer, Maricel G. Kann, Predrag Radivojac, Randy Heiland, and Sean D. Mooney. “MutDB: Update on Development of Tools for the Biochemical Analysis of Genetic Variation.” Nucleic Acids Research 36 (2008): D815-819. Link

Mooney, Sean D., and Peter H. Baenziger. “Extensible Open Source Content Management Systems and Frameworks: A Solution for Many Needs of a Bioinformatics Group.” Briefings In Bioinformatics 9.1 (2008): 69-74. Link

2007

Altman, Russ, Neal Benowitz, David Gurwitz, Jeantine Lunshof, Mary Relling, Eric Wieben, Sean Mooney, Scott Weiss, Julie Johnson, Howard McLeod, Alan Shuldiner, Dan Roden, Ronald Krauss, and Mark Ratain. “Genetic Nondiscrimination Legislation: A Critical Prerequisite for Pharmacogenomics Data Sharing.” Pharmacogenomics 8.5 (2007): 519. Link

Youn, Eunseog, Brandon Peters, Predrag Radivojac, and Sean D. Mooney. “Evaluation of Features for Catalytic Residue Prediction in Novel Folds.” Protein Science 16.2 (2007): 216-26. Link

Heiland, Randy; Mooney, Sean; Boverhof, Joshua; Jackson, Keith; Swat, Maciek; Balter, Ariel; Christie, Marcus; Insley, Joseph. “Python for scientific gateways development.” Grid Computing Environments (2007). Link

2006

Sadat, Mohammed, Sara Dirscherl, Nancy Pech, Robert Getty, Scott Cross, Cecilia Barese, W. Scott Goebel, Mervin C. Yoder, Sean Mooney, Manuel Grez, Kenneth Cornetta, and Mary C. Dinauer. “Biased Engraftment of Retrovirus-transduced Marrow in Murine X-CGD following Submyeloablative Conditioning.” Blood 108.11 (2006): 937A-38A. Link

Peters, Brandon, Charles Moad, Eunseog Youn, Kris Buffington, Randy Heiland, and Sean Mooney. “Identification of Similar Regions of Protein Structures Using Integrated Sequence and Structure Analysis Tools.” BMC Structural Biology 6 (2006): 4. Link

Farrow, Emily G., Siobhan I. Davis, Sean D. Mooney, Peter Beighton, Leo Mascarenhas, Yvonne R. Gutierrez, Pisit Pitukcheewanont, and Kenneth E. White. “Extended Mutational Analyses of FGFR1 in Osteoglophonic Dysplasia.” American Journal of Medical Genetics Part A 140.5 (2006): 537-39. Link

2005

Mooney, Sean D., Mike Hsin‐Ping Liang, Rob DeConde, and Russ B. Altman. “Structural Characterization of Proteins Using Residue Environments.” Proteins: Structure, Function, and Bioinformatics 61.4 (2005): 741-47. Link

Sadat, Barese, Pech, Goebel, Yoder, Mooney, Cornetta, Grez, and Dinauer. “Reconstitution of Neutrophil NADPH Oxidase Activity in Murine X-CGD following Transplantation of Retrovirus-transduced Marrow: Potential Impact of Submyeloablative Conditioning.” Blood 106.11 (2005): 853A-54A. Link

Larsson, Tem, SS Davis, Hj Garringer, SD Mooney, MS Draman, Mj Cullen, and Ke White. “FGF23 Mutants Causing Familial Ttumoral Calcinosis Are Differentially Processed.” Journal Of Bone And Mineral Research 20.9 (2005): S98. Link

Larsson, T., Si Davis, Hj Garringer, SD Mooney, MS Draman, Mj Cullen, and Ke White. “Fibroblast Growth Factor-23 Mutants Causing Familial Tumoral Calcinosis Are Differentially Processed.” Endocrinology 146.9 (2005): 3883-891. Link

Dantzer, Jessica, Charles Moad, Randy Heiland, and Sean Mooney. “MutDB Services: Interactive Structural Analysis of Mutation Data.” Nucleic Acids Research 33.Web Server Issue (2005): W311-314. Link

Larsson, T., Xj Yu, Si Davis, MS Draman, SD Mooney, Mj Cullen, and Ke White. “A Novel Recessive Mutation in Fibroblast Growth Factor-23 Causes Familial Tumoral Calcinosis.” Journal Of Clinical Endocrinology & Metabolism 90.4 (2005): 2424-427. Link

Mooney, S. “Bioinformatics Approaches and Resources for Single Nucleotide Polymorphism Functional Analysis.” Briefings In Bioinformatics 6.1 (2005): 44-56. Link 

Babbitt, Patricia C, Philip E Bourne, and Sean D Mooney. “Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular Structure.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2005): 319-21. Link

2004

Mooney, Sean. “Bioinformatics for Geneticists.” Briefings in Bioinformatics 5.2 (2004): 209-10. Link

Sean D. Mooney, PE Bourne, PC Babbitt. “INTRODUCTION TO INFORMATICS APPLICATIONS IN STRUCTURAL GENOMICS.” Proceedings of the Pacific Symposium (2004). Link

Babbitt, Patricia C, Philip E Bourne, and Sean D Mooney. “Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular Structure.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2004): 372-74. Link

2003

Mooney, Sean. “Microarrays for an Integrative Genomics.” Briefings in Bioinformatics 4.4 (2003): 383-84. Link

Mooney, SD, and Rb Altman. “MutDB: Annotating Human Variation with Functionally Relevant Data.” Bioinformatics 19.14 (2003): 1858-860. Link

Knudsen, Gm, CR Nishida, SD Mooney, and PRO De Montellano. “Nitric-oxide Synthase (NOS) Reductase Domain Models Suggest a New Control Element in Endothelial NOS That Attenuates Calmodulin-dependent Activity.” Journal Of Biological Chemistry 278.34 (2003): 31814-1824. Link

Hewett, Rattikorn, John Leuchner, Sean D. Mooney, and Teri E. Klein. “Analysis of Mutations in the COLIA1 Gene with Second-Order Rule Induction.” International Journal of Pattern Recognition and Artificial Intelligence (IJPRAI) 17.05 (2003): 721-40. Link

Knudsen, Gm, CR Nishida, SD Mooney, and PRO De Montellano. “Nitric-oxide Synthase (NOS) Reductase Domain Models Suggest a New Control Element in Endothelial NOS That Attenuates Calmodulin-dependent Activity.” Journal Of Biological Chemistry 278.34 (2003): 31814-1824. Link

Mooney, Sean D D., Teri E E. Klein, Russ B B. Altman, Mark A A. Trifiro, and Bruce Gottlieb. “A Functional Analysis of Disease-associated Mutations in the Androgen Receptor Gene.” Nucleic Acids Research 31.8 (2003): E42. Link

Giselle M Knudsen, Clinton R Nishida, Sean D Mooney, Paul R Ortiz de Montellano.”ENZYME CATALYSIS AND REGULATION-Nitric-oxide Synthase (NOS) Reductase Domain Models Suggest a New Control Element in Endothelial NOS That Attenuates Calmodulin-dependent Activity.” Journal of Biological Chemistry 278.34 (2003): 31814-31824. Link

2002

Mooney, SD, and Te Klein. “Structural Models of Osteogenesis Imperfecta-associated Variants in the COL1A1 Gene.” Molecular & Cellular Proteomics 1.11 (2002): 868-75. Link

Mooney, SD, and Te Klein. “The Functional Importance of Disease-associated Mutation.” Bmc Bioinformatics 3 (2002): Bmc Bioinformatics, 2002, Vol.3. Link

Mooney, Sean D., Peter A. Kollman, and Teri E. Klein. “Conformational Preferences of Substituted Prolines in the Collagen Triple Helix.” Biopolymers 64.2 (2002): 63-71. Link

Rattikorn Hewett, John Leuchner, Choh Man Teng, Sean D Mooney, Teri E Klein. “Compression-Based Induction and Genome Data.” Proceedings of the Fifteenth International Florida Artificial Intelligence Research Society Conference (2002): 344-348. Link

Mooney, SD, PA Kollman, and Te Klein. “Conformational Preferences of Substituted Proline Residues in the Triple Helix of Collagen.” Abstracts Of Papers Of The American Chemical Society 222 (2001): U415-416. Link

2001

Mooney, SD, Cc Huang, PA Kollman, and Te Klein. “Computed Free Energy Differences between Point Mutations in a Collagen-like Peptide.” Biopolymers 58.3 (2001): 347-53. Link

Encyclopedia

Sean Mooney, Jeffery T. Chang. “Encyclopedia of Biopharmaceutical Statistics”. Link