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2015 Published Articles

2015

Bisignano, P., Burford, N.T., Shang, Y., Marlow, B., Livingston, K.E., Fenton, A.M., Rockwell,K., Budenholzer, L., Traynor, J., Gerritz, S.W., Alt, A., and Filizola, M. “Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the mu-Opioid Receptor” (2015) Journal of Chemical Information & Modeling 55(9):1836-43 [PMID:26347990] http://www.ncbi.nlm.nih.gov/pubmed/26347990

Schneider, S., Provasi, D. & Filizola, M. “The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics” (2015) Methods in Molecular Biology, 1335:277-294 [PMID:26260607] http://www.ncbi.nlm.nih.gov/pubmed/26260607

Shang, Y. and Filizola, M. “Opioid receptors: Structural and mechanistic insights into pharmacology and signaling” (2015) European Journal of Pharmacology, http://dx.doi.org/10.1016/j.ejphar.2015.05.012; [PMID: 25981301] http://www.ncbi.nlm.nih.gov/pubmed/25981301

Burford, N., Livingston, K., Canals, M., Ryan, M., Budenholzer, L., Han, Y., Shang, Y., Herbst, J., O’Connell, J., Banks, M., Zhang, L., Filizola, M., Bassoni, D., Wehrman, T., Christopoulos, A., Traynor, J., Gerritz, S., Alt, A. “Discovery, Synthesis and Molecular Pharmacology of Selective Positive Allosteric Modulators of the d-Opioid Receptor” (2015) Journal of Medicinal Chemistry Apr 22. [Epub ahead of print]; [PMID: 25901762] http://www.ncbi.nlm.nih.gov/pubmed/25901762

Provasi, D., Boz, M.B., Johnston, J.M., Filizola, M. “Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association” PLOS Computational Biology (2015) Mar 30;11(3):e1004148; [PMID: 25822938] http://www.ncbi.nlm.nih.gov/pubmed/25822938

R. Osman, M. Mezei, S. Engel, The Role of Protein ‘Stability Patches’ in Molecular Recognition: a Case Study of the Human Growth Hormone-Receptor Complex, J. Comput. Chem., (2015). DOI:10.1002/jcc.24276

M. Mezei, Use of circular variance to quantify the deviation of a macromolecule from the spherical shape, J. Math. Chem., 53, 2184-2189 (2015). DOI:10.1007/s10910-015-0540-4.

M. Mezei, Statistical properties of protein-protein interfaces, Algorithms, 8, 92-99 (2015). DOI:10.3390/a70x000x.

F. Petralia, P. Wang, J. Yang, Z. Tu, “A General Framework of Integrative Random Forest for Gene Regulatory Network Inference”, Bioinformatics 2015, Jun; 15;31(12), i197-205. PMCID: PMC4542785 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542785/

Sia, D., Losic, B., Moeini, A., Cabellos, L., Hao, K., Revill, K., Bonal, D., Miltiadous, O., Zhang, Z., Hoshida, Y., Cornella, H., Castillo-Martin, M., Pinyol, R., Kasai, Y., Roayaie, S., Thung, S.N., Fuster, J., Schwartz, M.E., Waxman, S., Cordon-Cardo, C., Schadt, E., Mazzaferro, V. & Llovet, J.M. (2015) Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma. Nature Communications, 6:6087. PMID: 25608663
http://www.ncbi.nlm.nih.gov/pubmed/25608663

Cornella, H., Alsinet, C., Sayols, S., Zhang, Z., Hao, K., Cabellos, L., Hoshida, Y., Villanueva, A., Thung, S., Ward, S.C., Rodriguez-Carunchio, L., Vila-Casadesús, M., Imbeaud, S., Lachenmayer, A., Quaglia, A., Nagorney, D.M., Minguez, B., Carrilho, F., Roberts, L.R., Waxman, S., Mazzaferro, V., Schwartz, M., Esteller, M., Heaton, N.D., Zucman-Rossi, J. & Llovet, J.M. (2015) Unique genomic profile of fibrolamellar hepatocellular carcinoma. Gastroenterology, 148(4): 806-818. PMCID: PMC4521774
www.ncbi.nlm.nih.gov/pubmed/25557953

Zhang Z., Hao K. (2015) SAAS-CNV: A joint segmentation approach on aggregated and allele specific signals for the identification of somatic copy number alterations with next-generation sequencing data. PLoS Computational Biology, 11(11): e1004618. PMCID: PMC4652904
http://www.ncbi.nlm.nih.gov/pubmed/26583378

Vardabasso C, Gaspar-Maia A, Pünzeler S, Valle-Garcia D, Hasson D, Straub T, Keilhauer EC, Strub T, Dong J, Panda T, Segura M, Chung CY, Yao JL, Singh R, Verma A, Mann M, Hernando E, Hake SB, Bernstein E. Histone variant H2A.Z.2 regulates proliferation and drug sensitivity of malignant melanoma. Molecular Cell 2015, 59(1):75-88.

Qiao W*, Yang Y*, Sebra R, Mendiratta G, Gaedigk A, Desnick RJ, Scott SA. Long-read single molecule real-time (SMRT) full gene sequencing of cytochrome P450-2D6 (CYP2D6). Hum Mutat. 2016;37:315-23. [Epub 2015 Nov 25.] (* equal contribution) PMCID: PMC4752389

Qiao W, Wang J, Pullman BS, Chen R, Yang Y, Scott SA. The CYP2D6 VCF translator. Pharmacogenomics J. [Epub 2016 Mar 15.] PMID: 26975230 http://www.nature.com/tpj/journal/vaop/ncurrent/full/tpj201614a.html

Yang Y, Sebra R, Pullman B, Peter I, Desnick RJ, Geyer CR, DeCoteau JF, Scott SA. Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS). BMC Genomics, 2015 May 6;16:350. PMCID: PMC4422326 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422326/

Schmidt B, Wei L, DePeralta DK, Hoshida Y, Tan PS, Sun X, Sventek JP, Lanuti M, Tanabe KK, Fuchs BC. Molecular subclasses of hepatocellular carcinoma predict sensitivity to fibroblast growth factor receptor inhibition. Int J Cancer. 2016 Mar 15;138(6):1494-505. doi: 10.1002/ijc.29893. Epub 2015 Nov 9. PubMed PMID:
26481559. http://www.ncbi.nlm.nih.gov/pubmed/26481559

Tan PS, Nakagawa S, Goossens N, Venkatesh A, Huang T, Ward SC, Sun X, Song WM, Koh A, Canasto-Chibuque C, Deshmukh M, Nair V, Mahajan M, Zhang B, Fiel MI, Kobayashi M, Kumada H, Hoshida Y. Clinicopathological indices to predict hepatocellular carcinoma molecular classification. Liver Int. 2016 Jan;36(1):108-18. doi: 10.1111/liv.12889. Epub 2015 Jun 29. PubMed PMID: 26058462; PubMed Central PMCID: PMC4674393. http://www.ncbi.nlm.nih.gov/pubmed/26058462

Miltiadous O, Sia D, Hoshida Y, Fiel MI, Harrington AN, Thung SN, Tan PS, Dong H, Revill K, Chang CY, Roayaie S, Byrne TJ, Mazzaferro V, Rakela J, Florman S, Schwartz M, Llovet JM. Progenitor cell markers predict outcome of patients with hepatocellular carcinoma beyond Milan criteria undergoing liver transplantation. J Hepatol. 2015 Dec;63(6):1368-77. doi: 10.1016/j.jhep.2015.07.025. Epub 2015 Jul 26. PubMed PMID: 26220754. http://www.ncbi.nlm.nih.gov/pubmed/26220754

El-Shamy A, Eng FJ, Doyle EH, Klepper AL, Sun X, Sangiovanni A, Iavarone M, Colombo M, Schwartz RE, Hoshida Y, Branch AD. A cell culture system for distinguishing hepatitis C viruses with and without liver cancer-related mutations in the viral core gene. J Hepatol. 2015 Dec;63(6):1323-33. doi: 10.1016/j.jhep.2015.07.024. Epub 2015 Jul 26. PubMed PMID: 26220749; PubMed Central PMCID: PMC4654634. http://www.ncbi.nlm.nih.gov/pubmed/26220749

Finkin S, Yuan D, Stein I, Taniguchi K, Weber A, Unger K, Browning JL,Goossens N, Nakagawa S, Gunasekaran G, Schwartz ME, Kobayashi M, Kumada H, Berger M, Pappo O, Rajewsky K, Hoshida Y, Karin M, Heikenwalder M, Ben-Neriah Y, Pikarsky E. Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma. Nat Immunol. 2015 Dec;16(12):1235-44. doi: 10.1038/ni.3290. Epub 2015 Oct 26. PubMed PMID: 26502405; PubMed Central PMCID: PMC4653079. http://www.ncbi.nlm.nih.gov/pubmed/26502405

Goossens N, Hoshida Y, Song WM, Jung M, Morel P, Nakagawa S, Zhang B, Frossard JL, Spahr L, Friedman SL, Negro F, Rubbia-Brandt L, Giostra E. Nonalcoholic Steatohepatitis Is Associated With Increased Mortality in Obese Patients Undergoing Bariatric Surgery. Clin Gastroenterol Hepatol. 2015 Oct 20. pii: S1542-3565(15)01406-8. doi: 10.1016/j.cgh.2015.10.010. [Epub ahead of print] PubMed PMID: 26492845; PubMed Central PMCID: PMC4838546. http://www.ncbi.nlm.nih.gov/pubmed/26492845

Kocabayoglu P, Zhang DY, Kojima K, Hoshida Y, Friedman SL. Induction and contribution of beta platelet-derived growth factor signalling by hepatic stellate cells to liver regeneration after partial hepatectomy in mice. Liver Int. 2015 Aug 10. doi: 10.1111/liv.12933. [Epub ahead of print] PubMed PMID: 26256287; PubMed Central PMCID: PMC4749477. http://www.ncbi.nlm.nih.gov/pubmed/26256287

King LY, Canasto-Chibuque C, Johnson KB, Yip S, Chen X, Kojima K, Deshmukh M, Venkatesh A, Tan PS, Sun X, Villanueva A, Sangiovanni A, Nair V, Mahajan M, Kobayashi M, Kumada H, Iavarone M, Colombo M, Fiel MI, Friedman SL, Llovet JM, Chung RT, Hoshida Y. A genomic and clinical prognostic index for hepatitis C-related early-stage cirrhosis that predicts clinical deterioration. Gut. 2015 Aug;64(8):1296-302. doi: 10.1136/gutjnl-2014-307862. Epub 2014 Aug 20. PubMed PMID: 25143343; PubMed Central PMCID: PMC4336233. http://www.ncbi.nlm.nih.gov/pubmed/25143343

Kocabayoglu P, Lade A, Lee YA, Dragomir AC, Sun X, Fiel MI, Thung S, Aloman C, Soriano P, Hoshida Y, Friedman SL. ß-PDGF receptor expressed by hepatic stellate cells regulates fibrosis in murine liver injury, but not carcinogenesis. J Hepatol. 2015 Jul;63(1):141-7. doi: 10.1016/j.jhep.2015.01.036. Epub 2015 Feb 9. PubMed PMID: 25678385; PubMed Central PMCID: PMC4475471. http://www.ncbi.nlm.nih.gov/pubmed/25678385

Zhang DY, Goossens N, Guo J, Tsai MC, Chou HI, Altunkaynak C, Sangiovanni A, Iavarone M, Colombo M, Kobayashi M, Kumada H, Villanueva A, Llovet JM, Hoshida Y, Friedman SL. A hepatic stellate cell gene expression signature associated with outcomes in hepatitis C cirrhosis and hepatocellular carcinoma after curative
resection. Gut. 2015 Jun 4. pii: gutjnl-2015-309655. doi: 10.1136/gutjnl-2015-309655. [Epub ahead of print] PubMed PMID: 26045137; PubMed Central PMCID: PMC4848165. http://www.ncbi.nlm.nih.gov/pubmed/26045137

Whalen S, Pandey OP, Pandey G. Predicting protein function and other biomedical characteristics with heterogeneous ensembles. Methods 93(15):92-102.

Pandey G, Arora S, Manocha S, Whalen S. Enhancing the functional content of eukaryotic protein interaction networks. PLoS One 9(10): e109130.

Whalen S, Pandey G. A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics. Proceedings of the IEEE International Conference on Data Mining, pp. 807-816.

Pandey G, Cohain A, Miller J, Merad M. Decoding dendritic cell function through module and network analysis. Journal of Immunological Methods 387(1-2):71-80.

Jinlian Wang, Jun Liao, Jinglan Zhang, Wei-yi Cheng, Jorg Hakenberg, Meng Ma, Bryn D. Webb, Rajasekar Ramasamudram-chakravarthi, Lisa Karger, Lakshmi Mehta, Ruth Kornreich, George A. Diaz, Shuyu Li, Lisa Edelmann, Rong Chen (2015). "ClinLabGeneticist: A tool for clinical management of genetic variants from whole exome sequencing in clinical genetic laboratories." Genome Med 7(1):77.
http://link.springer.com/article/10.1186%2Fs13073-015-0207-6.

Benjamin S. Glicksberg, Li Li, Wei-yi Cheng, Khader Shameer, Jorg Hakenberg, Rafael Castellanos, Meng Ma, Lisong Shi, Hardik Shah, Joel T. Dudley, Rong Chen (2015). "An integrated pipeline for multi-modal discovery of disease relationships." Pac Symp Biocomput. 407-18. http://www.ncbi.nlm.nih.gov/pubmed/25592600

Sean Whalen, Om Prakash Pandey and Gaurav Pandey (2015). "Predicting protein function and other biomedical characteristics with heterogeneous ensembles." Methods. doi:10.1016/j.ymeth.2015.08.016. http://www.sciencedirect.com/science/article/pii/S1046202315300566

"Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia" Antimicrob Agents Chemother. 2015 Aug 31. pii: AAC.01723-15. [Epub ahead of print] PubMed PMID: 26324280. Theodore R. Pak, Oliver Attie, Robert Sebra, Martha Lewis, Gintaras Deikus, Leah C. Newman, Gang Fang, Eric E. Schadt, Harm van Bakel, Andrew Kasarskis, Ali Bashir, et al. http://aac.asm.org/content/early/2015/08/25/AAC.01723-15.full.pdf+html.

M. Mezei,Use of circular variance to quantify the deviation of a macromolecule from the spherical shape, J. Math. Chem., in print (2015). DOI: 10.1007/s10910-015-0540-4. http://link.springer.com/article/10.1007/s10910-015-0540-4/fulltext.html

Webb BD, Wheeler PG, Hagen JJ, Cohen N, Linderman MD, Diaz GA, Naidich TP, Rodenburg RJ, Houten SM, Schadt EE. "Novel, Compound Heterozygous, Single-Nucleotide Variants in MARS2 Associated with Developmental Delay, Poor Growth, and Sensorineural Hearing Loss." Hum Mutat. 2015 Mar 9. doi: 10.1002/humu.22781. [Epub ahead of print] PMID: 25754315. http://www.ncbi.nlm.nih.gov/pubmed/25754315

Brohl AS, Li Li, Andikyan V, Običan SG, Cioffi A, Hao K, Dudley JT, Ascher-Walsh C, Kasarskis A, Maki RG, “Age-Stratified Risk of Unexpected Uterine Sarcoma Following Surgery for Presumed Benign Leiomyoma,” The Oncologist (2015) Mar 12. [Epub ahead of print], The Oncologist

Nonnenmacher M, van Bakel H, Hajjar RJ, Weber T. High Capsid-Genome Correlation Facilitates Creation of AAV Libraries for Directed Evolution. Mol Ther. 2015 Jan 13; doi:10.1038/mt.2015.3. http://www.nature.com/mt/journal/v23/n4/abs/mt20153a.html

Miller MS, Rialdi A, Ho JSY, Tilove M, Martinez-Gil L, Moshkina NP, Peralta Z, Noel J, Melegari C, Maestre AM, Mitsopoulos P, Madrenas J, Heinz S, Benner C, Young JAT, Feagins AR, Basler C, Fernandez-Sesma A, Becherel OJ, Lavin MF, Harm van Bakel*†, Ivan Marazzi*†. Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis. Nat Immunol. 2015 Mar 30;doi:10.1038/ni.3132. http://www.ncbi.nlm.nih.gov/pubmed/25822250

Mezei, M. (2015, April 2). "Statistical Properties of Protein-Protein Interfaces." Algorithms. Multidisciplinary Digital Publishing Institute. doi:10.3390/a8020092. http://www.mdpi.com/1999-4893/8/2/92

Ke Xu, Eric E. Schadt, Katherine S. Pollard, Panos Roussos, and Joel T. Dudley, "Genomic and Network Patterns of Schizophrenia Genetic Variation in Human Evolutionary Accelerated Regions," Mol Biol Evol (2015) doi: 10.1093/molbev/msv031
http://mbe.oxfordjournals.org/content/early/2015/03/15/molbev.msv031

Provasi, D., Boz, M.B., Johnston, J.M., Filizola, M. “Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association” PLOS Computational Biology (2015) Mar 30;11(3):e1004148. http://www.ploscompbiol.org/article/fetchObject.action?uri=info%3Adoi%2F...

Buitrago, L., Rendon, A., Liang, Y., Turro, E., Simeoni, I., Negri, A., ThromboGenomics Consortium, Filizola, M., Ouwehand, W.H., Coller, B.S. “αIIbβ3 Variants Defined by Next Generation Sequencing: Predicting Variants Likely to Cause Glanzmann Thrombasthenia” (2015) Proceedings of the National Academy of Science USA, published ahead of print March 31, 2015, doi:10.1073/pnas.1422238112. http://www.pnas.org/content/early/2015/03/30/1422238112.full.pdf

Simchoni, N. and Cunningham-Rundles, C. "TLR7- and TLR9-Responsive Human B Cells Share Phenotypic and Genetic Characteristics.” The Journal of Immunology April 1, 2015 vol. 194 no. 7 3035-3044. http://www.jimmunol.org/content/194/7/3035.long.

Cunningham-Rundles, C., Simchoni, N., et al. "Clonal and constricted T cell repertoire in Common Variable Immune Deficiency." Clinical Immunology. 2015 Jan 14. pii: S1521-6616(15)00004-2. doi: 10.1016/j.clim.2015.01.002. [Epub ahead of print] Link: http://www.ncbi.nlm.nih.gov/pubmed/25596453

Glicksberg, B. S. et al. "An integrative pipeline for multi-modal discovery of disease relationships." Pac. Symp. Biocomput. 20, 407–18 (2015). Link: http://www.worldscientific.com/doi/pdf/10.1142/9789814644730_0039

Teumer A, Tin A, Sorice R, Gorski M, Yeo NC, Chu AY, Li M, Li Y, Mijatovic V , Ko YA, Taliun D, Luciani A, Chen MH, Yang Q, Foster MC, Olden M, Hiraki LT, Tay o BO, Fuchsberger C, Dieffenbach AK, Shuldiner AR, Smith AV, Zappa AM, Lupo A, Kollerits B, Ponte B, Stengel B, Krämer BK, Paulweber B, Mitchell BD, Hayward C , Helmer C, Meisinger C, Gieger C, Shaffer CM, Müller C, Langenberg C, Ackermann D, Siscovick D; DCCT/EDIC, Boerwinkle E, Kronenberg F, Ehret GB, Homuth G, Waeber G, Navis G, Gambaro G, Malerba G, Eiriksdottir G, Li G, Wichmann HE, Grallert H, Wallaschofski H, Völzke H, Brenner H, Kramer H, Mateo Leach I, Rudan I, Hillege HL, Beckmann JS, Lambert JC, Luan J, Zhao JH, Chalmers J, Coresh J, Denny JC, Butterbach K, Launer LJ, Ferrucci L, Kedenko L, Haun M, Metzger M, Woodward M, Hoffman MJ, Nauck M, Waldenberger M, Pruijm M, Bochud M, Rheinberger M, Verweij N, Wareham NJ, Endlich N, Soranzo N, Polasek O, van der Harst P, Pramstaller PP , Vollenweider P, Wild PS, Gansevoort RT, Rettig R, Biffar R, Carroll RJ, Katz R, Loos RJ, Hwang SJ, Coassin S, Bergmann S, Rosas SE, Stracke S, Harris TB, Corre T, Zeller T, Illig T, Aspelund T, Tanaka T, Lendeckel U, Völker U, Gudnason V, Chouraki V, Koenig W, Kutalik Z, O'Connell JR, Parsa A, Heid IM, Paterson AD, d e Boer IH, Devuyst O, Lazar J, Endlich K, Susztak K, Tremblay J, Hamet P, Jacob H J, Böger CA, Fox CS, Pattaro C, Köttgen A. Genome-wide Association Studies Identif y Genetic Loci Associated With Albuminuria in Diabetes. Diabetes. 2016 Mar;65(3):803-17. doi: 10.2337/db15-1313. Epub 2015 Dec 2. PubMed PMID: 2663173 7; PubMed Central PMCID: PMC4764151.
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CHARGE Consortium; DIAGRAM Consortium; GLGC Consortium; Global-BPGen Consortium; ICBP Consortium; MAGIC Consortium, Chakravarti A, Clegg DJ, Cupples LA, Gordon-Larsen P, Jaquish CE, R ao DC, Abecasis GR, Assimes TL, Barroso I, Berndt SI, Boehnke M, Deloukas P, Fox C S, Groop LC, Hunter DJ, Ingelsson E, Kaplan RC, McCarthy MI, Mohlke KL, O'Connell JR, Schlessinger D, Strachan DP, Stefansson K, van Duijn CM, Hirschhorn JN, Lindgren CM, Heid IM, North KE, Borecki IB, Kutalik Z, Loos RJ. 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