Below is a list of the lab’s publications. See also the lab pre-prints (more recent work at various stages of manuscript preparation and/or peer-review).

Recent publications

  • Tacrolimus rescues the signaling and gene expression signature of endothelial ALK1 loss-of-function and improves HHT vascular pathology.Santiago Ruiz, Pallavi Chandakkar, Haitian Zhao, Prodyot K Chatterjee, Erica Christen, Christine N. Metz, Lionel Blanc, Fabien Campagne, Philippe Marambaud. Human Molecular Genetics, in press.
  • A mouse model of hereditary hemorrhagic telangiectasia generated by transmammary-delivered immunoblocking of BMP9 and BMP10. Ruiz S, Zhao H, Chandakkar P, Chatterjee PK, Papoin J, Blanc L, Metz CN, Campagne F, Marambaud P. Sci Rep. 2016 Nov 22;5:37366. doi: 10.1038/srep37366.

  • Exome Sequencing and Prediction of Long-Term Kidney Allograft Function. Mesnard L, Muthukumar T, Burbach M, Li C, Shang H, Dadhania D, Lee JR, Sharma VK, Xiang J, Suberbielle C, Carmagnat M, Ouali N, Rondeau E, Friedewald JJ, Abecassis MM, Suthanthiran M, Campagne F. PLoS Comput Biol. 2016 Sep 29;12(9):e1005088. doi: 10.1371/journal.pcbi.1005088. eCollection 2016 Sep.

  • Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA. Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. JAMA Oncol. 2015 Jul;1(4):466-74. doi: 10.1001/jamaoncol.2015.1313.
  • Heineman TE, Evans DG, Campagne F, Selesnick SH. In Silico Analysis of NF2 Gene Missense Mutations in Neurofibromatosis Type 2: From Genotype to Phenotype. Otol Neurotol. 2015 Jun;36(5):908-14. doi: 10.1097/MAO.0000000000000639
  • Victoria M. Benson and Fabien Campagne. Language Workbench user interfaces for data analysis. PeerJ. in press 2015.
  • Nyasha Chambwe, Matthias Kormaksson, Huimin Geng, Subhajyoti De, Franziska Michor, Nathalie Johnson, Ryan Morin, David Scott, Lucy Godley, Randy Gascoyne, Ari Melnick, Fabien Campagne*, Rita Shaknovich*. Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood. 2015 [PubMed].
  • Effect of the CALHM1 G330D and R154H human variants on the control of cytosolic Ca2+ and Aβ levels. Vingtdeux V, Tanis JE, Chandakkar P, Zhao H, Dreses-Werringloer U, Campagne F, Foskett JK, Marambaud P. PLoS One. 2014 Nov 11;9(11):e112484. doi: 10.1371/journal.pone.0112484. eCollection 2014.
  • Manuele Simi and Fabien Campagne. Composable languages for bioinformatics: the NYoSh experiment. PeerJ. 2014. doi:10.7717/peerj.241.

  • Fabien Campagne, Kevin C. Dorff, Nyasha Chambwe, James T. Robinson, Jill P. Mesirov. Compression of structured high-throughput sequencing data. PLOS One, 2013, 8(11): e79871. doi:10.1371/journal.pone.0079871
  • Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Manuele Simi, Rita Shaknovich, and Fabien CampagneGobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLOS One, 2013, 8(7): e69666. doi:10.1371/journal.pone.0069666 [pre-print at arXiv:1211.6666pdf]

Books

Book chapters

  • Filizola M, Visiers I, Skrabanek L, Campagne F, Weinstein H. Functional mechanisms of GPCRs in a structural context. In Molecular Neuropharmacology, Strategies and Methods, Eds., A. Schousboe and H. Bräuner-Osborne, Humana Press. Dec. 2003.
  • Chan E, Campagne F, Applications, Representation and Management of Signaling Pathway Information: Introduction to the SigPath Project. In Introduction to Systems Biology, chapter 19, Ed. Sangdun Choi, Humana Press. ISBN13: 978-1-58829-706-8
  • Deng X, and Campagne F. Biomarker discovery and validation with high-throughput measurement technologies. Statistical Methods in Molecular Biology. Editors: Bang H, Zhou XK, Van Epps HL, Mazumdar M, Humana Press, in press.

All publications (in chronological order)

  1. Campagne, F. and B. Maigret, Multiple sequence alignment in HTML: colored, possibly hyperlinked, compact representations. J Mol Graph Model, 1998. 16(1): p. 6-10, 34-5.
  2. Horn F, Weare J, Beukers MW, Horsch S, Bairoch A, Chen W, Edvardsen O, Campagne F, Vriend G., GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res, 1998. 26(1): p. 275-9.
  3. Campagne, F. and H. Weinstein, Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins. J Mol Graph Model, 1999. 17(3-4): p. 207-13.
  4. Campagne, F., et al., Visualisation and integration of G protein-coupled receptor related information help the modelling: description and applications of the Viseur program. J Comput Aided Mol Des, 1999 13(6): p. 625-43.
  5. Konvicka, K., F. Campagne, and H. Weinstein, Interactive construction of residue-based diagrams of proteins: the RbDe web service. Protein Eng, 2000. 13(6): p. 395-6.
  6. Campagne, F., Clustalnet: the joining of clustal and CORBA. Bioinformatics, 2000. 16(7): p. 606-12.
  7. Max,. M., Shanker, Y.G., Huang, L., Rong, M., Liu, Z., Campagne, F., Weinstein, H., Damak, S. and Margolskee, R.F. Tas1r3, encoding a new candidate taste receptor, is allelic to the sweet responsiveness locus Sac. Nat. Gen. 2001. 28: p58-63
  8. Skrabanek, L. and Campagne F. TissueInfo: high-throughput identification of tissue expression profiles and specificity. Nucleic Acids Res. 2001 Nov 1;29(21):E102-2.
  9. Campagne, F. Interoperability calls for an unusual mix of skills. Nature. 2002 Jul 11;418(6894):125.
  10. Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G. GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res. 2003 Jan 1;31(1):294-7.
  11. Filizola M, Visiers I, Skrabanek L, Campagne F, Weinstein H. Functional mechanisms of GPCRs in a structural context. In Molecular Neuropharmacology, Strategies and Methods, Eds., A. Schousboe and H. Bräuner-Osborne, Humana Press. Dec. 2003,
  12. Skrabanek L, Campagne F, Weinstein H. Building protein diagrams on the web with the Residue-based diagram editor RbDe. Nucleic Acids Res. Jul 2003, 1;31(13):3856-8.
  13. Campagne F, Bettler E, Vriend G, Weinstein H. Batch mode generation of residue-based diagrams of proteins. Bioinformatics. 2003, Sep 22;19(14):1854-1855.
  14. Characterization of the mouse AAVS1 ortholog, Dutheil N, Yoon-Robarts M, Ward P, Henckaerts E, Skrabanek L, Berns KI, Campagne F, and Linden RM, J. Virol. 2004 Aug;78(16):8917-21.
  15. Quantitative information management for the biochemical computation of cellular networks. Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Science STKE. 2004 Aug 24;(248):pl11.
  16. Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Marco Palma, Juan Zurita, Julian Ferreras, Stefan Worgall,  Lei Shi, Fabien Campagne, and Luis E. N. Quadri. Infection and Immunity. 2005 73(5):2958-66.
  17. T1r3 a novel taste receptor. Robert Margolskee, Marianna Max, Harel Weinstein, Fabien Campagne, Gopi Y. Shanker. US Patent #20040219632 11/04/2004.
  18. Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. Srdanovic, M., Schenk, U., Schwieger, M., Campagne, F. BMC Bioinformatics 2005, 6:5.
  19. Building a protein name dictionary from full text: a machine learning term extraction approach. Lei Shi, Fabien Campagne BMC Bioinformatics 2005, 6:88.
  20. Crooked tail (Cd) Model of Human Folate Responsive NTD is Mutated in Wnt Co-receptor LRP6. Carter M, Chen X, Minnerath S, Slowinska B, Glickstein S, Shi L, Campagne F, Weinstein H and Ross ME. Proc Natl Acad Sci USA 2005 Sep 6;102(36):12843-8.
  21. Minimal Information Requested In the Annotation of biochemical Models (MIRIAM). N Le Novère, N. Finney, A. Hucka, M. Bhalla, U. Campagne, F. Collado-Vides, J. Crampin, E. Halstead, M. Klipp, E. Mendes, P. Nielsen, P. Sauro, H. Shapiro B., Snoep, J.L. Spence, H.D. Wanner, B.L. Nat Biotechnol. 2005 Dec;23(12):1509-15.
  22. SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Gang Hao, Behrad Derakhshan, Lei Shi, Fabien Campagne and Steven S. Gross. Proc Natl Acad Sci U S A. 2006 Feb; 103(4):1012-17.
  23. Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies vesicular transport and cell junction proteins as differentially expressed genes. Stephen Rohan, Jiangling J. Tu, Jean Kao, Piali Mukherjee, Fabien Campagne, Xi K. Zhou, Elizabeth Hyjek, Miguel A. Alonso, Yao-Tseng Chen. Clin. Cancer Res.. 2006.
  24. Mining expressed sequence tags identifies cancer markers of clinical interest. Campagne F, Skrabanek L. BMC Bioinformatics. 2006 Nov 1;7(1):481.
  25. Lucy Skrabanek, Marta Murcia, Michel Bouvier, Lakshmi Devi, Susan R George, Martin J Lohse, Graeme Milligan, Richard Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend, Jonathan A Javitch, Fabien Campagne and Marta Filizola. Requirements and Ontology for a G Protein-Coupled Receptor Oligomerization Knowledge Base. BMC Bioinformatics. 2007, 8:177
  26. Eliza Chan and Fabien Campagne. Applications, representation and management of signaling pathway information. Introduction to the SigPath project. Introduction to Systems Biology, chapter 19. Humana Press. July 2007, Humana Press. ISBN13: 978-1-58829-706-8
  27. Fabien Campagne. Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols. BMC Bioinformatics. 2008 Feb 29;9:132.
  28. Beyond TissueInfo: Functional Prediction using Tissue Expression Profile Similarity Searches
  29. Daniel Aguilar, Lucy Skrabanek, Steven S. Gross, Baldomero Oliva, Fabien Campagne. Nucleic Acids Research, 2008 Jun; 36(11):3728-37
  30. Ute Dreses-Werringloer, Jean-Charles Lambert, Valérie Vingtdeux, Haitian Zhao, Horia Vais, Adam Siebert, Ankit Jain, Jeremy Koppel, Anne Rovelet-Lecrux, Didier Hannequin, Florence Pasquier, Daniela Galimberti, Elio Scarpini, David Mann, Corinne Lendon, Dominique Campion, Philippe Amouyel, Peter Davies, J. Kevin Foskett, Fabien Campagne, and Philippe Marambaud. A polymorphism in CALHM1 influences Ca2+ homeostasis, Ab levels, and Alzheimer’s disease risk. Cell, 2008 Jun 27;133(7):1149-61.
  31. LIM Kinase and Cofilin regulate actin filament population required for dynamin-dependent apical carrier fission for TGN. Susana B. Salvarezza, Sylvie Deborde, Ryan Schreiner, Fabien Campagne, Michael M. Kessels, Britta Qualmann, Alfredo Caceres, Geri Kreitzer and Enrique Rodriguez-Boulan, Mol Biol Cell. 2009 Nov 19.
  32. [CALHM1, a novel gene to blame in Alzheimer disease.] Lambert JC, Campagne F, Marambaud P. Médecine et Sciences (Paris). 2008 Nov;24(11):923-924. French.
  33. Xutao Deng and Fabien Campagne, Biomarker discovery and validation with high-throughput measurement technologies. Book chapter. Humana Press. Statistical Methods in Molecular Biology: a Beginner’s Guide, in press.
  34. Response: CALHM1 Association with Alzheimer’s Disease Risk Fabien Campagne, Jean-Charles Lambert, Ute Dreses-Werringloer, Valérie Vingtdeux, Corinne Lendon, Dominique Campion, Philippe Amouyel, Annette T. Lee, Peter K. Gregersen, Peter Davies and Philippe Marambaud. Cell, 2008.
  35. 34. Xutao Deng and Fabien Campagne. Biomarker discovery and validation with high-throughput measurement technologies. Statistical Methods in Molecular Biology. Editors: Bang H, Zhou XK, Van Epps HL & Mazumdar M, Human Press, in press.
  36. Alex Kentsis, Flavio Monigatti, Kevin Dorff, Fabien Campagne, Richard Bachur, Hanno Steen. Urine proteomics for profiling of human disease using high accuracy mass spectrometry. Proteomics Clinical Applications, 2009, 3, 1052–1061.
  37. Alex Kentsis, Yin Yin Lin, Kyle Kurek, Monica Calicchio, Yan Yan Wang, Flavio Monigatti, Fabien Campagne, Richard Lee, Bruce Horwitz, Hanno Steen, Richard Bachur. Discovery and validation of urine markers of acute pediatric appendicitis using high accuracy mass spectrometry. Annals of Emergency Medicine, 2009 Jun 25.
  38. Maria E. Figueroa, Sanne Lugthart, Yushan Li, Claudia Erpelinck-Verschueren, Xutao Deng, Paul J. Christos, Elizabeth Schifano, James Booth, Wim van Putten, Lucy Skrabanek, Fabien Campagne, Madhu Mazumdar, John M. Greally, Peter J.M. Valk, Bob Löwenberg, Ruud Delwel, and Ari Melnick. DNA methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia. Cancer Cell, Cancer Cell. 2010 Jan 19;17(1):13-27.
  39. George Khelashvili, Kevin Dorff et al. GPCR-OKB: The G Protein Coupled Receptor Oligomer Knowledge Base. Bioinformatics (2010) Jul 15;26(14):1804-5 [Pubmed]
  40. MAQC Consortium, Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 2010 Jul 30 [Pubmed]
  41. Kevin C. Dorff, Nyasha Chambwe, Marko Srdanovic and Fabien Campagne. BDVal: reproducible large scale predictive model development and validation in high-throughput datasets. Bioinformatics, in press.
  42. Chapuis J, Vingtdeux V, Campagne F, et al. Growth arrest specific 1 binds to and controls the maturation and processing of the amyloid beta precursor protein. Human Molecular Genetics. 2011.
  43. Koppel J, Campagne F, Vingtdeux V, et al. Calhm1 P86L polymorphism modulates CSF Aβ levels in cognitively healthy individuals at risk for alzheimer s disease. Molecular Medicine. 2011.
  44. Ji-eun Oh, Nyasha Chambwe, Judit Gal, Stuart Andrews, Georgia Gleason, Rita Shaknovich, Ari Melnick, Fabien Campagne, Miklos Toth. Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment. Translational Psychiatry. 2012, in press.
  45. Fabien Campagne, Kevin C. Dorff, Nyasha Chambwe, James T. Robinson, Jill P. Mesirov. Compression of structured high-throughput sequencing data. PLOS One, 2013,  8(11): e79871. doi:10.1371/journal.pone.0079871
  46. Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Manuele Simi, Rita Shaknovich, and Fabien CampagneGobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLOS One, 2013, 8(7): e69666. doi:10.1371/journal.pone.0069666 [pre-print at arXiv:1211.6666pdf]
  47. Manuele Simi and Fabien Campagne. Composable languages for bioinformatics: the NYoSh experiment. PeerJ. 2014. in press. [pre-print at PeerJ]
  48. Nyasha Chambwe, Matthias Kormaksson, Huimin Geng, Subhajyoti De, Franziska Michor, Nathalie Johnson, Ryan Morin, David Scott, Lucy Godley, Randy Gascoyne, Ari Melnick, Fabien Campagne*, Rita Shaknovich*. Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood. 2014.
  49. Victoria M. Benson and Fabien Campagne. Language Workbench user interfaces for data analysis. PeerJ. in press 2015.
  50. Heineman TE, Evans DG, Campagne F, Selesnick SH. In Silico Analysis of NF2 Gene Missense Mutations in Neurofibromatosis Type 2: From Genotype to Phenotype. Otol Neurotol. 2015 Jun;36(5):908-14. doi: 10.1097/MAO.0000000000000639
  51. Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA. Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. JAMA Oncol. 2015 Jul;1(4):466-74. doi: 10.1001/jamaoncol.2015.1313.
  52. Mesnard L, Muthukumar T, Burbach M, Li C, Shang H, Dadhania D, Lee JR, Sharma VK, Xiang J, Suberbielle C, Carmagnat M, Ouali N, Rondeau E, Friedewald JJ, Abecassis MM, Suthanthiran M, Campagne F. Exome Sequencing and Prediction of Long-Term Kidney Allograft Function.  PLoS Comput Biol. 2016 Sep 29;12(9):e1005088. doi: 10.1371/journal.pcbi.1005088. eCollection 2016 Sep.
  53. A mouse model of hereditary hemorrhagic telangiectasia generated by transmammary-delivered immunoblocking of BMP9 and BMP10. Ruiz S, Zhao H, Chandakkar P, Chatterjee PK, Papoin J, Blanc L, Metz CN, Campagne F, Marambaud P. Sci Rep. 2016 Nov 22;5:37366. doi: 10.1038/srep37366.