Publications

For the most up-to-date publication list, please see my page on Pubmed or Google Scholar.

Publications

  1. Waldron L, Riester M, Ramos M, Parmigiani G, Birrer M: The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles. J. Natl. Cancer Inst. 2016, 108. (pdf)
  2. Pasolli E, Truong DT, Malik F, Waldron L, Segata N: Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights. PLoS Comput. Biol. 2016, 12:e1004977. (pdf)
  3. Spratt DE, Chan T, Waldron L, Speers C, Feng FY, Ogunwobi OO, Osborne JR: Racial/Ethnic Disparities in Genomic Sequencing. JAMA Oncol 2016. (pdf)
  4. Gao J, Zheng X, Zheng Y-Y, Zuo G-Q, Ran H-T, Auh YH, Waldron L, Chan T, Wang Z-G: Shear Wave Elastography of the Spleen for Monitoring Transjugular Intrahepatic Portosystemic Shunt Function: A Pilot Study. J. Ultrasound Med. 2016, 35:951–958. (pdf)
  5. Waldron L, Riester M: Meta-Analysis in Gene Expression Studies. Methods Mol. Biol. 2016, 1418:161–176. (pdf)
  6. Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DMA, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L: Public data and open source tools for multi-assay genomic investigation of disease. Brief. Bioinform. 2015. (link)
  7. Tyekucheva S, Martin NE, Stack EC, Wei W, Vathipadiekal V, Waldron L, Fiorentino M, Lis RT, Stampfer MJ, Loda M, Parmigiani G, Mucci LA, Birrer M: Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues. J. Mol. Diagn. 2015, 17:374–381. (pdf)
  8. Vathipadiekal V, Wang V, Wei W, Waldron L, Drapkin R, Gillette M, Skates S, Birrer M: Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array. Clin. Cancer Res. 2015. (pdf)
  9. Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C: Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol. 2015, 16:67. (pdf)
  10. Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C: A reproducible approach to high-throughput biological data acquisition and integration. PeerJ 2015, 3:e791. (link)
  11. Trippa L, Waldron L, Huttenhower C, Parmigiani G: Bayesian nonparametric cross-study validation of prediction methods. Ann. Appl. Stat. 2015, 9:402–428. (pdf)
  12. Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M: Orchestrating high-throughput genomic analysis with Bioconductor. Nat. Methods 2015, 12:115–121. (pdf)
  13. Zhao SD, Parmigiani G, Huttenhower C, Waldron L: Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics 2014, 30:3062–3069. (link)
  14. Waldron L, Riester M, Birrer M: Molecular subtypes of high-grade serous ovarian cancer: the holy grail? J. Natl. Cancer Inst. 2014, 106. (pdf)
  15. Re A, Workman CT, Waldron L, Quattrone A, Brunak S: Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells. Stem Cell Res. 2014, 13:316–328. (pdf)
  16. Bernau C, Riester M, Boulesteix A-L, Parmigiani G, Huttenhower C, Waldron L, Trippa L: Cross-study validation for the assessment of prediction algorithms. Bioinformatics 2014, 30:i105–12. (link)
  17. Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C: Relating the metatranscriptome and metagenome of the human gut. Proc. Natl. Acad. Sci. U. S. A. 2014, 111:E2329–38.
  18. Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G: Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. J. Natl. Cancer Inst. 2014, 106. (pdf)
  19. Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim S-H, Michor F, Huttenhower C, Parmigiani G, Birrer MJ: Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. J. Natl. Cancer Inst. 2014, 106. (pdf)
  20. Morgan XC, Segata N, Waldron L: Relating the metatranscriptome and metagenome of the human gut. Proceedings of the 2014.
  21. Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C: Two-stage microbial community experimental design. ISME J. 2013, 7:2330–2339.
  22. Goswami RS, Atenafu EG, Xuan Y, Waldron L, Reis PP, Sun T, Datti A, Xu W, Kuruvilla J, Good DJ, Lai R, Church AJ, Lam WS, Baetz T, Lebrun DP, Sehn LH, Farinha P, Jurisica I, Bailey DJ, Gascoyne RD, Crump M, Kamel-Reid S: MicroRNA signature obtained from the comparison of aggressive with indolent non-Hodgkin lymphomas: potential prognostic value in mantle-cell lymphoma. J. Clin. Oncol. 2013, 31:2903–2911.
  23. Hui ABY, Lin A, Xu W, Waldron L, Perez-Ordonez B, Weinreb I, Shi W, Bruce J, Huang SH, O’Sullivan B, Waldron J, Gullane P, Irish JC, Chan K, Liu F-F: Potentially prognostic miRNAs in HPV-associated oropharyngeal carcinoma. Clin. Cancer Res. 2013, 19:2154–2162.
  24. Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L: curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database 2013, 2013:bat013. (link)
  25. Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE: A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput. Biol. 2013, 9:e1002863.
  26. Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, Golub TR, Fuchs CS, Parmigiani G, Huttenhower C: Expression profiling of archival tumors for long-term health studies. Clin. Cancer Res. 2012, 18:6136–6146. (pdf)
  27. Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C: Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 2012, 9:811–814.
  28. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J: Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 2012, 13:R42.
  29. Yamauchi M, Morikawa T, Kuchiba A, Imamura Y, Qian ZR, Nishihara R, Liao X, Waldron L, Hoshida Y, Huttenhower C, Chan AT, Giovannucci E, Fuchs C, Ogino S: Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum. Gut 2012, 61:847–854.
  30. Waldron L, Simpson P, Parmigiani G, Huttenhower C: Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. BMC Cancer 2012, 12:124.
  31. Singh N, Shirdel EA, Waldron L, Zhang R-H, Jurisica I, Comelli EM: The murine caecal microRNA signature depends on the presence of the endogenous microbiota. Int. J. Biol. Sci. 2012, 8:171–186.
  32. Waldron L, Coller HA, Huttenhower C: Integrative Approaches for Microarray Data Analysis. In Next Generation Microarray Bioinformatics. edited by Wang J, Tan AC, Tian T Humana Press; 2012, 802:157–182.
  33. Waldron L, Pintilie M, Tsao M-S, Shepherd FA, Huttenhower C, Jurisica I: Optimized application of penalized regression methods to diverse genomic data. Bioinformatics 2011, 27:3399–3406.
  34. Reis PP, Waldron L, Perez-Ordonez B, Pintilie M, Galloni NN, Xuan Y, Cervigne NK, Warner GC, Makitie AA, Simpson C, Goldstein D, Brown D, Gilbert R, Gullane P, Irish J, Jurisica I, Kamel-Reid S: A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence. BMC Cancer 2011, 11:437.
  35. Eppert K, Takenaka K, Lechman ER, Waldron L, Nilsson B, van Galen P, Metzeler KH, Poeppl A, Ling V, Beyene J, Canty AJ, Danska JS, Bohlander SK, Buske C, Minden MD, Golub TR, Jurisica I, Ebert BL, Dick JE: Stem cell gene expression programs influence clinical outcome in human leukemia. Nat. Med. 2011, 17:1086–1093.
  36. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C: Metagenomic biomarker discovery and explanation. Genome Biol. 2011, 12:R60.
  37. Reis PP, Waldron L, Goswami RS, Xu W, Xuan Y, Perez-Ordonez B, Gullane P, Irish J, Jurisica I, Kamel-Reid S: mRNA transcript quantification in archival samples using multiplexed, color-coded probes. BMC Biotechnol. 2011, 11:46.
  38. Shi W, Gerster K, Alajez NM, Tsang J, Waldron L, Pintilie M, Hui AB, Sykes J, P’ng C, Miller N, McCready D, Fyles A, Liu F-F: MicroRNA-301 mediates proliferation and invasion in human breast cancer. Cancer Res. 2011, 71:2926–2937.
  39. Goswami RS, Waldron L, Machado J, Cervigne NK, Xu W, Reis PP, Bailey DJ, Jurisica I, Crump MR, Kamel-Reid S: Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples. BMC Biotechnol. 2010, 10:47.
  40. Hui ABY, Lenarduzzi M, Krushel T, Waldron L, Pintilie M, Shi W, Perez-Ordonez B, Jurisica I, O’Sullivan B, Waldron J, Gullane P, Cummings B, Liu F-F: Comprehensive MicroRNA profiling for head and neck squamous cell carcinomas. Clin. Cancer Res. 2010, 16:1129–1139.
  41. Waldron L, Cooper PA, Ung YT: Modeling the leaching of inorganic components of wood preservatives in service. In Environmental Impacts of Treated Wood. edited by Townsend T, Solo-Gabriele H Taylor & Francis; 2010:157–172.
  42. Wilkins O, Waldron L, Nahal H, Provart NJ, Campbell MM: Genotype and time of day shape the Populus drought response. Plant J. 2009, 60:703–715.
  43. Waldron L, Cooper PA: Modeling of simultaneous three-dimensional leaching and chemical reaction of CCA components in unfixed wood exposed to water. Wood Sci. Technol. 2009, 44:129–147.
  44. Hui ABY, Shi W, Boutros PC, Miller N, Pintilie M, Fyles T, McCready D, Wong D, Gerster K, Waldron L, Jurisica I, Penn LZ, Liu F-F: Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues. Lab. Invest. 2009, 89:597–606.
  45. Newman L, Waldron L, Dale A, Carriere K: Sustainable urban community development from the grassroots: Challenges and opportunities in a pedestrian street initiative. Local Environ. 2008, 13:129–139.
  46. Waldron L, Cooper P: Modeling of simultaneous unidirectional leaching and reduction of Cr6+ in unfixed CCA treated wood. Wood Sci. Technol. 2007, 42:299–312.
  47. Waldron L, Cooper PA, Ung TY: Prediction of long-term leaching potential of preservative-treated wood by diffusion modeling. Holzforschung 2005, 59:581–588.
  48. Waldron L, Liu W-K, Le Roy RJ: Collisional broadening and shifting of Raman lines, and the potential energy surface for H2–Ar. Journal of Molecular Structure: THEOCHEM 2002, 591:245–253.
  49. Waldron L, Liu W: Hydrogen-rare gas interactions and Raman line shapes. Journal of the Chinese Chemical Society 2001, 48:439–448.