For an always up-to-date publication list, see my Google Scholar profile or My Bibliography on NCBI. Most of my publications are freely available either here, from PubMed Central, or from bioRxiv. If you are unable to access a manuscript, please let me know.


  1. Rosenbaum J, Usyk M, Chen Z, Zolnik CP, Jones HE, Waldron L, Dowd JB, Thorpe LE, Burk RD: Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota. Sci. Rep. 2019, 9:1531.

  2. Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L: HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor. Am. J. Epidemiol. 2019 (pre-print). Commentary by Griffith and Morgan (PDF).

  3. Waldron L, Schiffer L, Azhar R, Ramos M, Geistlinger L, Segata N: Improving Accessibility of the Human Microbiome Project Data Through Integration With R/Bioconductor. Am. J. Epidemiol. 2019. (PDF)


  1. Davis S, Ramos M, Shepherd L, Turaga N, Geistlinger L, Morgan MT, Haibe-Kains B, Waldron L: Orchestrating a community-developed computational workshop and accompanying training materials. F1000Res. 2018;7.

  2. Ma S, Ogino S, Parsana P, Nishihara R, Qian Z, Shen J, Mima K, Masugi Y, Cao Y, Nowak JA, Shima K, Hoshida Y, Giovannucci EL, Gala MK, Chan AT, Fuchs CS, Parmigiani G, Huttenhower C, Waldron L: Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biol. 2018, 19:142.

  3. Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L: Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. Clin. Cancer Res. 2018:clincanres.0784.2018.

  4. Zhang Y, Bernau C, Parmigiani G, Waldron L: The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models. Biostatistics 2018. doi:

  5. Robertson MM, Penrose K, Irvine MK, Robbins RS, Kulkarni S, Braunstein SL, Waldron L, Harriman G, Nash D: Impact of an HIV Care Coordination Program on Durable Viral Suppression. J. Acquir. Immune Defic. Syndr. 2018.

  6. Robertson MM, Waldron L, Robbins RS, Chamberlin S, Penrose K, Levin B, Kulkarni S, Braunstein SL, Irvine MK, Nash D: Using Registry Data to Construct a Comparison Group for Programmatic Effectiveness Evaluation: The New York City HIV Care Coordination Program. Am. J. Epidemiol. 2018, 187:1980–1989.

  7. Nash D, Robertson MM, Penrose K, Chamberlin S, Robbins RS, Braunstein SL, Myers JE, Abraham B, Kulkarni S, Waldron L, Levin B, Irvine MK: Short-term effectiveness of HIV care coordination among persons with recent HIV diagnosis or history of poor HIV outcomes. PLoS One 2018, 13:e0204017.

  8. Waldron L: Data and Statistical Methods To Analyze the Human Microbiome. mSystems 2018, 3.

  9. Raimann JG, Waldron L, Koh E, Miller GA, Sor MH, Gray RJ, Kotanko P: Meta-analysis and commentary: Preemptive correction of arteriovenous access stenosis. Hemodial. Int. 2018, 22:279–280.

  10. McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C: bioBakery: a meta’omic analysis environment. Bioinformatics 2018, 34:1235–1237.


  1. Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, Huttenhower C, Morgan M, Segata N, Waldron L: Accessible, curated metagenomic data through ExperimentHub. Nat. Methods 2017, 14:1023–1024.

  2. Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L: Software for the Integration of Multiomics Experiments in Bioconductor. Cancer Res. 2017, 77:e39–e42.

  3. Gao J, Perlman A, Kalache S, Berman N, Seshan S, Salvatore S, Smith L, Wehrli N, Waldron L, Kodali H, Chevalier J: Multiparametric Quantitative Ultrasound Imaging in Assessment of Chronic Kidney Disease. J. Ultrasound Med. 2017, 36:2245–2256.


  1. Re A, Waldron L, Quattrone A: Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites. PLoS Comput. Biol. 2016, 12:e1005198.

  2. Nelms BD, Waldron L, Barrera LA, Weflen AW, Goettel JA, Guo G, Montgomery RK, Neutra MR, Breault DT, Snapper SB, Orkin SH, Bulyk ML, Huttenhower C, Lencer WI: CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biol. 2016, 17:201.

  3. Spratt DE, Chan T, Waldron L, Speers C, Feng FY, Ogunwobi OO, Osborne JR: Racial/Ethnic Disparities in Genomic Sequencing. JAMA Oncol 2016, 2:1070–1074.

  4. 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.

  5. 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.

  6. 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.

  7. Waldron L, Riester M: Meta-Analysis in Gene Expression Studies. In Statistical Genomics: Methods and Protocols. edited by Mathé E, Davis S New York, NY: Springer New York; 2016, 1418:161–176. (PDF)

  8. 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. 2016, 17:603–615.

  9. Ramos M, Gbedemah M, Jones H, Waldron L: Engagement of introductory biostatistics students in a novel hybrid course format. F1000Res. 2016, 5:2624.


  1. 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.

  2. 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, 21:4960–4969.

  3. 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.

  4. Trippa L, Waldron L, Huttenhower C, Parmigiani G: Bayesian nonparametric cross-study validation of prediction methods. Ann. Appl. Stat. 2015, 9:402–428.

  5. 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.

  6. 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.


  1. 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.

  2. 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.

  3. Waldron L, Riester M, Birrer M: Molecular subtypes of high-grade serous ovarian cancer: the holy grail? J. Natl. Cancer Inst. 2014, 106.

  4. 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.

  5. 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.

  6. 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.

  7. 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.


  1. Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C: Two-stage microbial community experimental design. ISME J. 2013, 7:2330–2339.

  2. 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.

  3. 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.

  4. 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.

  5. 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.


  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.


  1. 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.

  2. 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.

  3. 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.

  4. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C: Metagenomic biomarker discovery and explanation. Genome Biol. 2011, 12:R60.

  5. 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.

  6. 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.

  7. 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.


  1. 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.

  2. 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. 2010, 44:129–147.

  3. 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.

2009 and earlier

  1. 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.

  2. 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.

  3. Waldron L, Cooper P: Modeling of simultaneous unidirectional leaching and reduction of Cr6+ in unfixed CCA treated wood. Wood Sci. Technol. 2008, 42:299.

  4. 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.

  5. Waldron L, Cooper PA, Ung TY: Prediction of long-term leaching potential of preservative-treated wood by diffusion modeling. Holzforschung 2005, 59:90.

  6. 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.

  7. Waldron L, Liu W: Hydrogen-rare gas interactions and Raman line shapes. Journal of the Chinese Chemical Society 2001, 48:439–448.