Levi Waldron

Levi Waldron

Professor of Biostatistics at CUNY Graduate School of Public Health and Health Policy.

Curriculum Vitae
Slides from presentations

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.

2025

  1. Sarhan MS, Antonello G, Weissensteiner H, Mengoni C, Mascalzoni D, Waldron L, Segata N, Fuchsberger C: Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat? Cell 2025, 188(10):2561-2566. (PMID: 40378832)

2024

  1. Basso M, Gori A, Nardella C, Palviainen M, Holcar M, Sotiropoulos I, Bobis-Wozowicz S, D’Agostino VG, Casarotto E, Ciani Y, Suetsugu S, Gualerzi A, Martin-Jaular L, Boselli D, Kashkanova A, Parisse P, Lippens L, Pagliuca M, Blessing M, Frigerio R, Fourniols T, Meliciano A, Fietta A, Fioretti PV, Soroczyńska K, Picciolini S, Salviano-Silva A, Bergese P, Zocco D, Chiari M, Jenster G, Waldron L, Milosavljevic A, Nolan J, Monopoli MP, Witwer KW, Bussolati B, Di Vizio D, Falcon Perez J, Lenassi M, Cretich M, Demichelis F: International Society for Extracellular Vesicles Workshop. QuantitatEVs: multiscale analyses, from bulk to single extracellular vesicle. J Extracell Biol 2024, 3(1):e137. (PMID: 38405579, PMCID: PMC10883470, full-text)
  2. Björk JR, Bolte LA, Maltez Thomas A, Lee KA, Rossi N, Wind TT, Smit LM, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Spector TD, Bataille V, Segata N, Hospers GAP, Weersma RK: Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma. Nat Med 2024, 30(3):785-796. (PMID: 38365950, PMCID: PMC10957474)
  3. Asnicar F, Thomas AM, Passerini A, Waldron L, Segata N: Machine learning for microbiologists. Nat Rev Microbiol 2024, 22(4):191-205. (*co-corresponding) (PMID: 37968359, PMCID: PMC11980903)
  4. Bhosle A, Bae S, Zhang Y, Chun E, Avila-Pacheco J, Geistlinger L, Pishchany G, Glickman JN, Michaud M, Waldron L, Clish CB, Xavier RJ, Vlamakis H, Franzosa EA, Garrett WS, Huttenhower C: Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease. Mol Syst Biol 2024, 20(4):338-361. (PMID: 38467837, PMCID: PMC10987656)
  5. Geistlinger L, Mirzayi C, Zohra F, Azhar R, Elsafoury S, Grieve C, Wokaty J, Gamboa-Tuz SD, Sengupta P, Hecht I, Ravikrishnan A, Gonçalves RS, Franzosa E, Raman K, Carey V, Dowd JB, Jones HE, Davis S, Segata N, Huttenhower C, Waldron L: BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures. Nat Biotechnol 2024, 42(5):790-802. (PMID: 37697152, PMCID: PMC11098749)
  6. Oh S, Gravel-Pucillo K, Ramos M, Davis S, Carey V, Morgan M, Waldron L: AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines. Res Sq 2024, rs.3.rs-4370115. (PMID: 38798429, PMCID: PMC11118690, full-text)
  7. Afiaz A, Ivanov AA, Chamberlin J, Hanauer D, Savonen CL, Goldman MJ, Morgan M, Reich M, Getka A, Holmes A, Pati S, Knight D, Boutros PC, Bakas S, Caporaso JG, Del Fiol G, Hochheiser H, Haas B, Schloss PD, Eddy JA, Albrecht J, Fedorov A, Waldron L, Hoffman AM, Bradshaw RL, Leek JT, Wright C: Best practices to evaluate the impact of biomedical research software-metric collection beyond citations. Bioinformatics 2024, 40(8):btae469. (PMID: 39067017, PMCID: PMC11297485, full-text)
  8. Oh S, Gravel-Pucillo K, Ramos M, Schatz MC, Davis S, Carey V, Morgan M, Waldron L: AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines. F1000Res 2024, 13:1257. (PMID: 39669685, PMCID: PMC11635187, full-text)
  9. Manghi P, Filosi M, Zolfo M, Casten LG, Garcia-Valiente A, Mattevi S, Heidrich V, Golzato D, Perini S, Thomas AM, Montalbano S, Cancellieri S, Waldron L, Hall JB, Xu S, Volfovsky N, Green Snyder L, Feliciano P, Asnicar F, Valles-Colomer M, Michaelson JJ, Segata N, Domenici E: Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders. Nat Commun 2024, 15(1):9743. (PMID: 39528484, PMCID: PMC11555315)
  10. Khleborodova A, Gamboa-Tuz SD, Ramos M, Segata N, Waldron L, Oh S: lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R. Bioinformatics 2024, 40(12):btae707. (PMID: 39585730, PMCID: PMC11665633, full-text)

2023

  1. Eckenrode KB, Righelli D, Ramos M, Argelaguet R, Vanderaa C, Geistlinger L, Culhane AC, Gatto L, Carey V, Morgan M, Risso D, Waldron L: Curated single cell multimodal landmark datasets for R/Bioconductor. PLoS Comput Biol 2023, 19:e1011324. (PMID: 37624866, PMCID: PMC10497156)
  2. Ramos M, Morgan M, Geistlinger L, Carey VJ, Waldron L: RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor. Bioinformatics 2023, 39(6):btad330. (PMID: 37208161, PMCID: PMC10272705, full-text)
  3. Nash D, Rane MS, Robertson MM, Chang M, Kulkarni SG, Zimba R, You W, Berry A, Mirzayi C, Kochhar S, Maroko A, Westmoreland DA, Parcesepe AM, Waldron L, Grov C: Severe acute respiratory syndrome Coronavirus 2 incidence and risk factors in a national, community-based prospective cohort of US adults. Clin Infect Dis 2023, 76:e375–e384. (PMID: 35639911, PMCID: PMC9213857)

2022

  1. Nash D, Qasmieh S, Robertson M, Rane M, Zimba R, Kulkarni SG, Berry A, You W, Mirzayi C, Westmoreland D, Parcesepe A, Waldron L, Kochhar S, Maroko AR, Grov C, CHASING COVID Cohort Study Team: Household factors and the risk of severe COVID-like illness early in the U.S. pandemic. PLoS One 2022, 17:e0271786. (PMID: 35862418, PMCID: PMC9302833)
  2. Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S: GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun 2022, 13:3695. (PMID: 35760813, PMCID: PMC9237024)
  3. Ghazi AR, Sucipto K, Rahnavard A, Franzosa EA, McIver LJ, Lloyd-Price J, Schwager E, Weingart G, Moon YS, Morgan XC, Waldron L, Huttenhower C: High-sensitivity pattern discovery in large, paired multiomic datasets. Bioinformatics 2022, 38:i378–i385. (PMID: 35758795, PMCID: PMC9235493)
  4. Khaliq AM, Erdogan C, Kurt Z, Turgut SS, Grunvald MW, Rand T, Khare S, Borgia JA, Hayden DM, Pappas SG, Govekar HR, Kam AE, Reiser J, Turaga K, Radovich M, Zang Y, Qiu Y, Liu Y, Fishel ML, Turk A, Gupta V, Al-Sabti R, Subramanian J, Kuzel TM, Sadanandam A, Waldron L, Hussain A, Saleem M, El-Rayes B, Salahudeen AA, Masood A: Refining colorectal cancer classification and clinical stratification through a single-cell atlas. Genome Biol 2022, 23:113. (PMID: 35538548, PMCID: PMC9092724)
  5. Lee KA, Thomas AM, Bolte LA, Björk JR, de Ruijter LK, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Leeming ER, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Vijay A, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Bataille V, Hospers GAP, Spector TD, Weersma RK, Segata N: Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nat Med 2022, 28(3):535-544. (PMID: 35228751, PMCID: PMC8938272)
  6. Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, Mosher S, Morgan M, Nekrutenko A, O’Connor BD, Osborn K, Paten B, Patterson C, Tan FJ, Taylor CO, Vessio J, Waldron L, Wang T, Wuichet K: Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom 2022, 2(1):100085. (PMID: 35199087, PMCID: PMC8863334, full-text)

2021

  1. Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C: Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol 2021, 17:e1009442. (PMID: 34784344, PMCID: PMC8714082)
  2. Zimba RN, Romo ML, Kulkarni SG, Berry A, You W, Mirzayi C, Westmoreland DA, Parcesepe AM, Waldron L, Rane MS, Kochhar S, Robertson MM, Maroko AR, Grov C, Nash D: Patterns of SARS-CoV-2 testing preferences in a national cohort in the United States: Latent class analysis of a discrete choice experiment. JMIR Public Health Surveill 2021. (PMID: 34793320, PMCID: PMC8722498, full-text)
  3. Mirzayi C, Renson A, Genomic Standards Consortium, …, Waldron L: Reporting guidelines for human microbiome research: the STORMS checklist. Nat Med 2021, 27:1885–1892. (PMID: 34789871, PMCID: PMC9105086)
  4. Robertson MM, Kulkarni SG, Rane M, Kochhar S, Berry A, Chang M, Mirzayi C, You W, Maroko A, Zimba R, Westmoreland D, Grov C, Parcesepe AM, Waldron L, Nash D, CHASING COVID Cohort Study Team: Cohort profile: a national, community-based prospective cohort study of SARS-CoV-2 pandemic outcomes in the USA-the CHASING COVID Cohort study. BMJ Open 2021, 11:e048778. (PMID: 34548354, PMCID: PMC8458000)
  5. Tomic A, Tomic I, Waldron L, Geistlinger L, Kuhn M, Spreng RL, Dahora LC, Seaton KE, Tomaras G, Hill J, Duggal NA, Pollock RD, Lazarus NR, Harridge SDR, Lord JM, Khatri P, Pollard AJ, Davis MM: SIMON: Open-Source Knowledge Discovery Platform. Patterns (N Y) 2021, 2:100178. (PMID: 33511368, PMCID: PMC7815964, full-text)
  6. Asnicar F, Berry SE, Valdes AM, Nguyen LH, Piccinno G, Drew DA, Leeming E, Gibson R, Le Roy C, Khatib HA, Francis L, Mazidi M, Mompeo O, Valles-Colomer M, Tett A, Beghini F, Dubois L, Bazzani D, Thomas AM, Mirzayi C, Khleborodova A, Oh S, Hine R, Bonnett C, Capdevila J, Danzanvilliers S, Giordano F, Geistlinger L, Waldron L, Davies R, Hadjigeorgiou G, Wolf J, Ordovás JM, Gardner C, Franks PW, Chan AT, Huttenhower C, Spector TD, Segata N: Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat Med 2021. (PMID: 33432175, PMCID: PMC8353542)
  7. Geistlinger L, Csaba G, Santarelli M, Ramos M, Schiffer L, Turaga N, Law C, Davis S, Carey V, Morgan M, Zimmer R, Waldron L: Toward a gold standard for benchmarking gene set enrichment analysis. Brief Bioinform 2021, 22:545-556. (PMID: 32026945, PMCID: PMC7820859)

2020

  1. Geistlinger L, Oh S, Ramos M, Schiffer L, LaRue RS, Henzler CM, Munro SA, Daughters C, Nelson AC, Winterhoff BJ, Chang Z, Talukdar S, Shetty M, Mullany SA, Morgan M, Parmigiani G, Birrer MJ, Qin LX, Riester M, Starr TK, Waldron L: Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma. Cancer Res 2020, 80(20):4335-4345. (PMID: 32747365, PMCID: PMC7572645)
  2. Zhang Y, Bernau C, Parmigiani G, Waldron L: The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models. Biostatistics 2020, 21(2):253-268. (PMID: 30202918, PMCID: PMC7868050)
  3. Oh S, Abdelnabi J, Al-Dulaimi R, Aggarwal A, Ramos M, Davis S, Riester M, Waldron L: HGNChelper: identification and correction of invalid gene symbols for human and mouse. F1000Res 2020, 9:1493. (PMID: 33564398, PMCID: PMC7856679)
  4. Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Hugo J W: Transparency and reproducibility in artificial intelligence. Nature 2020, 586:E14–E16. (PMID: 33057217, PMCID: PMC8144864)
  5. Renson A, Kasselman LJ, Dowd JB, Waldron L, Jones HE, Herd P: Gut bacterial taxonomic abundances vary with cognition, personality, and mood in the Wisconsin Longitudinal Study. Brain Behav Immun Health 2020, 100155. (PMID: 34589897, PMCID: PMC8474555, full-text)
  6. Calgaro M, Romualdi C, Waldron L, Risso D, Vitulo N: Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data. Genome Biol 2020, 21:191. (PMID: 32746888, PMCID: PMC7398076)
  7. Oh S, Geistlinger L, Ramos M, Morgan M, Waldron L, Riester M: Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data. JCO Clin Cancer Inform 2020, 4:321–335. (PMID: 32282230, PMCID: PMC7259876)
  8. Carey VJ, Ramos M, Stubbs BJ, Gopaulakrishnan S, Oh S, Turaga N, Waldron L, Morgan M: Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale. JCO Clin Cancer Inform 2020, 4:472–479. (PMID: 32453635, PMCID: PMC7265787)
  9. Moon JI, Zhang H, Waldron L, Iyer KR: “Stoma or no stoma”: First report of intestinal transplantation without stoma. Am J Transplant 2020. (PMID: 32431016)
  10. Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC: Orchestrating single-cell analysis with Bioconductor. Nat Methods 2020, 17:137–145. (preprint, PMID: 31792435, PMCID: PMC7358058)
  11. Schwede M, Waldron L, Mok SC, Wei W, Basunia A, Merritt MA, Mitsiades CS, Parmigiani G, Harrington DP, Quackenbush J, Birrer MJ, Culhane AC: The impact of stroma admixture on molecular subtypes and prognostic gene signatures in serous ovarian cancer. Cancer Epidemiol Biomarkers Prev 2020, 29(2):509-519. (PDF, PMID: 31871106, PMCID: PMC7448721)

2019

  1. Brown P; RELISH Consortium; Zhou Y: Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database (Oxford) 2019, 2019:baz085. (PMID: 33326193, PMCID: PMC7291946, full-text)
  2. da Silva V, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho L, Zimmer R, Waldron L, Geistlinger L: CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. Bioinformatics 2019. (PMID: 31392308, PMCID: PMC9887538)
  3. Gendoo DMA, Zon M, Sandhu V, Manem VSK, Ratanasirigulchai N, Chen GM, Waldron L, Haibe-Kains B: MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature. Sci Rep 2019, 9:8770. (PMID: 31217513, PMCID: PMC6584731)
  4. 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, 188:1023–1026. (preprint, PMID: 30649166, PMCID: PMC6545282)
  5. Waldron L, Schiffer L, Azhar R, Ramos M, Geistlinger L, Segata N: Reply to “Commentary on the HMP16SData Bioconductor Package.” Am J Epidemiol 2019, 188:1031–1032. (Invited commentary by Griffith and Morgan, PMID: 30689687, PMCID: PMC6545274)
  6. Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE, Waldron L: Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study. Ann Epidemiol 2019, 34:18–25.e3. (preprint, PMID: 31076212, PMCID: PMC6548637)
  7. Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L, Dowd JB: Sociodemographic variation in the oral microbiome. Ann Epidemiol 2019, 35:73–80.e2. (preprint, PMID: 31151886, PMCID: PMC6626698)
  8. Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat Med 2019, 25:667–678. (PDF, PMID: 30936548, PMCID: PMC9533319)
  9. Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G: Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. Nat Med 2019, 25:679–689. (PDF, PMID: 30936547, PMCID: PMC7984229)
  10. 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. (PMID: 30728424, PMCID: PMC6365504)
  11. Gopaulakrishnan S, Pollack S, Stubbs BJ, Pagès H, Readey J, Davis S, Waldron L, Morgan M, Carey V: restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor. F1000Res 2019, 8:21. (PMID: 30828438, PMCID: PMC6392152)
  12. 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 2019, 80(1):46-55. (PMID: 30299346, PMCID: PMC6289598)

2018

  1. Geistlinger L, da Silva VH, Cesar ASM, Tizioto PC, Waldron L, Zimmer R, Regitano LCA, Coutinho LL: Widespread modulation of gene expression by copy number variation in skeletal muscle. Sci Rep 2018, 8(1):1399. (PMID: 29362391, PMCID: PMC5780461)
  2. 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. (PMID: 30473781, PMCID: PMC6234736)
  3. 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. (PMID: 30253799, PMCID: PMC6154428)
  4. 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. (PMID: 30084834, PMCID: PMC6207081)
  5. 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. (PMID: 29788080, PMCID: PMC6118060)
  6. 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. (PMID: 30248136, PMCID: PMC6152971)
  7. Waldron L: Data and Statistical Methods To Analyze the Human Microbiome. mSystems 2018, 3. (PMID: 29556541, PMCID: PMC5850081)
  8. 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. (PMID: 28972691)
  9. 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. (PMID: 29194469, PMCID: PMC6030947)

2017

  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. (PMID: 29088129, PMCID: PMC5862039)
  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. (PMID: 29092936, PMCID: PMC5679241)
  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. (PMID: 28407281, PMCID: PMC5640470)

2016

  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. (PMID: 27923063, PMCID: PMC5140048)
  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. (PMID: 27687735, PMCID: PMC5043525)
  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. (PMID: 27366979, PMCID: PMC5123755)
  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. (PMID: 27381624, PMCID: PMC5241903)
  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. (PMID: 27400279, PMCID: PMC4939962)
  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. (PMID: 27036168)
  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, PMID: 27008014)
  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. (PMID: 26463000, PMCID: PMC4945830)
  9. Ramos M, Gbedemah M, Jones H, Waldron L: Engagement of introductory biostatistics students in a novel hybrid course format. F1000Res 2016, 5:2624. (PMID: 28239459, PMCID: PMC5318556)

2015

  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. (PMID: 25887922, PMCID: PMC4414286)
  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. (PMID: 25944803)
  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. (PMID: 25937617, PMCID: PMC4483460)
  4. Trippa L, Waldron L, Huttenhower C, Parmigiani G: Bayesian nonparametric cross-study validation of prediction methods. Ann Appl Stat 2015, 9:402–428. (PMID: 26640642, PMCID: PMC4662493)
  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. (PMID: 26157642, PMCID: PMC4493686)
  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. (PMID: 25633503, PMCID: PMC4509590)

2014

  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. (PMID: 24843156, PMCID: PMC4050606)
  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. (PMID: 24700803, PMCID: PMC4580556)
  3. Waldron L, Riester M, Birrer M: Molecular subtypes of high-grade serous ovarian cancer: the holy grail? J Natl Cancer Inst 2014, 106(10):dju297. (PMID: 25269490)
  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. (PMID: 25173649)
  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. (PMID: 25061068, PMCID: PMC4201155)
  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. (PMID: 24931973, PMCID: PMC4058929)
  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. (PMID: 24700801, PMCID: PMC4580554)

2013

  1. Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C: Two-stage microbial community experimental design. ISME J 2013, 7:2330–2339. (PMID: 23949665, PMCID: PMC3834858)
  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. (PMID: 23835716)
  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. (PMID: 23459718)
  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. (PMID: 23550061, PMCID: PMC3625954)
  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. (PMID: 23326225, PMCID: PMC3542080)

2012

  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. (PMID: 23136189, PMCID: PMC3500412)
  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. (PMID: 22698087, PMCID: PMC3446314)
  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. (PMID: 22688413, PMCID: PMC3443552)
  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. (PMID: 22427238, PMCID: PMC3345105)
  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. (PMID: 22458912, PMCID: PMC3342119)
  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. (PMID: 22211115, PMCID: PMC3248702)
  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. (PMID: 22130880)

2011

  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. (PMID: 22156367, PMCID: PMC3232376)
  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. (PMID: 21989116, PMCID: PMC3198722)
  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. (PMID: 21873988)
  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. (PMID: 21702898, PMCID: PMC3218848)
  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. (PMID: 21549012, PMCID: PMC3103428)
  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. (PMID: 21393507)

2010

  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. (PMID: 20145181)
  2. 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. (PMID: 20573258, PMCID: PMC2902407)
  3. 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.
  4. 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. (PMID: 19682285)
  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. (PMID: 19290006)
  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.