Joel Dudley is a Consulting Faculty Member in the Division of Systems Medicine in the Department of Pediatrics at Stanford University. His work involves the development of a genomics-based classification of human disease, known as the Genomic Nosology, and other projects in genomic medicine and translational bioinformatics. Prior to joining Butte Lab, Joel was the Chief Technical Officer at the Center for Evolutionary Functional Genomics where he participated in the development of the popular Molecular Evolutionary Genetics Analysis (MEGA) software package.

• Personal website
• MEGA Software
• My twitter Account Page

1. Quantifying multi-ethnic representation in genetic studies of high mortality diseases.
   Chen R, Dudley JT, Ruau D, Butte AJ
   AMIA Summits Transl Sci Proc2012p11-8(2012)
2. Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases.
   Ruau D, Dudley JT, Chen R, Phillips NG, Swan GE, Lazzeroni LC, Clark JD, Butte AJ, Angst MS
   PLoS Comput Biol8pe1002538(2012 Jun)
3. Human genomic disease variants: A neutral evolutionary explanation.
   Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S
   Genome Resp(2012 Jun 4)
4. Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases.
   Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB, Ruau D, Lincoln SE, Bustamante CD, Butte AJ
   PLoS Genet8pe1002621(2012 Apr)
5. Personal omics profiling reveals dynamic molecular and medical phenotypes.
   Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M
   Cell148p1293-307(2012 Mar 16)
6. Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery.
   Dudley JT, Chen R, Sanderford M, Butte AJ, Kumar S
   Mol Biol Evolp(2012 Mar 1)
7. Interpretome: a freely available, modular, and secure personal genome interpretation engine.
   Karczewski KJ, Tirrell RP, Cordero P, Tatonetti NP, Dudley JT, Salari K, Snyder M, Altman RB, Kim SK
   Pac Symp Biocomputp339-50(2012)
8. ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.
   Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ
   Bioinformaticsp(2011 Oct 3)
9. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.
   Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA
   PLoS Genet7pe1002280(2011 Sep)
10. Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease.
    Dudley JT, Sirota M, Shenoy M, Pai RK, Roedder S, Chiang AP, Morgan AA, Sarwal MM, Pasricha PJ, Butte AJ
    Sci Transl Med3p96ra76(2011 Aug 17)
11. Discovery and preclinical validation of drug indications using compendia of public gene expression data.
    Sirota M, Dudley JT, Kim J, Chiang AP, Morgan AA, Sweet-Cordero A, Sage J, Butte AJ
    Sci Transl Med3p96ra77(2011 Aug 17)
12. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations.
    Kumar S, Dudley JT, Filipski A, Liu L
    Trends Genetp(2011 Jul 15)
13. Exploiting drug-disease relationships for computational drug repositioning.
    Dudley JT, Deshpande T, Butte AJ
    Brief Bioinformp(2011 Jun 20)
14. Comparison of Automated and Human Assignment of MeSH Terms on Publicly-Available Molecular Datasets.
    Ruau D, Mbagwu M, Dudley JT, Krishnan V, Butte AJ
    J Biomed Informp(2011 Mar 17)
15. Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes.
    Sharaf RN, Butte AJ, Montgomery KD, Pai R, Dudley JT, Pasricha PJ
    BMC Gastroenterol11p5(2011 Jan 20)
16. Content-based microarray search using differential expression profiles.
    Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ
    BMC Bioinformatics11p603(2010 Dec 21)
17. Matching cancer genomes to established cell lines for personalized oncology.
    Dudley JT, Chen R, Butte AJ
    Pac Symp Biocomputp243-52(2011)
18. An integrative method for scoring candidate genes from association studies: application to warfarin dosing.
    Tatonetti NP, Dudley JT, Sagreiya H, Butte AJ, Altman RB
    BMC Bioinformatics11 Suppl 9pS9(2010 Oct 28)
19. Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays.
    Chen DP, Dudley JT, Butte AJ
    BMC Bioinformatics11 Suppl 9pS4(2010 Oct 28)
20. In silico research in the era of cloud computing.
    Dudley JT, Butte AJ
    Nat Biotechnol28p1181-5(2010 Nov)
21. Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
    Chen R, Sigdel TK, Li L, Kambham N, Dudley JT, Hsieh SC, Klassen RB, Chen A, Caohuu T, Morgan AA, Valantine HA, Khush KK, Sarwal MM, Butte AJ
    PLoS Comput Biol6p(2010 Sep 23)
22. Extreme Evolutionary Disparities Seen in Positive Selection across Seven Complex Diseases.
    Corona E, Dudley JT, Butte AJ
    PLoS One5p(2010 Aug 17)
23. Translational bioinformatics in the cloud: an affordable alternative.
    Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ
    Genome Med2p51(2010 Aug 6)
24. Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks.
    Dudley JT, Schadt E, Sirota M, Butte AJ, Ashley E
    J Cardiovasc Transl Resp(2010 Jul 31)
25. Biomarker and Drug Discovery for Gastroenterology through Translational Bioinformatics.
    Dudley JT, Butte AJ
    Gastroenterologyp(2010 Jul 19)
26. Clinical assessment incorporating a personal genome.
    Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB
    Lancet375p1525-35(2010 May 1)
27. Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets.
    Suthram S, Dudley JT, Chiang AP, Chen R, Hastie TJ, Butte AJ
    PLoS Comput Biol6pe1000662(2010 Feb 5)
28. A quick guide for developing effective bioinformatics programming skills.
    Dudley JT, Butte AJ
    PLoS Comput Biol5pe1000589(2009 Dec)
29. Dynamism in Gene Expression Across Multiple Studies.
    Morgan AA, Dudley JT, Deshpande T, Butte AJ
    Physiol Genomicsp(2009 Nov 17)
30. Disease signatures are robust across tissues and experiments.
    Dudley JT, Tibshirani R, Deshpande T, Butte AJ
    Mol Syst Biol5p307(2009)
31. Identification of discriminating biomarkers for human disease using integrative network biology.
    Dudley JT, Butte AJ
    Pac Symp Biocomputp27-38(2009)
32. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease.
    Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ
    Genome Biol9pR170(2008 Dec 5)
33. Using SNOMED-CT for Translational Genomics Data Integration.
    Dudley J, Chen DP, Butte AJ.
    Proceedings of the Third International Conference on Knowledge Representation in Medicine (KR-MED 2008). (PDF)
34. Enabling integrative genomic analysis of high-impact human diseases through text mining.
    Dudley J, Butte AJ
    Pac Symp Biocomputp580-91(2008)
35. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences.
    Kumar S, Nei M, Dudley J, Tamura K
    Brief Bioinform9p299-306(2008 Jul)
36. Bioinformatics software for biologists in the genomics era.
    Kumar S, Dudley J
    Bioinformatics23p1713-7(2007 Jul 15)
37. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
    Tamura K, Dudley J, Nei M, Kumar S
    Mol Biol Evol24p1596-9(2007 Aug)
38. TimeTree: a public knowledge-base of divergence times among organisms.
    Hedges SB, Dudley J, Kumar S
    Bioinformatics22p2971-2(2006 Dec 1)

• Interviewed in Science Careers magazine about job prospects for computational biologists.
• Video interview I did with the Mendelspod show to discuss my new drug discovery startup, NuMedii.
• Wall Street Journal article reporting on our drug repositioning work which was published in Science Translational Medicine
• GenomeWeb article on our cloud computing paper in Nature Biotechnology discussing reproducible computing
• GenomeWeb article on our paper in Genome Medicine discussing translational bioinformatics and cloud computing
• Blog post from famous science writer Carl Zimmer that shows and mentions a figure I created for our Lancet paper analyzing Steve Quake's genome
• Science/AAAS feature article on protein biomarkers that uses images from my PSB protein biomarker network paper.
• GenomeWeb story mentioning some of the work from our lab.
• Quoted in a news item from Emerging Health Threats for my reaction to a paper on disease networks that was published in PLoS Computational Biology.
• Article in the Nov. 2008 issue of The New Scientist on careers in genetics in which I was interviewed.
• Interview by ScienceWatch to discuss our highly-cited MEGA paper in Briefings in Bioinformatics
• A summary of a talk I gave at Stanford was featured on GenomeWeb
• A talk I gave on Bioinformatics at Stanford in 2009 was the topic of Coast to Coast Bio Podcast Episode 13