Publications

N.B. Most of these papers are also indexed on PubMed.
* denotes equal authorship.

Michlmayr D,* Pak TR,* Rahman A, Amir ED, Kim E-Y, Kim-Schulze S, Suprun M, Stewart MG, Thomas G, Balmaseda A, Wang L, Zhu J, Suarez-Farinas M, Wolinsky SM, Kasarskis A, Harris E. “Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases.” Mol Syst Biol. 2018 Aug; 14(8): e7862. doi:10.15252/msb.20177862. [PDF]

Altman D, Sullivan M, Chacko KI, Balasubramanian D, Pak TR, Sause W, Kumar K, Sebra R, Deikus G, Attie O, Rose H, Lewis M, Fulmer Y, Bashir A, Kasarskis A, Schadt EE, Richardson A, Torres V, Shopsin B, van Bakel H. “Genome plasticity of agr-defective Staphylococcus aureus during clinical infection.” Infect Immun. 2018 Jul 30; pii: IAI.00331-18. doi:10.1128/IAI.00331-18.

Chacko K, Sullivan M, Beckford C, Altman D, Ciferri B, Pak TR, Sebra R, Kasarskis A, Hamula C, van Bakel H. “The genetic basis of emerging vancomycin, linezolid, and daptomycin heteroresistance in a case of persistent Enterococcus faecium bacteremia.” Antimicrob Agents Chemother. 2018 Jan 16. pii:AAC.02007-17. doi:10.1128/AAC.02007-17. [PDF]

Pak TR, Chacko KI, O’Donnell T, Huprikar S, van Bakel H, Kasarskis A, Scott ER. “Estimating local costs associated with Clostridium difficile infection using machine learning and electronic medical records.” Infect Control Hosp Epidemiol. 2017 Dec;38(12):1478-1486. doi:10.1017/ice.2017.214. [PDF]

Hamlin RE, Rahman A, Pak TR, Maringer K, Mena I, Bernal-Rubio D, Potla U, Maestre AM, Fredericks AC, Amir ED, Kasarskis A, Ramos I, Merad M, Fernandez-Sesma A. “High-dimensional CyTOF analysis of dengue virus-infected human DCs reveals distinct viral signatures.” JCI Insight. 2017 Jul 6;2(13). pii: 92424. doi: 10.1172/jci.insight.92424. [PDF]

Bashir A, Attie O, Sullivan M, Sebra R, Singh KV, Altman D, Pak TR, Dutta J, Chacko K, Webster E, Lewis M, Hamula C, Delli Carpini KW, Murray BE, Kasarskis A, van Bakel H, Huprikar S. Genomic confirmation of vancomycin-resistant Enterococcus transmission from deceased donor to liver transplant recipient. PLoS One. 2017 Mar 16;12(3):e0170449. doi: 10.1371/journal.pone.0170449. [PDF]

Pak TR, Altman DR, Attie O, Sebra R, Hamula CL, Lewis M, Deikus G, Newman LC, Fang G, Hand J, Patel G, Wallach F, Schadt EE, Huprikar S, van Bakel H, Kasarskis A, Bashir A. “Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.” Antimicrob Agents Chemother. 2015 Aug 31. pii: AAC.01723-15. doi:10.1128/AAC.01723-15. [PDF]

Pak TR, Kasarskis A. “How next-generation sequencing and multiscale data analysis will transform infectious disease management.” Clin Infect Dis. 2015 Aug 6. pii: civ670. doi:10.1093/cid/civ670. [PDF]

Pak TR, Rodriguez MD, Roth FP. “Why clinical trials are terminated.” bioRxiv doi: 10.1101/021543. [PDF]

  • Highlighted in Science: Couzin-Frankel J. “Researchers seek clear reasons when clinical trials end early.” 349(6245):222. doi: 10.1126/science.349.6245.222. [PDF]

Finkelstein M, Siddiqui A, Pak TR, Hu K, Ciccariello C, Knabben V, Chiang D, Thomas DC, Meah YS. “A user-editable web-based platform to streamline clinical information flow.” Stud Health Technol Inform. 2015;210:909-13. doi: 10.3233/978-1-61499-512-8-909. [PDF]

Pak TR, Roth FP. “ChromoZoom: a flexible, fluid, web-based genome browser.” Bioinformatics. 2013 Feb 1;29(3):384-6. doi: 10.1093/bioinformatics/bts695. Epub 2012 Dec 6. [PDF]

Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M. “Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.” Nature. 2012 Jul 26;487(7408):491-5. doi: 10.1038/nature11288. [PDF]

Legendre M, Pochet N, Pak TR, Verstrepen KJ. “Sequence-based estimation of minisatellite and microsatellite repeat variability.” Genome Res. 2007 Dec;17(12):1787-96. Epub 2007 Oct 31. doi: 10.1101/gr.6554007 [PDF]

Camillone N 3rd, Pak TR, Adib K, Osgood RM Jr. “Tuning molecule-surface interactions with sub-nanometer-thick covalently bound organic monolayers.” J Phys Chem B. 2006 Jun 15;110(23):11334-43. doi: 10.1021/jp0606659 [PDF]

Pak TR, Cadet P, Mantione KJ, Stefano GB. “Morphine via nitric oxide modulates beta-amyloid metabolism: a novel protective mechanism for Alzheimer’s disease.” Med Sci Monit. 2005 Oct;11(10):BR357-66. Epub 2005 Sep 26. [PDF]

Presentations

ChromoZoom, a flexible, fluid, web-based genome browser. Workshop speaker, Computational Tools Workshop, Yeast Genetics & Molecular Biology Meeting; Princeton University, August 2012.

UCSC interactive: rethinking the UI of genome browsers. Invited speaker, UCSC Genecats Seminar Series; UC Santa Cruz, April 2012.

Variability of an artificial tandem repeat. Plenary speaker, Harvard Undergraduate Research Symposium; Harvard University, November 2007.