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- A. L. Charbonneau, A. Brady, K. Czajkowski, J. Aluvathingal, S. Canchi, R. Carter, K. Chard, D. J. B. Clarke, J. Crabtree, H. H. Creasy, M. D’Arcy, V. Felix, M. Giglio, A. Gingrich, R. M. Harris, T. K. Hodges, O. Ifeonu, M. Jeon, E. Kropiwnicki, M. C. W. Lim, R. L. Liming, J. Lumian, A. A. Mahurkar, M. Mandal, J. B. Munro, S. Nadendla, R. Richter, C. Romano, P. Rocca-Serra, M. Schor, R. E. Schuler, H. Tangmunarunkit, A. Waldrop, C. Williams, K. Word, S. Sansone, A. Ma’ayan, R. Wagner, I. Foster, C. Kesselman, C. T. Brown, O. White
Making Common Fund data more findable: Catalyzing a Data Ecosystem
GigaScience, (in press) (Sep 2022)
- A. L. Charbonneau, A. Brady, K. Czajkowski, J. Aluvathingal, S. Canchi, R. Carter, K. Chard, D. J. B. Clarke, J. Crabtree, H. H. Creasy, M. D’Arcy, V. Felix, M. Giglio, A. Gingrich, R. M. Harris, T. K. Hodges, O. Ifeonu, M. Jeon, E. Kropiwnicki, M. C. W. Lim, R. L. Liming, J. Lumian, A. A. Mahurkar, M. Mandal, J. B. Munro, S. Nadendla, R. Richter, C. Romano, P. Rocca-Serra, M. Schor, R. E. Schuler, H. Tangmunarunkit, A. Waldrop, C. Williams, K. Word, S. Sansone, A. Ma’ayan, R. Wagner, I. Foster, C. Kesselman, C. T. Brown, O. White
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- Y. Zhang, A. Brady, C. Jones, Y. Song, T. C. Darton, C. Jones, C. J. Blohmke, A. J. Pollard, L. S. Magder, A. Fasano, M. B. Sztein, C. M. Fraser
Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi
mBio Vol. 9, No. 3, p. e00686-18 (May/June 2018) [DOI]
- Y. Zhang, A. Brady, C. Jones, Y. Song, T. C. Darton, C. Jones, C. J. Blohmke, A. J. Pollard, L. S. Magder, A. Fasano, M. B. Sztein, C. M. Fraser
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- J. Lloyd-Price, A. Mahurkar, G. Rahnavard, J. Crabtree, J. Orvis, A. B. Hall, A. Brady, H. H. Creasy, C. McCracken, M. G. Giglio, D. McDonald, E. A. Franzosa, R. Knight, O. White, C. Huttenhower
Strains, functions and dynamics in the expanded Human Microbiome Project
Nature 550, p. 61-66 (Oct 2017) [DOI]
- J. Lloyd-Price, A. Mahurkar, G. Rahnavard, J. Crabtree, J. Orvis, A. B. Hall, A. Brady, H. H. Creasy, C. McCracken, M. G. Giglio, D. McDonald, E. A. Franzosa, R. Knight, O. White, C. Huttenhower
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- E. Eloe-Fadrosh, A. Brady, J. Crabtree, E. Drabek, B. Ma, A. Mahurkar, J. Ravel, M. Haverkamp, A. Fiorino, C. Botelho, I. Andreyeva, P. Hibberd, C. Fraser
Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption
mBio Vol. 6, No. 2, p. e00231-15 (Apr 2015) [DOI]
- E. Eloe-Fadrosh, A. Brady, J. Crabtree, E. Drabek, B. Ma, A. Mahurkar, J. Ravel, M. Haverkamp, A. Fiorino, C. Botelho, I. Andreyeva, P. Hibberd, C. Fraser
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- J. Madan, A. G. Hoen, A. Brady, E. Drabek, E. Mongodin
Aberrant intestinal colonization and microbial metabolic patterns in infancy in CF
Pediatric Pulmonology Vol. 49, p. 418 (Sep 2014)
- J. Madan, A. G. Hoen, A. Brady, E. Drabek, E. Mongodin
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- K. Huang, A. Brady, A. Mahurkar, O. White, D. Gevers, C. Huttenhower, N. Segata
MetaRef: a pan-genomic database for comparative and community microbial genomics
Nucleic Acids Research Vol. 42 (database issue), pp. 617-624 (Jan 2014; Epub Nov 2013) [DOI]
- K. Huang, A. Brady, A. Mahurkar, O. White, D. Gevers, C. Huttenhower, N. Segata
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- S. L. Salzberg, B. Novak, A. Brady, M. Kuch, C. King, H. Poinar, T. Kaye, M. Fitzgibbon, G. Merrihew, M. MacCoss, P. Pevzner, J. Kyowan, M. McIntosh
DNA, dinosaurs and metagenomics: a new tool for mass identification of DNA from fossil bone
Supplement to the online Journal of Vertebrate Paleontology, November 2011 issue, p. 185 (abstract)
(Society of Vertebrate Paleontology, 71st Annual Meeting, November 2011)
- S. L. Salzberg, B. Novak, A. Brady, M. Kuch, C. King, H. Poinar, T. Kaye, M. Fitzgibbon, G. Merrihew, M. MacCoss, P. Pevzner, J. Kyowan, M. McIntosh
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- A. Brady, S. L. Salzberg
PhymmBL expanded: confidence scores, custom databases, parallelization and more
Nature Methods Vol. 8, No. 5, p. 367 (May 2011) [DOI]
- A. Brady, S. L. Salzberg
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- A. Brady, S. L. Salzberg
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
Nature Methods Vol. 6, No. 9, pp. 673-676 (September 2009) [DOI]
- A. Brady, S. L. Salzberg
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- A. Brady, K. Maxwell, N. Daniels, L. Cowen
Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways
PLoS ONE 4(4): e5364, 28 April 2009 [DOI]
/\ A poster describing this paper won a Best Poster Award at RECOMB 2009. /\
- A. Brady, K. Maxwell, N. Daniels, L. Cowen
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- A. Brady
Detecting high-level gene function and inferring genetic pathway relationships using machine learning methods
Doctoral dissertation, Tufts University Department of Computer Science, July 2008
- A. Brady
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- X. Wei, L. Cowen, C. Brodley, A. Brady, D Sculley and D. Slonim
A distance-based method for detecting horizontal gene transfer in whole genomes
Proceedings of the 4th International Symposium on Bioinformatics Research and Applications (ISBRA 2008)
- X. Wei, L. Cowen, C. Brodley, A. Brady, D Sculley and D. Slonim
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- D. Krioukov, kc claffy, K. Fall, A. Brady
On compact routing for the Internet
ACM SIGCOMM Computer Communication Review, Vol. 37, Issue 3, pp. 41-52 (July 2007)
- D. Krioukov, kc claffy, K. Fall, A. Brady
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- A. Brady, L. Cowen
Exact distance labelings yield additive-stretch compact routing schemes
Proceedings of the 20th International Symposium on Distributed Computing (DISC 2006), pp. 339-354
/\ This paper won the Best Student Paper Award at DISC 2006. /\
- A. Brady, L. Cowen
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- A. Brady, L. Cowen
Brief Announcement: Compact routing with additive stretch using distance labelings
Proceedings of the 18th ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2006), p. 233
- A. Brady, L. Cowen
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- A. Brady, L. Cowen
Compact routing on power-law graphs with additive stretch
Proceedings of the 8th Workshop on Algorithm Engineering and Experiments (ALENEX 2006), pp. 119-128 - A. Brady
A compact routing scheme for power-law networks using empirical discoveries in power-law graph topology
Master's thesis, Tufts University Department of Computer Science, May 2005
- A. Brady, L. Cowen