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Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

Journal Article

Sundermann, L. K.; Wintersinger, J.; Rätsch, G.; Stoye, J.; Morris, Q.
PLoS Computational Biology (2021)

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Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence

Journal Article

Liao, C.; Wang, T.; Maslov, S.; Xavier, J. B.
PLoS Computational Biology (2020)

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Compositional Lotka-Volterra describes microbial dynamics in the simplex

Journal Article

Joseph, T. A.; Shenhav, L.; Xavier, J. B.; Halperin, E.; Pe’er, I.
PLoS Computational Biology (2020)

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Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection

Journal Article

Yan, J.; Estanbouli, H.; Liao, C.; Kim, W.; Monk, J. M.; Rahman, R.; Kamboj, M.; Palsson, B. O.; Qiu, W.; Xavier, J. B.
PLoS Computational Biology (2019)

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BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

Journal Article

Cline, M. S.; Liao, R. G.; Parsons, M. T.; Paten, B.; Alquaddoomi, F.; Antoniou, A.; Baxter, S.; Brody, L.; Cook-Deegan, R.; Coffin, A.; more...
PLoS Genetics (2018)

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Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Journal Article

Nguyen, T. H.; Rustenburg, A. S.; Krimmer, S. G.; Zhang, H.; Clark, J. D.; Novick, P. A.; Branson, K.; Pande, V. S.; Chodera, J. D.; Minh, D. D. L.
PLoS ONE (2018)

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Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network

Journal Article

Yan, J.; Deforet, M.; Boyle, K. E.; Rahman, R.; Liang, R.; Okegbe, C.; Dietrich, L. E. P.; Qiu, W.; Xavier, J. B.
PLoS Computational Biology (2017)

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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Journal Article

Eastman, P.; Swails, J.; Chodera, J. D.; McGibbon, R. T.; Zhao, Y.; Beauchamp, K. A.; Wang, L. P.; Simmonett, A. C.; Harrigan, M. P.; Stern, C. D.; more...
PLoS Computational Biology (2017)

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Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes

Journal Article

Loupasakis, K.; Kuo, D.; Sokhi, U. K.; Sohn, C.; Syracuse, B.; Giannopoulou, E. G.; Park, S. H.; Kang, H.; Rätsch, G.; Ivashkiv, L. B.; more...
PLoS ONE (2017)

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Learning to predict miRNA-mRNA interactions from AGO CLIP sequencing and CLASH data

Journal Article

Lu, Y.; Leslie, C. S.
PLoS Computational Biology (2016)

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