Benjamin Kaehler

Lecturer of Industrial and Applied Mathematics
Lecturer

Dr Ben Kaehler is a Lecturer of Industrial and Applied Mathematics in the School of Science at UNSW Canberra. He develops mathematical techniques to extract meaning from biological information. He has drawn on the fields of machine learning and stochastic processes to build tools for microbial ecology and create fundamental insights in molecular evolution. He is a core developer for the QIIME 2 microbiome bioinformatics platform and regular contributor to the cogent3 comparative genomics library.

PhD Opportunities and Scholarships

Scholarships of $35,000 (AUD) are available for PhD students who achieved H1/High Distinction in their UG program and/or have completed a Masters by Research.

If you are interested in working on a PhD to develop mathematical, statistical, or computational techniques for analysing biological data contact Dr Ben Kaehler.

PUBLICATIONS

Preprints
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Bokulich NA; Kaehler BD; Rideout JR; Dillon M; Bolyen E; Knight R; Huttley GA; Caporaso JG, 2018, Optimizing taxonomic classification of marker gene amplicon sequences, http://dx.doi.org/10.7287/peerj.preprints.3208
2018
Bolyen E; Rideout JR; Dillon MR; Bokulich NA; Abnet C; Al-Ghalith GA; Alexander H; Alm EJ; Arumugam M; Asnicar F; Bai Y; Bisanz JE; Bittinger K; Brejnrod A; Brislawn CJ; Brown CT; Callahan BJ; Caraballo-Rodríguez AM; Chase J; Cope E; Da Silva R; Dorrestein PC; Douglas GM; Durall DM; Duvallet C; Edwardson CF; Ernst M; Estaki M; Fouquier J; Gauglitz JM; Gibson DL; Gonzalez A; Gorlick K; Guo J; Hillmann B; Holmes S; Holste H; Huttenhower C; Huttley G; Janssen S; Jarmusch AK; Jiang L; Kaehler B; Kang KB; Keefe CR; Keim P; Kelley ST; Knights D; Koester I; Kosciolek T; Kreps J; Langille MG; Lee J; Ley R; Liu Y-X; Loftfield E; Lozupone C; Maher M; Marotz C; Martin BD; McDonald D; McIver LJ; Melnik AV; Metcalf JL; Morgan SC; Morton J; Naimey AT; Navas-Molina JA; Nothias LF; Orchanian SB; Pearson T; Peoples SL; Petras D; Preuss ML; Pruesse E; Rasmussen LB; Rivers A; Robeson, II MS; Rosenthal P; Segata N; Shaffer M; Shiffer A; Sinha R; Song SJ; Spear JR; Swafford AD; Thompson LR; Torres PJ; Trinh P; Tripathi A; Turnbaugh PJ; Ul-Hasan S; van der Hooft JJ; Vargas F; Vázquez-Baeza Y; Vogtmann E; von Hippel M; Walters W; Wan Y; Wang M; Warren J; Weber KC; Williamson CH; Willis AD; Xu ZZ; Zaneveld JR; Zhang Y; Zhu Q; Knight R; Caporaso JG, 2018, QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science, http://dx.doi.org/10.7287/peerj.preprints.27295
2018
Kaehler BD; Yap VB; Huttley GA, 2016, Standard codon substitution models overestimate purifying selection for non-stationary data, http://dx.doi.org/10.7287/peerj.preprints.2218
2016
Kaehler BD, 2016, Full Reconstruction of Non-Stationary Strand-Symmetric Models on Rooted Phylogenies
2016
Buchmann B; Kaehler B; Maller R; Szimayer A, 2015, Multivariate Subordination using Generalised Gamma Convolutions with Applications to V.G. Processes and Option Pricing
2015
Robeson MS; O’Rourke DR; Kaehler BD; Ziemski M; Dillon MR; Foster JT; Bokulich NA, RESCRIPt: Reproducible sequence taxonomy reference database management for the masses, http://dx.doi.org/10.1101/2020.10.05.326504
Bolyen E; Rideout JR; Dillon MR; Bokulich NA; Abnet C; Al-Ghalith GA; Alexander H; Alm EJ; Arumugam M; Asnicar F; Bai Y; Bisanz JE; Bittinger K; Brejnrod A; Brislawn CJ; Brown CT; Callahan BJ; Caraballo-Rodríguez AM; Chase J; Cope E; Da Silva R; Dorrestein PC; Douglas GM; Durall DM; Duvallet C; Edwardson CF; Ernst M; Estaki M; Fouquier J; Gauglitz JM; Gibson DL; Gonzalez A; Gorlick K; Guo J; Hillmann B; Holmes S; Holste H; Huttenhower C; Huttley G; Janssen S; Jarmusch AK; Jiang L; Kaehler B; Kang KB; Keefe CR; Keim P; Kelley ST; Knights D; Koester I; Kosciolek T; Kreps J; Langille MGI; Lee J; Ley R; Liu Y-X; Loftfield E; Lozupone C; Maher M; Marotz C; Martin BD; McDonald D; McIver LJ; Melnik AV; Metcalf JL; Morgan SC; Morton J; Naimey AT; Navas-Molina JA; Nothias LF; Orchanian SB; Pearson T; Peoples SL; Petras D; Preuss ML; Pruesse E; Rasmussen LB; Rivers A; Robeson, II MS; Rosenthal P; Segata N; Shaffer M; Shiffer A; Sinha R; Song SJ; Spear JR; Swafford AD; Thompson LR; Torres PJ; Trinh P; Tripathi A; Turnbaugh PJ; Ul-Hasan S; van der Hooft JJJ; Vargas F; Vázquez-Baeza Y; Vogtmann E; von Hippel M; Walters W; Wan Y; Wang M; Warren J; Weber KC; Williamson CHD; Willis AD; Xu ZZ; Zaneveld JR; Zhang Y; Zhu Q; Knight R; Caporaso JG, QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science, http://dx.doi.org/10.7287/peerj.preprints.27295v2
Bolyen E; Rideout JR; Dillon MR; Bokulich NA; Abnet C; Al-Ghalith GA; Alexander H; Alm EJ; Arumugam M; Asnicar F; Bai Y; Bisanz JE; Bittinger K; Brejnrod A; Brislawn CJ; Brown CT; Callahan BJ; Caraballo-Rodríguez AM; Chase J; Cope E; Da Silva R; Dorrestein PC; Douglas GM; Durall DM; Duvallet C; Edwardson CF; Ernst M; Estaki M; Fouquier J; Gauglitz JM; Gibson DL; Gonzalez A; Gorlick K; Guo J; Hillmann B; Holmes S; Holste H; Huttenhower C; Huttley G; Janssen S; Jarmusch AK; Jiang L; Kaehler B; Kang KB; Keefe CR; Keim P; Kelley ST; Knights D; Koester I; Kosciolek T; Kreps J; Langille MGI; Lee J; Ley R; Liu Y-X; Loftfield E; Lozupone C; Maher M; Marotz C; Martin BD; McDonald D; McIver LJ; Melnik AV; Metcalf JL; Morgan SC; Morton J; Naimey AT; Navas-Molina JA; Nothias LF; Orchanian SB; Pearson T; Peoples SL; Petras D; Preuss ML; Pruesse E; Rasmussen LB; Rivers A; Robeson, II MS; Rosenthal P; Segata N; Shaffer M; Shiffer A; Sinha R; Song SJ; Spear JR; Swafford AD; Thompson LR; Torres PJ; Trinh P; Tripathi A; Turnbaugh PJ; Ul-Hasan S; van der Hooft JJJ; Vargas F; Vázquez-Baeza Y; Vogtmann E; von Hippel M; Walters W; Wan Y; Wang M; Warren J; Weber KC; Williamson CHD; Willis AD; Xu ZZ; Zaneveld JR; Zhang Y; Knight R; Caporaso JG, QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science, http://dx.doi.org/10.7287/peerj.preprints.27295v1
Kaehler BD; Yap VB; Huttley GA, Standard codon substitution models overestimate purifying selection for non-stationary data, http://dx.doi.org/10.7287/peerj.preprints.2218v1
Bokulich NA; Kaehler BD; Rideout JR; Dillon M; Bolyen E; Knight R; Huttley GA; Caporaso JG, Optimizing taxonomic classification of marker gene sequences, http://dx.doi.org/10.7287/peerj.preprints.3208v1
Bokulich NA; Kaehler BD; Rideout JR; Dillon M; Bolyen E; Knight R; Huttley GA; Caporaso JG, Optimizing taxonomic classification of marker gene amplicon sequences, http://dx.doi.org/10.7287/peerj.preprints.3208v2
Bokulich NA; Dillon M; Bolyen E; Kaehler BD; Huttley GA; Caporaso JG, q2-sample-classifier: machine-learning tools for microbiome classification and regression, http://dx.doi.org/10.1101/306167
Kaehler BD; Bokulich NA; McDonald D; Knight R; Gregory Caporaso J; Huttley GA, Species abundance information improves sequence taxonomy classification accuracy, http://dx.doi.org/10.1101/406611
Journal articles
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Dillon MR; Bolyen E; Adamov A; Belk A; Borsom E; Burcham Z; Debelius JW; Deel H; Emmons A; Estaki M; Herman C; Keefe CR; Morton JT; Oliveira RRM; Sanchez A; Simard A; Vázquez-Baeza Y; Ziemski M; Miwa HE; Kerere TA; Coote C; Bonneau R; Knight R; Oliveira G; Gopalasingam P; Kaehler BD; Cope EK; Metcalf JL; Robeson MS; Bokulich NA; Gregory Caporaso J, 2021, 'Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops', PLoS Computational Biology, vol. 17, pp. e1009056, http://dx.doi.org/10.1371/journal.pcbi.1009056
2021
Ziemski M; Wisanwanichthan T; Bokulich NA; Kaehler BD, 2021, 'Beating Naive Bayes at Taxonomic Classification of 16S rRNA Gene Sequences', Frontiers in Microbiology, vol. 12, http://dx.doi.org/10.3389/fmicb.2021.644487
2021
Bokulich NA; Ziemski M; Robeson MS; Kaehler BD, 2020, 'Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods', Computational and Structural Biotechnology Journal, vol. 18, pp. 4048 - 4062, http://dx.doi.org/10.1016/j.csbj.2020.11.049
2020
Kaehler BD; Bokulich NA; McDonald D; Knight R; Caporaso JG; Huttley GA, 2019, 'Species abundance information improves sequence taxonomy classification accuracy', Nature Communications, vol. 10, pp. 4643, http://dx.doi.org/10.1038/s41467-019-12669-6
2019
McDonald D; Kaehler B; Gonzalez A; DeReus J; Ackermann G; Marotz C; Huttley G; Knight R, 2019, 'Redbiom: A rapid sample discovery and feature characterization system', mSystems, vol. 4, http://dx.doi.org/10.1128/mSystems.00215-19
2019
Bolyen E; Rideout JR; Dillon MR; Bokulich NA; Abnet CC; Al-Ghalith GA; Alexander H; Alm EJ; Arumugam M; Asnicar F; Bai Y; Bisanz JE; Bittinger K; Brejnrod A; Brislawn CJ; Brown CT; Callahan BJ; Caraballo-Rodríguez AM; Chase J; Cope EK; Da Silva R; Diener C; Dorrestein PC; Douglas GM; Durall DM; Duvallet C; Edwardson CF; Ernst M; Estaki M; Fouquier J; Gauglitz JM; Gibbons SM; Gibson DL; Gonzalez A; Gorlick K; Guo J; Hillmann B; Holmes S; Holste H; Huttenhower C; Huttley GA; Janssen S; Jarmusch AK; Jiang L; Kaehler BD; Kang KB; Keefe CR; Keim P; Kelley ST; Knights D; Koester I; Kosciolek T; Kreps J; Langille MGI; Lee J; Ley R; Liu YX; Loftfield E; Lozupone C; Maher M; Marotz C; Martin BD; McDonald D; McIver LJ; Melnik AV; Metcalf JL; Morgan SC; Morton JT; Naimey AT; Navas-Molina JA; Nothias LF; Orchanian SB; Pearson T; Peoples SL; Petras D; Preuss ML; Pruesse E; Rasmussen LB; Rivers A; Robeson MS; Rosenthal P; Segata N; Shaffer M; Shiffer A; Sinha R; Song SJ; Spear JR; Swafford AD; Thompson LR; Torres PJ; Trinh P; Tripathi A; Turnbaugh PJ; Ul-Hasan S; van der Hooft JJJ; Vargas F; Vázquez-Baeza Y; Vogtmann E; von Hippel M; Walters W, 2019, 'Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2', Nature Biotechnology, vol. 37, pp. 852 - 857, http://dx.doi.org/10.1038/s41587-019-0209-9
2019
Bolyen E; Rideout JR; Dillon MR; Bokulich NA; Abnet CC; Al-Ghalith GA; Alexander H; Alm EJ; Arumugam M; Asnicar F; Bai Y; Bisanz JE; Bittinger K; Brejnrod A; Brislawn CJ; Brown CT; Callahan BJ; Caraballo-Rodríguez AM; Chase J; Cope EK; Da Silva R; Diener C; Dorrestein PC; Douglas GM; Durall DM; Duvallet C; Edwardson CF; Ernst M; Estaki M; Fouquier J; Gauglitz JM; Gibbons SM; Gibson DL; Gonzalez A; Gorlick K; Guo J; Hillmann B; Holmes S; Holste H; Huttenhower C; Huttley GA; Janssen S; Jarmusch AK; Jiang L; Kaehler BD; Kang KB; Keefe CR; Keim P; Kelley ST; Knights D; Koester I; Kosciolek T; Kreps J; Langille MGI; Lee J; Ley R; Liu YX; Loftfield E; Lozupone C; Maher M; Marotz C; Martin BD; McDonald D; McIver LJ; Melnik AV; Metcalf JL; Morgan SC; Morton JT; Naimey AT; Navas-Molina JA; Nothias LF; Orchanian SB; Pearson T; Peoples SL; Petras D; Preuss ML; Pruesse E; Rasmussen LB; Rivers A; Robeson MS; Rosenthal P; Segata N; Shaffer M; Shiffer A; Sinha R; Song SJ; Spear JR; Swafford AD; Thompson LR; Torres PJ; Trinh P; Tripathi A; Turnbaugh PJ; Ul-Hasan S; van der Hooft JJJ; Vargas F; Vázquez-Baeza Y; Vogtmann E; von Hippel M; Walters W, 2019, 'Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 (Nature Biotechnology, (2019), 37, 8, (852-857), 10.1038/s41587-019-0209-9)', Nature Biotechnology, vol. 37, pp. 1091, http://dx.doi.org/10.1038/s41587-019-0252-6
2019
Bokulich NA; Dillon MR; Bolyen E; Kaehler BD; Huttley GA; Caporaso JG, 2018, 'q2-sample-classifier: machine-learning tools for microbiome classification and regression.', J Open Res Softw, vol. 3, pp. 934 - 934, http://dx.doi.org/10.21105/joss.00934
2018
Sutherland TD; Sriskantha A; Rapson TD; Kaehler BD; Huttley GA, 2018, 'Did aculeate silk evolve as an antifouling material?', PLOS ONE, vol. 13, http://dx.doi.org/10.1371/journal.pone.0203948
2018
Bokulich NA; Kaehler BD; Rideout JR; Dillon M; Bolyen E; Knight R; Huttley GA; Caporaso JG, 2018, 'Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2 ' s q2-feature-classifier plugin', MICROBIOME, vol. 6, http://dx.doi.org/10.1186/s40168-018-0470-z
2018
Buchmann B; Kaehler B; Maller R; Szimayer A, 2017, 'Multivariate subordination using generalised Gamma convolutions with applications to Variance Gamma processes and option pricing', STOCHASTIC PROCESSES AND THEIR APPLICATIONS, vol. 127, pp. 2208 - 2242, http://dx.doi.org/10.1016/j.spa.2016.10.008
2017
Kaehler BD, 2017, 'Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies', JOURNAL OF THEORETICAL BIOLOGY, vol. 420, pp. 144 - 151, http://dx.doi.org/10.1016/j.jtbi.2017.03.007
2017
Kaehler BD; Yap VB; Huttley GA, 2017, 'Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data', GENOME BIOLOGY AND EVOLUTION, vol. 9, pp. 134 - 149, http://dx.doi.org/10.1093/gbe/evw308
2017
Zhang C; Stadler T; Klopfstein S; Heath TA; Ronquist F, 2016, 'Total-Evidence Dating under the Fossilized Birth-Death Process', SYSTEMATIC BIOLOGY, vol. 65, pp. 228 - 249, http://dx.doi.org/10.1093/sysbio/syv080
2016
Maitip J; Trueman HE; Kaehler BD; Huttley GA; Chantawannakul P; Sutherland TD, 2015, 'Folding behavior of four silks of giant honey bee reflects the evolutionary conservation of aculeate silk proteins', INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY, vol. 59, pp. 72 - 79, http://dx.doi.org/10.1016/j.ibmb.2015.02.007
2015
Kaehler BD; Maller RA, 2010, 'A Generalized Skewness Statistic for Stationary Ergodic Martingale Differences', MATHEMATICAL METHODS OF STATISTICS, vol. 19, pp. 267 - 282, http://dx.doi.org/10.3103/S106653071003004X
2010
Theses / Dissertations
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Kaehler B, 2009, Option pricing for alternative risky asset price models, and model verification results
2009
Organisational units
lensSchool of Science
Sub Theme
lensApplied & Industrial Mathematics