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| Issue Date | Title | Author(s) |
| 2023-07-25 | Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics. | Brito, BP; Frost, MJ; Anantanawat, K; Jaya, F; Batterham, T; Djordjevic, SP; Chang, W-S; Holmes, EC; Darling, AE; Kirkland, PD |
| 2023-03 | Rhometa: Population recombination rate estimation from metagenomic read datasets. | Krishnan, S; DeMaere, MZ; Beck, D; Ostrowski, M; Seymour, JR; Darling, AE; Didelot, X |
| 2022-06-16 | Fidelity of Hyperbolic Space for Bayesian Phylogenetic Inference | Macaulay, M; Darling, AE; Fourment, M |
| 2022-04 | Critical Assessment of Metagenome Interpretation: the second round of challenges. | Meyer, F; Fritz, A; Deng, Z-L; Koslicki, D; Lesker, TR; Gurevich, A; Robertson, G; Alser, M; Antipov, D; Beghini, F; Bertrand, D; Brito, JJ; Brown, CT; Buchmann, J; Buluç, A; Chen, B; Chikhi, R; Clausen, PTLC; Cristian, A; Dabrowski, PW; Darling, AE; Egan, R; Eskin, E; Georganas, E; Goltsman, E; Gray, MA; Hansen, LH; Hofmeyr, S; Huang, P; Irber, L; Jia, H; Jørgensen, TS; Kieser, SD; Klemetsen, T; Kola, A; Kolmogorov, M; Korobeynikov, A; Kwan, J; LaPierre, N; Lemaitre, C; Li, C; Limasset, A; Malcher-Miranda, F; Mangul, S; Marcelino, VR; Marchet, C; Marijon, P; Meleshko, D; Mende, DR; Milanese, A; Nagarajan, N; Nissen, J; Nurk, S; Oliker, L; Paoli, L; Peterlongo, P; Piro, VC; Porter, JS; Rasmussen, S; Rees, ER; Reinert, K; Renard, B; Robertsen, EM; Rosen, GL; Ruscheweyh, H-J; Sarwal, V; Segata, N; Seiler, E; Shi, L; Sun, F; Sunagawa, S; Sørensen, SJ; Thomas, A; Tong, C; Trajkovski, M; Tremblay, J; Uritskiy, G; Vicedomini, R; Wang, Z; Wang, Z; Wang, Z; Warren, A; Willassen, NP; Yelick, K; You, R; Zeller, G; Zhao, Z; Zhu, S; Zhu, J; Garrido-Oter, R; Gastmeier, P; Hacquard, S; Häußler, S; Khaledi, A; Maechler, F; Mesny, F; Radutoiu, S; Schulze-Lefert, P; Smit, N; Strowig, T; Bremges, A; Sczyrba, A; McHardy, AC |
| 2022-01 | Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction. | Gaio, D; Anantanawat, K; To, J; Liu, M; Monahan, L; Darling, AE |
| 2022 | Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig. | Gaio, D; DeMaere, MZ; Anantanawat, K; Eamens, GJ; Falconer, L; Chapman, TA; Djordjevic, S; Darling, AE |
| 2021-10 | qc3C: Reference-free quality control for Hi-C sequencing data. | DeMaere, MZ; Darling, AE |
| 2021-08-09 | Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes. | Gaio, D; DeMaere, MZ; Anantanawat, K; Chapman, TA; Djordjevic, SP; Darling, AE |
| 2021-07-26 | STRONG: metagenomics strain resolution on assembly graphs | Quince, C; Nurk, S; Raguideau, S; James, R; Soyer, OS; Summers, JK; Limasset, A; Eren, AM; Chikhi, R; Darling, AE |
| 2021-07-26 | STRONG: metagenomics strain resolution on assembly graphs | Quince, C; Nurk, S; Raguideau, S; James, R; Soyer, OS; Summers, JK; Limasset, A; Eren, AM; Chikhi, R; Darling, AE |
| 2021-07-26 | STRONG: metagenomics strain resolution on assembly graphs | Quince, C; Nurk, S; Raguideau, S; James, R; Soyer, OS; Summers, JK; Limasset, A; Eren, AM; Chikhi, R; Darling, AE |
| 2021-07-23 | Strainberry: automated strain separation in low-complexity metagenomes using long reads | Vicedomini, R; Quince, C; Darling, AE; Chikhi, R |
| 2021-06-03 | A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen | Gaio, D; DeMaere, MZ; Anantanawat, K; Eamens, GJ; Liu, M; Zingali, T; Falconer, L; Chapman, TA; Djordjevic, SP; Darling, AE |
| 2021-03 | Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit. | Meyer, F; Lesker, T-R; Koslicki, D; Fritz, A; Gurevich, A; Darling, AE; Sczyrba, A; Bremges, A; McHardy, AC |
| 2021-02-25 | Automated strain separation in low-complexity metagenomes using long reads | Vicedomini, R; Quince, C; Darling, AE; Chikhi, R |
| 2020-08-12 | Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit | Meyer, F; Lesker, T-R; Koslicki, D; Fritz, A; Gurevich, A; Darling, AE; Sczyrba, A; Bremges, A; McHardy, AC |
| 2020-06-04 | Whole Genome Sequencing Analysis of Porcine Faecal Commensal Escherichia coli Carrying Class 1 Integrons from Sows and Their Offspring. | Zingali, T; Reid, CJ; Chapman, TA; Gaio, D; Liu, M; Darling, AE; Djordjevic, SP |
| 2020-02-06 | Metagenomic Hi-C of a Healthy Human Fecal Microbiome Transplant Donor. | DeMaere, MZ; Liu, MYZ; Lin, E; Djordjevic, SP; Charles, IG; Worden, P; Burke, CM; Monahan, LG; Gardiner, M; Borody, TJ; Darling, AE |
| 2020-01-01 | Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups | Bogema, DR; McKinnon, J; Liu, M; Hitchick, N; Miller, N; Venturini, C; Iredell, J; Darling, AE; Chowdury, PR; Djordjevic, SP |
| 2020-01 | Whole genome analysis of ExPEC ST73 from a single hospital over a 2-year period identified different circulating clonal groups | Bogema, DR; McKinnon, J; Liu, M; Hitchick, N; Miller, N; Venturini, C; Iredell, J; Darling, AE; Roy Chowdury, P; Djordjevic, SP |
