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| Issue Date | Title | Author(s) |
| 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 |
| 2014-01-01 | Alignathon: A competitive assessment of whole-genome alignment methods | Earl, D; Nguyen, N; Hickey, G; Harris, RS; Fitzgerald, S; Beal, K; Seledtsov, I; Molodtsov, V; Raney, BJ; Clawson, H; Kim, J; Kemena, C; Chang, JM; Erb, I; Poliakov, A; Hou, M; Herrero, J; Kent, WJ; Solovyev, V; Darling, AE; Ma, J; Notredame, C; Brudno, M; Dubchak, I; Haussler, D; Paten, B |
| 2018-04-27 | Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes | Bogema, DR; Micallef, ML; Liu, M; Padula, MP; Djordjevic, SP; Darling, AE; Jenkins, C |
| 2009 | Are protein domains modules of lateral genetic transfer? | Chan, CX; Darling, AE; Beiko, RG; Ragan, MA |
| 2009-02-20 | Are protein domains modules of lateral genetic transfer? | Chan, CX; Darling, AE; Beiko, RG; Ragan, MA |
| 2021-02-25 | Automated strain separation in low-complexity metagenomes using long reads | Vicedomini, R; Quince, C; Darling, AE; Chikhi, R |
| 2016-01-01 | Bacterial communities vary between sinuses in chronic rhinosinusitis patients | Joss, TV; Burke, CM; Hudson, BJ; Darling, AE; Forer, M; Alber, DG; Charles, IG; Stow, NW |
| 2019-11-01 | BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics | Ayres, DL; Cummings, MP; Baele, G; Darling, AE; Lewis, PO; Swofford, DL; Huelsenbeck, JP; Lemey, P; Rambaut, A; Suchard, MA |
| 2019-02-26 | Bin3C: Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes | Demaere, MZ; Darling, AE |
| 2019-02-08 | CAMISIM: Simulating metagenomes and microbial communities | Fritz, A; Hofmann, P; Majda, S; Dahms, E; Dröge, J; Fiedler, J; Lesker, TR; Belmann, P; Demaere, MZ; Darling, AE; Sczyrba, A; Bremges, A; McHardy, AC |
| 2018-04-13 | CAMISIM: Simulating metagenomes and microbial communities | Darling, AE; Fritz, A; Hofmann, P; Majda, S; Dahms, E; Droge, J; Fiedler, J; Lesker, TR; Belmann, P; DeMaere, MZ; Sczyrba, A; Bremges, A; McHardy, AC |
| 2014-01-01 | The Common Oceanographer: Crowdsourcing the Collection of Oceanographic Data | Lauro, FM; Senstius, SJ; Cullen, J; Neches, R; Jensen, RM; Brown, MV; Darling, AE; Givskov, M; McDougald, D; Hoeke, R; Ostrowski, M; Philip, GK; Paulsen, IT; Grzymski, JJ |
| 2015-03-10 | Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs | Wyrsch, E; Chowdhury, PR; Abraham, S; Santos, J; Darling, AE; Charles, IG; Chapman, TA; Djordjevic, SP |
| 2015-03-10 | Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs | Wyrsch, E; Chowdhury, PR; Abraham, S; Santos, J; Darling, AE; Charles, IG; Chapman, TA; Djordjevic, SP |
| 2016-03-12 | Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease | Roy Chowdhury, P; Demaere, M; Chapman, T; Worden, P; Charles, IG; Darling, AE; Djordjevic, SP |
| 2015-01-01 | Comparative genomics of the genus porphyromonas identifies adaptations for heme synthesis within the prevalent canine oral species porphyromonas cangingivalis | O'Flynn, C; Deusch, O; Darling, AE; Eisen, JA; Wallis, C; Davis, IJ; Harris, SJ |
| 2017-10-31 | Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software | Sczyrba, A; Hofmann, P; Belmann, P; Koslicki, D; Janssen, S; Dröge, J; Gregor, I; Majda, S; Fiedler, J; Dahms, E; Bremges, A; Fritz, A; Garrido-Oter, R; Jørgensen, TS; Shapiro, N; Blood, PD; Gurevich, A; Bai, Y; Turaev, D; Demaere, MZ; Chikhi, R; Nagarajan, N; Quince, C; Meyer, F; Balvočiutė, M; Hansen, LH; Sørensen, SJ; Chia, BKH; Denis, B; Froula, JL; Wang, Z; Egan, R; Don Kang, D; Cook, JJ; Deltel, C; Beckstette, M; Lemaitre, C; Peterlongo, P; Rizk, G; Lavenier, D; Wu, YW; Singer, SW; Jain, C; Strous, M; Klingenberg, H; Meinicke, P; Barton, MD; Lingner, T; Lin, HH; Liao, YC; Silva, GGZ; Cuevas, DA; Edwards, RA; Saha, S; Piro, VC; Renard, BY; Pop, M; Klenk, HP; Göker, M; Kyrpides, NC; Woyke, T; Vorholt, JA; Schulze-Lefert, P; Rubin, EM; Darling, AE; Rattei, T; McHardy, AC |
| 2017-01-09 | Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software | Darling, AE |
| 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 |
| 2016-01-01 | Deconvoluting simulated metagenomes: The performance of hard- and softclustering algorithms applied to metagenomic chromosome conformation capture (3C) | DeMaere, MZ; Darling, AE |
