Publications

Nucleic acids research. 2025-01-06; 53.D1: D678-D690.
MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration
Zdouc MM, Blin K, Louwen NLL, Navarro J, Loureiro C, Bader CD, Bailey CB, Barra L, Booth TJ, Bozhüyük KAJ, Cediel-Becerra JDD, Charlop-Powers Z, Chevrette MG, Chooi YH, D'Agostino PM, de Rond T, Del Pup E, Duncan KR, Gu W, Hanif N, Helfrich EJN, Jenner M, Katsuyama Y, Korenskaia A, Krug D, Libis V, Lund GA, Mantri S, Morgan KD, Owen C, Phan CS, Philmus B, Reitz ZL, Robinson SL, Singh KS, Teufel R, Tong Y, Tugizimana F, Ulanova D, Winter JM, Aguilar C, Akiyama DY, Al-Salihi SAA, Alanjary M, Alberti F, Aleti G, Alharthi SA, Rojo MYA, Arishi AA, Augustijn HE, Avalon NE, Avelar-Rivas JA, Axt KK, Barbieri HB, Barbosa JCJ, Barboza Segato LG, Barrett SE, Baunach M, Beemelmanns C, Beqaj D, Berger T, Bernaldo-Agüero J, Bettenbühl SM, Bielinski VA, Biermann F, Borges RM, Borriss R, Breitenbach M, Bretscher KM, Brigham MW, Buedenbender L, Bulcock BW, Cano-Prieto C, Capela J, Carrion VJ, Carter RS, Castelo-Branco R, Castro-Falcón G, Chagas FO, Charria-Girón E, Chaudhri AA, Chaudhry V, Choi H, Choi Y, Choupannejad R, Chromy J, Donahey MSC, Collemare J, Connolly JA, Creamer KE, Crüsemann M, Cruz AA, Cumsille A, Dallery JF, Damas-Ramos LC, Damiani T, de Kruijff M, Martín BD, Sala GD, Dillen J, Doering DT, Dommaraju SR, Durusu S, Egbert S, Ellerhorst M, Faussurier B, Fetter A, Feuermann M, Fewer DP, Foldi J, Frediansyah A, Garza EA, Gavriilidou A, Gentile A, Gerke J, Gerstmans H, Gomez-Escribano JP, González-Salazar LA, Grayson NE, Greco C, Gomez JEG, Guerra S, Flores SG, Gurevich A, Gutiérrez-García K, Hart L, Haslinger K, He B, Hebra T, Hemmann JL, Hindra H, Höing L, Holland DC, Holme JE, Horch T, Hrab P, Hu J, Huynh TH, Hwang JY, Iacovelli R, Iftime D, Iorio M, Jayachandran S, Jeong E, Jing J, Jung JJ, Kakumu Y, Kalkreuter E, Kang KB, Kang S, Kim W, Kim GJ, Kim H, Kim HU, Klapper M, Koetsier RA, Kollten C, Kovács ÁT, Kriukova Y, Kubach N, Kunjapur AM, Kushnareva AK, Kust A, Lamber J, Larralde M, Larsen NJ, Launay AP, Le NT, Lebeer S, Lee BT, Lee K, Lev KL, Li SM, Li YX, Licona-Cassani C, Lien A, Liu J, Lopez JAV, Machushynets NV, Macias MI, Mahmud T, Maleckis M, Martinez-Martinez AM, Mast Y, Maximo MF, McBride CM, McLellan RM, Bhatt KM, Melkonian C, Merrild A, Metsä-Ketelä M, Mitchell DA, Müller AV, Nguyen GS, Nguyen HT, Niedermeyer THJ, O'Hare JH, Ossowicki A, Ostash BO, Otani H, Padva L, Paliyal S, Pan X, Panghal M, Parade DS, Park J, Parra J, Rubio MP, Pham HT, Pidot SJ, Piel J, Pourmohsenin B, Rakhmanov M, Ramesh S, Rasmussen MH, Rego A, Reher R, Rice AJ, Rigolet A, Romero-Otero A, Rosas-Becerra LR, Rosiles PY, Rutz A, Ryu B, Sahadeo LA, Saldanha M, Salvi L, Sánchez-Carvajal E, Santos-Medellin C, Sbaraini N, Schoellhorn SM, Schumm C, Sehnal L, Selem N, Shah AD, Shishido TK, Sieber S, Silviani V, Singh G, Singh H, Sokolova N, Sonnenschein EC, Sosio M, Sowa ST, Steffen K, Stegmann E, Streiff AB, Strüder A, Surup F, Svenningsen T, Sweeney D, Szenei J, Tagirdzhanov A, Tan B, Tarnowski MJ, Terlouw BR, Rey T, Thome NU, Torres Ortega LR, Tørring T, Trindade M, Truman AW, Tvilum M, Udwary DW, Ulbricht C, Vader L, van Wezel GP, Walmsley M, Warnasinghe R, Weddeling HG, Weir ANM, Williams K, Williams SE, Witte TE, Rocca SMW, Yamada K, Yang D, Yang D, Yu J, Zhou Z, Ziemert N, Zimmer L, Zimmermann A, Zimmermann C, van der Hooft JJJ, Linington RG, Weber T, Medema MH
PMID: 39657789
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2025-01-01; 30.711-716.
Earth Friendly Computation: Applying Indigenous Data Lifecycles in Medical and Sovereign AI
Fox K, Tsosie K, Ioannidis A, Wasik K, Calac A, Dawson E
PMID: 39670409
Science (New York, N.Y.). 2024-12-20; 386.6728: 1351-1353.
Confronting risks of mirror life
Adamala KP, Agashe D, Belkaid Y, Bittencourt DMC, Cai Y, Chang MW, Chen IA, Church GM, Cooper VS, Davis MM, Devaraj NK, Endy D, Esvelt KM, Glass JI, Hand TW, Inglesby TV, Isaacs FJ, James WG, Jones JDG, Kay MS, Lenski RE, Liu C, Medzhitov R, Nicotra ML, Oehm SB, Pannu J, Relman DA, Schwille P, Smith JA, Suga H, Szostak JW, Talbot NJ, Tiedje JM, Venter JC, Winter G, Zhang W, Zhu X, Zuber MT
PMID: 39666824
Cell host & microbe. 2024-12-11; 32.12: 2131-2147.e8.
A trivalent mucosal vaccine encoding phylogenetically inferred ancestral RBD sequences confers pan-Sarbecovirus protection in mice
Case JB, Sanapala S, Dillen C, Rhodes V, Zmasek C, Chicz TM, Switzer CE, Scheaffer SM, Georgiev G, Jacob-Dolan C, Hauser BM, Dos Anjos DCC, Adams LJ, Soudani N, Liang CY, Ying B, McNamara RP, Scheuermann RH, Boon ACM, Fremont DH, Whelan SPJ, Schmidt AG, Sette A, Grifoni A, Frieman MB, Diamond MS
PMID: 39561781
Biotechnology advances. 2024-12-01; 77.108462.
The current progress of tandem chemical and biological plastic upcycling
Hu Y, Tian Y, Zou C, Moon TS
PMID: 39395608
Clinical and translational gastroenterology. 2024-12-01; 15.12: e00796.
Correction to: Genetic Risk, Dysbiosis, and Treatment Stratification Using Host Genome and Gut Microbiome in Inflammatory Bowel Disease
Moustafa A, Li W, Anderson EL, MWong EH, Dulai PS, Sandborn WJ, Biggs W, Yooseph S, Jones MB, Venter CJ, Nelson KE, Chang JT, Telenti A, Boland BS
PMID: 39656168
Immunity. 2024-11-13;
Sialylated IgG induces the transcription factor REST in alveolar macrophages to protect against lung inflammation and severe influenza disease
Chakraborty S, Cheng BY, Edwards DL, Gonzalez JC, Chiu DK, Zheng H, Scallan C, Guo X, Tan GS, Coffey GP, Conley PB, Hume PS, Janssen WJ, Byers DE, Mudd PA, Taubenberger J, Memoli M, Davis MM, Chua KF, Diamond MS, Andreakos E, Khatri P, Wang TT
PMID: 39541970
Scientific reports. 2024-11-12; 14.1: 27637.
Major alteration of lung microbiome and the host responses in critically ill COVID-19 patients with high viral load
Bustos IG, Wiscovitch-Russo R, Singh H, Sievers BL, Matsuoka M, Freire M, Tan GS, Cala MP, Guerrero JL, Martin-Loeches I, Gonzalez-Juarbe N, Reyes LF
PMID: 39532981
Annual review of microbiology. 2024-11-07; 78.1: 213-232.
Molecular Mechanisms for Iron Uptake and Homeostasis in Marine Eukaryotic Phytoplankton
Lampe RH, Coale TH, McQuaid JB, Allen AE
PMID: 39018471
Nature communications. 2024-11-05; 15.1: 9525.
The gut microbiome is associated with susceptibility to febrile malaria in Malian children
Van Den Ham KM, Bower LK, Li S, Lorenzi H, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW
PMID: 39500866

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