Publications

 Google Scholar

(*co-first authors; ‡co-corresponding authors)

2020

  1. Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications. 2020. 11(1):2500.

  2. Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Knight R, Knights D. SHOGUN: a modular, accurate, and scalable framework for microbiome quantification. Bioinformatics. 2020. 36(13):4088-90.

  3. Estaki M*, Jiang L*, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R. QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data. Current Protocols in Bioinformatics. 2020. 70(1):e100.

  4. Poore GD*, Kopylova E*, Zhu Q, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf J, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Patel SP, Knight R. Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature. 2020. 579(7800):567-74.

  5. McCall L*, Callewaert C*, Zhu Q* (co-first author), Song SJ, Bouslimani A, Minich JJ, Ernst M, Ruiz-Calderon JF, Cavallin H, Pereira HS, Novoselac A, Hernandez J, Rios R, Branch OH, Blaser MJ, Paulino LC, Dorrestein PC, Knight R, Dominguez-Bello MG. Home chemical and microbial transitions across urbanization. Nature Microbiology. 2020. 5(1):108-15.


2019

  1. Zhu Q*, Mai U*, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao J, Wu Z, Xu ZZ, Sayyari E, Morton JT, Podell S, Knights D, Li W, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature Communications. 2019. 10(1):5477.

  2. Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome Biology. 2019. 20(1):226.

  3. 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 nd, 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. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. 2019. 37(8):852-57.

  4. Fu T, Coulter S, Yoshihara E, Oh TG, Fang S, Cayabyab F, Zhu Q, Zhang T, Leblanc M, Liu S, He M, Waizenegger W, Gasser E, Schnabl B, Atkins AR, Yu RT, Knight R, Liddle C, Downes M, Evans RM. FXR Regulates Intestinal Cancer Stem Cell Proliferation. Cell. 2019. 176(5):1098-1112.e18.

  5. Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, Smarr L, Knight R, Gonzalez DJ. Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. mSystems. 2019. 4(1):e00337-18.

  6. Xu ZZ, Amir A, Sanders J, Zhu Q, Morton JT, Bletz MC, Tripathi A, Huang S, McDonald D, Jiang L, Knight R. Calour: an Interactive, Microbe-Centric Analysis Tool. mSystems. 2019. 4(1):e00269-18.


2018

  1. Zhu Q, Dupont CL, Jones MB, Pham KM, Jiang ZD, DuPont HL, Highlander SK. Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. Microbiome. 2018. 6(1):201.

  2. Fang X, Monk J, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L. Metagenomics-based, strain-level analysis of Escherichia coli from a time-series of microbiome samples from a Crohn’s disease patient. Frontiers in Microbiology. 2018. 9:2559.

  3. Hillmann B, Al-Ghalith G, Shields-Cutler R, Zhu Q, Gohl D, Beckman K, Knight R, Knights D. Evaluating the information content of shallow shotgun metagenomics. mSystems. 2018. 3(6):e00069-18.

  4. Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R. Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). MicrobiologyOpen. 2018. e00716.

  5. Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R. Are microbiome studies ready for hypothesis-driven research? Current Opinion in Microbiology. 2018. 44:61-69.

  6. Hua ZS*, Qu YN*, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nature Communications. 2018. 9(1):2832.

  7. McDonald D*, Hyde E*, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, Goldasich LD, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, The American Gut Consortium, Knight R. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 3(3):e00031-18.

  8. He Y, Kosciolek T, Tang J, Zhou Y, Li Z, Ma X, Zhu Q, Yuan N, Yuan L, Li C, Jin K, Knight R, Tsuang MT, Chen X. Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis. European Psychiatry. 2018. 53:37-45.

  9. Washburne AD, Morton JT, Sanders J, McDonald D, Zhu Q, Oliverio AM, Knight R. Methods for phylogenetic analysis of microbiome data. Nature Microbiology. 2018. 3(6):652.

  10. Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. Best practices for analysing microbiomes. Nature Reviews Microbiology. 2018. 16(7):410-422.

  11. Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH, Allen EE, Venkateswaran K, Knight R. KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. mSystems. 2018. 3(3):e00218-17.

  12. Kapono CA, Morton JT, Bouslimani A, Melnik AV, Orlinsky K, Knaan TL, Garg N, Vázquez-Baeza Y, Protsyuk I, Janssen S, Zhu Q, Alexandrov T, Smarr L, Knight R, Dorrestein PC. Creating a 3D microbial and chemical snapshot of a human habitat. Scientific Reports. 2018. 8(1):3669.


2017 and before

  1. Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R, The Earth Microbiome Project Consortium. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017. 551(7681):457-63. (cover paper)

  2. Lin W*, Paterson GA*, Zhu Q, Wang Y, Kopylov E, Li Y, Knight R, Bazylinski DA, Zhu R, Kirschvink JL, Pan Y. Origin of microbial biomineralization and magnetotaxis during the Archean. Proceedings of the National Academy of Sciences. 2017. 114(9):2171-76.

  3. Yang Y, Zhu Q, Liu S, Zhao C, Wu C. The origin of Chinese domestic horses revealed with novel mtDNA variants. Animal Science Journal. 2017. 88(1):19-26.

  4. Li W, Richter RA, Jung Y, Zhu Q, Li RW. Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species. BMC Genomics. 2016. 17(1):761.

  5. Dittmar K, Zhu Q, Hastriter MW, Whiting MF: On the probability of dinosaur fleas. BMC Evolutionary Biology. 2016. 16(1):9.

  6. Liu Y, Yu Y, Duan W, Qu Q, Zhang Q, Zhao M, Zhu Q. Home storage significantly impairs Bifidobacteria survival in powered formula for infants and young children in the Chinese market. International Journal of Dairy Technology. 2015. 68(4):495-502.

  7. Han X, Chen Y, Wang L, Fang W, Zhang N, Zhu Q. RNA: an expanding view of function and evolution. Evolutionary Bioinformatics. 2015. Suppl. 1:77-9.

  8. Zhu Q, Hastriter MW, Whiting MF, Dittmar K. Fleas (Siphonaptera) are Cretaceous, and evolved with Theria. Molecular Phylogenetics and Evolution. 2015. 90:129-39.

  9. Brook CE, Bai Y, Dobson AP, Osikowicz LM, Ranaivoson HC, Zhu Q, Kosoy MY, Dittmar K. Bartonella spp. in fruit bats and blood-feeding ectoparasites in Madagascar. PLOS Neglected Tropical Diseases. 2015. 9(2):e0003532.

  10. Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genomics. 2014. 15:717.

  11. Zhu Q, Kosoy M, Olival KJ, Dittmar K. Horizontal transfers and gene losses in the phospholipid pathway of Bartonella reveal clues about early ecological niches. Genome Biology and Evolution. 2014. 6(8):2156-69.

  12. Kazemian M, Zhu Q, Halfon MS, Sinha S. Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. Nucleic Acids Research. 2011. 39(22):9463-72.

  13. Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Göttgens B, Halfon MS, Sinha S. Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Developmental Cell. 2009. 17(4):568-79.

  14. Liu Y*, Zhu Q*, Zhu N. Recent duplication and positive selection of the GAGE gene family. Genetica. 2008. 133(1):31-5.

  15. Liu Y, Zhu Q, Zhu N. Rapid HLA-DR fluorotyping based on melting curve analysis. Immunological Investigations. 2007. 36(4):507-21.


Book chapters

Dittmar K, Zhu Q, Hastriter MW, Whiting MF. Evolutionary history of Siphonaptera: fossils, origins, vectors. In Parasite Diversity and Diversification - Evolutionary Ecology Meets Phylogenetics. Ed. Morand S, Krasnov BR, Littlewood DTJ. Cambridge University Press. 2015.