Papers

Find our papers at Google Scholar or PubMed.

Preprints

MIOSTONE: Modeling microbiome-trait associations with taxonomy-adaptive neural networks

Jiang Y, Aton M, Zhu Q, Lu YY

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

Martino C, Kellman BP, Sandoval DR, Clausen TM, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido RA, Zhu Q, Armingol E, Vázquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, Belda-Ferre P, Liang C, Zhang Y, Schifanella L, Klatt NR, Havulinna AS, Jousilahti P, Huang S, Haiminen N, Parida L, Kim HC, Swafford AD, Zengler K, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Esko JD, Lewis NE, Knight R

2024

Cell Reports

An evolutionary optimum amid moderate heritability in prokaryotic cell size

Secaira-Morocho H, Chede A, Gonzalez-de-Salceda L, Garcia-Pichel F, Zhu Q

Cell Reports

Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology

Griffiths JA, Yoo BB, Thuy-Boun PS, Cantu V, Weldon KC, Challis C, Sweredoski MJ, Chan KY, Thron TM, Sharon G, Moradian A, Humphrey G, Zhu Q, Shaffer J, Wolan DW, Dorrestein PC, Knight R, Gradinaru V, Mazmanian SK

Nature Aging

Integration of polygenic and gut metagenomic risk prediction for common diseases

Liu Y, Ritchie S, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vazquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna A, Knight R, Méric G, Inouye M

Oncogene

Robustness of cancer microbiome signals over a broad range of methodological variation

Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R

Nature Microbiology (cover paper)

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables

Burcham Z, Belk AD, McGivern BB, Bouslimani A, Ghadermazi P, Martino C, Shenhav L, Zhang AR, Shi Z, Emmons A, Deel HL, Xu ZZ, Nieciecki V, Zhu Q, Shaffer M, Panitchpakdi M, Weldon KC, Cantrell K, Ben-Hur A, Reed SC, Humphry GC, Ackermann G, McDonald D, Chan SHJ, Conner M, Boyd D, Smith J, Watson JMS, Vidoli G, Steadman D, Lynne AM, Bucheli S, Dorrestein PC, Wrighton KC, Carter DO, Knight R, Metcalf JL

Featured in Decomposer communities are universal in death by Strickland MS and Lynch L

2023

Cell Reports

Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression

Fu T, Huan T, Rahman G, Zhi H, Xu Z, Oh TG, Guo J, Coulter S, Tripathi A, Martino C, McCarville JL, Zhu Q, Cayabyab F, He M, Xing S, Vargas F, Yu RT, Atkins AR, Liddle C, Ayres J, Raffatellu M, Dorrestein PC, Downes M, Knight R, Evans RM

Microbiome

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Pavia MJ, Chede A, Wu Z, Cadillo-Quiroz H, Zhu Q

Nature Biotechnology

Generation of accurate, expandable phylogenomic trees with uDANCE

Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S

Nature Biotechnology

Greengenes2 unifies microbial data in a single reference tree

McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R

Frontiers in Microbiology

Metagenomics reveals novel microbial signatures of farm exposures in house dust

Wang Z, Dalton KR, Lee M, Parks CG, Beane Freeman LE, Zhu Q, González A, Knight R, Zhao S, Motsinger-Reif AA, London SJ

Nature Neuroscience

Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cárdenas P, Baldeón ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, Taroncher-Oldenburg G

Featured in Microbiome alterations in autism spectrum disorder by Coley-O’Rourke & Hsaio

Cancer Nursing

Distinct Nausea Profiles Are Associated With Gastrointestinal Symptoms In Oncology Patients Receiving Chemotherapy

Singh K, Pituch P, Zhu Q, Gu H, Ernst B, Tofthagen C, Brewer M, Kober KM, Cooper BA, Paul SM, Conley YP, Hammer M, Levine JD, Miaskowski C

Systematic Biology

DEPP: Deep Learning Enables Extending Species Trees using Single Genes

Jiang Y, Balaban M, Zhu Q, Mirarab S

2022

Journal of Allergy and Clinical Immunology

The gut microbiome is a significant risk factor for future chronic lung disease

Liu Y, Teo SM, Meric G, Tang HHF, Zhu Q, Sanders JG, Vazquez-Baeza Y, Verspoor K, Vartiainen VA, Jousilahti P, Lahti L, Niiranen T, Havulinna AS, Knight R, Salomaa V, Inouye M

Nature Microbiology

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Shaffer JP, Nothias LF, Thompson LR, Sanders JG, Salido RA, Couvillion SP, Brejnrod AD, Lejzerowicz F, Haiminen N, Huang S, Lutz HL, Zhu Q, Martino C, Morton JT, Karthikeyan S, Nothias-Esposito M, Dührkop K, Böcker S, Kim HW, Aksenov AA, Bittremieux W, Minich JJ, Marotz C, Bryant MM, Sanders K, Schwartz T, Humphrey G, Vásquez-Baeza Y, Tripathi A, Parida L, Carrieri AP, Beck KL, Das P, González A, McDonald D, Karst SM, Albertsen M, Ackermann G, DeReus J, Thomas T, Petras D, Shade A, Stegen J, Song SJ, Metz TO, Swafford AD, Dorrestein PC, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project 500 (EMP500) Consortium

Cell (cover paper)

Pan-cancer analyses reveal cancer type-specific fungal ecologies and bacteriome interactions

Haziza LN, Sepich-Poore GD, Livyatan I, Asraf O, Martino C, Nejman D, Gavert N, Stajich JE, Amit G, González A, Wandro S, Perry G, Ariel R, Meltser A, Shaffer JP, Zhu Q, Balint-Lahat N, Barshack I, Dadiani M, Gal-Yam EN, Patel SP, Bashan A, Swafford AD, Pilpel Y, Knight R, Straussman R

mSystems

Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References

Hakim D, Wandro S, Zengler K, Zaramela L, Nowinski B, Swafford A, Zhu Q, Song SJ, González A, McDonald D, Knight R

Microbiome

Location-Specific Signatures of Crohn’s Disease at a Multi-omics Scale

Gonzalez CG, Mills RH, Zhu Q, Sauceda C, Knight R, Dulai PS, Gonzalez DJ

Nature Biotechnology

Enhancing untargeted metabolomics using metadata-based source annotation

Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP Jr, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC

mSystems

Phylogeny-aware analysis of metagenome community ecology based on matched reference genomes while bypassing taxonomy

Zhu Q (co-corresponding), Huang S, Gonzalez A, McGrath I, McDonald M, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R

mSystems

Swapping metagenomics preprocessing pipeline components offers speed and sensitivity increases

Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, Dereus J, Zhu Q, Roush D, McDonald D, Gonzalez A, Shaffer J, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford A, Moshiri N, Rosing T, Knight R

Cell Metabolism

Early prediction of incident liver disease using conventional risk factors and gut microbiome-augmented gradient boosting

Liu Y, Meric G, Havulinna AS, Teo SM, Aberg F, Ruuskanen M, Sanders J, Zhu Q, Tripathi A, Verspoor K, Cheng S, Jain M, Jousilahti P, Vazquez-Baeza Y, Loomba R, Lahti L, Niiranen T, Salomaa V, Knight R, Inouye M

Cellular and Molecular Gastroenterology and Hepatology

The Host-Microbiome Response to Hyperbaric Oxygen Therapy in Ulcerative Colitis Patients

Gonzalez CG, Mills RH, Kordahi M, Carrillo-Terrazas M, Secaira-Morocho H, Widjaja CE, Tsai MS, Mittal Y, Yee BA, Vargas F, Weldon K, Gauglitz JM, Delaroque C, Sauceda C, Rossitto LA, Ackermann G, Humphrey G, Swafford AD, Siegel CA, Buckey Jr JC, Raffals LE, Sadler C, Lindholm P, Fisch KM, Valaseck M, Suriawinata A, Yeo GW, Ghosh P, Chang JT, Chu H, Dorrestein P, Zhu Q, Chassaing B, Knight R, Gonzalez DJ, Dulai PS

Scientific Reports

Microbiome and metabolome profiles of high screen time in a cohort of healthy college students

Jasbi P, Mohr AE, Shi X, Mahmood T, Zhu Q, Bruening M, Gu H, Whisner C

Nature

A gut-derived metabolite alters brain activity and anxiety behavior in mice

Needham BD, Funabashi M, Adame MD, Wang Z, Boktor JC, Haney J, Wu WL, Rabut C, Ladinsky MS, Hwang SJ, Guo Y, Zhu Q, Griffiths JA, Knight R, Bjorkman PJ, Shapiro MG, Geschwind DH, Holschneider DP, Fischbach MA, Mazmanian SK

Nature Genetics

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

Qin Y, Havulinna AS, Liu Y, Jousilahti P, Ritchie SC, Tokolyi A, Sanders JG, Valsta L, Brożyńska M, Zhu Q, Tripathi A, Vázquez-Baeza Y, Loomba R, Cheng S, Jain M, Niiranen T, Lahti L, Knight R, Salomaa V, Inouye M, Méric G

Nature Microbiology

Multi-omics analyses of the ulcerative colitis gut microbiome link _Bacteroides vulgatus_ proteases with disease severity

Mills RH, Dulai PS, Vázquez-Baeza Y, Sauceda C, Daniel N, Gerner RR, Batachari LE, Malfavon M, Zhu Q, Weldon K, Humphrey G, Carrillo-Terrazas M, Goldasich LD, Bryant M, Raffatellu M, Quinn RA, Gewirtz AT, Chassaing B, Chu H, Sandborn WJ, Dorrestein PC, Knight R, Gonzalez DJ

Molecular Ecology Resources

Fast and Accurate Distance‐based Phylogenetic Placement using Divide and Conquer

Balaban M, Jiang Y, Roush D, Zhu Q, Mirarab S

Cancer Nursing

Multiple Gastrointestinal Symptoms Are Associated With Chemotherapy-Induced Nausea In Patients With Breast Cancer

Singh KP, Kober KM, Ernst B, Sachdev J, Brewer M, Zhu Q, Gu H, Melisko M, Paul SM, Cooper BA, Hammer M, Conley YP, Levine JD, Miaskowski C

2021

Genome Research

Efficient computation of Faith’s phylogenetic diversity with applications in characterizing microbiomes

Armstrong G, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri AP, Zhu Q, Gonzalez A, McGrath I, Beck K, Hakim D, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford AD, Kim HC, Parida L, Vázquez-Baeza Y, Knight R

The ISME Journal

Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers

Zhu Q, Hou Q, Huang S, Ou Q, Huo D, Vázquez-Baeza Y, Cen C, Cantu V, Estaki M, Chang H, Belda-Ferre P, Kim HC, Chen K, Knight R, Zhang J

Microbiome

Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome

Huang S, Jiang S, Huo D, Allaband C, Estaki M, Cantu V, Belda-Ferre P, Vázquez-Baeza Y, Zhu Q, Ma C, Li C, Zarrinpar A, Liu YY, Knight R, Zhang J

Nature Methods

Challenges in Benchmarking Metagenomic Profilers

Sun Z, Huang S, Zhang M, Zhu Q, Haiminen M, Carrieri AP, Vázquez-Baeza Y, Parida L, Kim HC, Knight R, Liu YY

The ISME Journal

Insight into the function and evolution of Wood-Ljungdahl pathway in Actinobacteria

Jiao JY, Fu L, Hua ZS, Liu L, Salam N, Liu PF, Lv AP, Wu G, Xian WD, Zhu Q, Zhou EM, Fang BZ, Oren A, Hedlund BP, Jiang HC, Knight R, Cheng L, Li WJ

Nature Methods

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

Karst SM, Ziels RM, Kirkegaard RH, Sørensen EA, McDonald D, Zhu Q, Knight R, Albertsen M

Nature Chemical Biology

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

Tripathi A, Vazquez-Baeza Y, Gauglitz JM, Wang M, Duhrkop K, Esposito-Nothias M, Acharya DD, Ernst M, van der Hooft JJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC

mSystems

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R

Environmental Science & Technology

Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing

Bhagwat G, Zhu Q, O'Connor W, Subashchandrabose S, Grainge, I, Knight R, Palanisami T

Marine Drugs

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria

Leão T, Wang M, Moss N, da Silva R, Sanders J, Nurk S, Gurevich A, Humphrey G, Reher R, Zhu Q, Belda-Ferre P, Glukhov E, Whitner S, Alexander KL, Rex R, Pevzner P, Dorrestein PC, Knight R, Bandeira N, Gerwick WH, Gerwick L

2020

Microbiome

Expanding magnetic organelle biogenesis in the domain Bacteria

Lin W, Zhang W, Paterson GA, Zhu Q, Zhao X, Knight R, Bazylinski DA, Roberts AP, Pan Y

Nature Communications

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

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

Bioinformatics

SHOGUN: a modular, accurate, and scalable framework for microbiome quantification

Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Knight R, Knights D

Current Protocols in Bioinformatics

QIIME 2 enables comprehensive end-to-end analysis of diverse microbiome data and comparative studies with publicly available data

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

Nature Microbiology

Home chemical and microbial transitions across urbanization

McCall L, Callewaert C, Zhu Q (co-first), 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

2019

Nature Communications

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

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

Among top 50 life and biological sciences articles of the journal in 2019.

Genome Biology

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

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

Nature Biotechnology

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

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

Cell

FXR Regulates Intestinal Cancer Stem Cell Proliferation

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

mSystems

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease

Mills RH, Vázquez-Baeza Y, Zhu Q, Jiang L, Gaffney J, Humphrey G, Smarr L, Knight R, Gonzalez DJ

mSystems

Calour: an Interactive, Microbe-Centric Analysis Tool

Xu ZZ, Amir A, Sanders J, Zhu Q, Morton JT, Bletz MC, Tripathi A, Huang S, McDonald D, Jiang L, Knight R

2018

Microbiome

Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea

Zhu Q, Dupont CL, Jones MB, Pham KM, Jiang ZD, DuPont HL, Highlander SK

Frontiers in Microbiology

Metagenomics-based, strain-level analysis of Escherichia coli from a time-series of microbiome samples from a Crohn’s disease patient

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

mSystems

Evaluating the information content of shallow shotgun metagenomics

Hillmann B, Al-Ghalith G, Shields-Cutler R, Zhu Q, Gohl D, Beckman K, Knight R, Knights D

MicrobiologyOpen

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus)

Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R

Current Opinion in Microbiology

Are microbiome studies ready for hypothesis-driven research?

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

Nature Communications

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota

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

mSystems

American Gut: an Open Platform for Citizen Science Microbiome Research

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

European Psychiatry

Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis

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

Nature Microbiology

Methods for phylogenetic analysis of microbiome data

Washburne AD, Morton JT, Sanders J, McDonald D, Zhu Q, Oliverio AM, Knight R

Nature Reviews Microbiology

Best practices for analysing microbiomes

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

mSystems

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

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

Scientific Reports

Creating a 3D microbial and chemical snapshot of a human habitat

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

2017 and before

2017, Nature

A communal catalogue reveals Earth’s multiscale microbial diversity

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

2017, Proceedings of the National Academy of Sciences

Origin of microbial biomineralization and magnetotaxis during the Archean

Lin W, Paterson GA, Zhu Q, Wang Y, Kopylov E, Li Y, Knight R, Bazylinski DA, Zhu R, Kirschvink JL, Pan Y

2017, Animal Science Journal

The origin of Chinese domestic horses revealed with novel mtDNA variants

Yang Y, Zhu Q, Liu S, Zhao C, Wu C

2016, BMC Genomics

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species

Li W, Richter RA, Jung Y, Zhu Q, Li RW

2016, BMC Evolutionary Biology

On the probability of dinosaur fleas

Dittmar K, Zhu Q, Hastriter MW, Whiting MF

2015, International Journal of Dairy Technology

Home storage significantly impairs Bifidobacteria survival in powered formula for infants and young children in the Chinese market

Liu Y, Yu Y, Duan W, Qu Q, Zhang Q, Zhao M, Zhu Q

2015, Evolutionary Bioinformatics

RNA: an expanding view of function and evolution

Han X, Chen Y, Wang L, Fang W, Zhang N, Zhu Q

2015, Molecular Phylogenetics and Evolution

Fleas (Siphonaptera) are Cretaceous, and evolved with Theria

Zhu Q, Hastriter MW, Whiting MF, Dittmar K

2015, PLOS Neglected Tropical Diseases

Bartonella spp. in fruit bats and blood-feeding ectoparasites in Madagascar

Brook CE, Bai Y, Dobson AP, Osikowicz LM, Ranaivoson HC, Zhu Q, Kosoy MY, Dittmar K

2014, BMC Genomics

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

Zhu Q (co-corresponding), Kosoy M, Dittmar K

2014, Genome Biology and Evolution

Horizontal transfers and gene losses in the phospholipid pathway of Bartonella reveal clues about early ecological niches

Zhu Q (co-corresponding), Kosoy M, Olival KJ, Dittmar K

2011, Nucleic Acids Research

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison

Kazemian M, Zhu Q, Halfon MS, Sinha S

2009, Developmental Cell

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse

Kantorovitz MR, Kazemian M, Kinston S, Miranda-Saavedra D, Zhu Q, Robinson GE, Göttgens B, Halfon MS, Sinha S

2008, Genetica

Recent duplication and positive selection of the GAGE gene family

Liu Y, Zhu Q (co-first), Zhu N

2007, Immunological Investigations

Rapid HLA-DR fluorotyping based on melting curve analysis

Liu Y, Zhu Q, Zhu N

Book chapters

2022, Environmental Microbial Evolution - Methods in Molecular Biology. Ed. Luo H. pp. 137-165. Humana, New York, NY

Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies

Zhu Q (corresponding), Mirarab S

2015, Parasite Diversity and Diversification - Evolutionary Ecology Meets Phylogenetics. Ed. Morand S, Krasnov BR, Littlewood DTJ. Cambridge University Press

Evolutionary history of Siphonaptera: fossils, origins, vectors

Dittmar K, Zhu Q, Hastriter MW, Whiting MF