Publications

Association rule mining of the human gut microbiome

Zhang Y, Ke, S, Wang X, Liu YY

Science China Life Sciences, in press

Demonstrating the beneficial effect of low protein diet in primary sclerosing cholangitis through a randomized clinical trial and multi-omics data analysis

Yin X, Sasson G, Sun Z, Ke, S, Babazadeh D, Mahmood SD, Andrews M, Hurwitz S, Chikowore T, Paul M, Javier N, Dave M, Austin A, Gray L, Steinberg F, Souza E, Bowlus S, Liu Y, Korzenik J

Cell Reports Medicine

Identification of antimicrobial peptides from urinary bacteria for the inhibition of uropathogenic Escherichia coli in urinary tract infections via deep learning

Ke, S, Wang X, Weiss ST, Liu YY

TBD

Investigating the Role of the Human Microbiome in Primary Sclerosing Cholangitis and Inflammatory Bowel Disease Through Multi-Omics Profiling Across Body Sites

Ke, S, Yin X, Zheng S, Mahmood S, Korzenik J, Liu YY

TBD

Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection

Ke, S, Gálvez JAV, Sun Z, Cao Y, Pollock NR, Chen X, Kelly CP, Liu, YY

The Journal of Infectious Diseases

Fulfilled mind, healthy gut? Relationships of eudaimonic psychological well-being with the gut microbiome in postmenopausal women

Guimond, AJ^#, Ke, S^#, Tworoger SS, Huang T, Chan AT, Kubzansky LD, Liu, Yang-Yu

Psychosomatic Medicine

Association of Post-Traumatic Stress Disorder with Dietary Pattern and Gut Microbiome in a Cohort of Women

Ke, S, Wang X, Ratanatharathorn A, Huang T, Roberts A, Grodstein F, Kubzansky L, Koenen KC, Liu, Yang-Yu

Nature Mental Health

A computational method to dissect colonization resistance of the gut microbiota against pathogens

Ke, S^#, Xiao, Y^#Weiss ST, Chen X, Kelly CP, Liu YY

Cell Reports Methods

The emerging role of the gut microbiome in posttraumatic stress disorder

Ke, S, Hartmann J, Ressler KJ, Liu YY, Koenen KC

Brain Behavior Immunity

Extensive identification of serum metabolites related to microbes in different gut locations and evaluating their associations with porcine fatness

Liu Q, He M, Zeng Z, Huang X, Fang S, Zhao Y, Ke, S, Wu J, Zhou Y, Xiong X, Li Z, Fu H, Huang L, Chen C

Microbial Biotechnology

Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women

Ke, S^#, Guimond, AJ^#, Tworoger SS, Huang T, Chan AT, Liu YY, Kubzansky LD

Microbial Biotechnology

. Benchmarking omics-based prediction of asthma development in children

Wang XW, Wang T, Schaub DP, Chen C, Sun Z, Ke, S, Hecker J, Maaser-Hecker A, Zeleznik OA, Zeleznik R, Litonjua AA, DeMeo DL, Lasky-Su J, Silverman EK, Liu YY, Weiss ST

Respiratory Research

Yak rumen microbiome elevates fiber degradation ability and alters rumen fermentation pattern to increase feed efficiency

Zhao C, Wang L, Ke, S, Chen X, Kenéz Á, Xu W, Wang D, Zhang F, Li Y, Cui Z, Qiao Y, Wang J, Sun W, Zhao J, Yao J, Yu Z, Cao Y

Animal Nutrition

Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes

Ke, S, Weiss ST, Liu YY

Nature Communications

Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort

Cao, Y^#, Wang,L^#, Ke, S^#, Kelly CP, Pollock NR, Villafuerte Gálvez JA, Daugherty K, Xu H, Yao J, Chen Y, Liu YY, Chen X

Microbiology Spectrum

Rejuvenating the human gut microbiome

Ke, S, Weiss ST, Liu YY

Trends Molecular Medicine

ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs

Yang H, Wu J, Huang X, Zhou Y, Zhang Y, Liu M, Liu Q, , Ke, S, He M, Fu H, Fang S, Xiong X, Jiang H, Chen Z, Wu Z, Gong H, Tong X, Huang Y, Ma J, Gao J, Charlier C, Coppieters W, Shagam L, Zhang Z, Ai H, Yang B, Georges M, Chen C, Huang L

Nature

Gut Microbiota Predicts Healthy Late-Life Aging in Male Mice

Ke, S, Mitchell SJ, MacArthur MR, Kane AE, Sinclair DA, Venable EM, Chadaideh KS, Carmody RN, Grodstein F, Mitchell JR, Liu YY

Nutrients

Deep Investigating the Changes of Gut Microbiome and Its Correlation With the Shifts of Host Serum Metabolome Around Parturition in Sows

Fu H, He M, Wu J, Zhou Y, Ke, S, Chen Z, Liu Q, Liu M, Jiang H, Huang L, Chen C

Frontiers in Microbiology.

Gut and Vagina Microbiota Associated With Estrus Return of Weaning Sows and Its Correlation With the Changes in Serum Metabolites

Zhang J, Liu M, Ke, S, Huang X, Fang S, He M, Fu H, Chen C, Huang L

Frontiers in Microbiology.

Fecal Mycobiota Combined With Host Immune Factors Distinguish Clostridioides difficile Infection From Asymptomatic Carriage

Cao, Y^#, Wang,L^#, Ke, S^#, Villafuerte Gálvez JA, Pollock NR, Barrett C, Sprague R, Daugherty K, Xu H, Lin Q, Yao J, Chen Y, Kelly CP, Liu YY, Chen X

Gastroenterology.

Integrating gut microbiome and host immune markers to understand the pathogenesis of Clostridioides difficile infection

Ke, S, Pollock NR, Wang XW, Chen X, Daugherty K, Lin Q, Xu H, Garey KW, Gonzales-Luna AJ, Kelly CP, Liu YY

Gut Microbes

Dramatic Remodeling of the Gut Microbiome Around Parturition and Its Relationship With Host Serum Metabolic Changes in Sows

Huang X, Gao J, Zhao Y, He M, Ke, S, Wu J, Zhou Y, Fu H, Yang H, Chen C, Huang L

Frontiers in Microbiology

Host Gender and Androgen Levels Regulate Gut Bacterial Taxa in Pigs Leading to Sex-Biased Serum Metabolite Profiles

He M, Gao J, Wu J, Zhou Y, Fu H, Ke, S, Yang H, Chen C, Huang L

Frontiers in Microbiology

Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition

Ke, S, Fang S, He M, Huang X, Yang H, Yang B, Chen C, Huang L

BMC Veterinary Research

Evaluating the profound effect of gut microbiome on host appetite in pigs

Yang H, Yang M, Fang S, Huang X, He M, Ke, S, Gao J, Wu J, Zhou Y, Fu H, Chen C, Huang L

BMC Microbiology

Evaluating the contribution of gut microbiome to the variance of porcine serum glucose and lipid concentration

Huang X, Fang S, Yang H, Gao J, He M, Ke, S, Zhao Y, Chen C, Huang L

Scientific Reports

Tanshinone IIA protects against pulmonary arterial hypertension in broilers

Hu, G^#, Song,Y^#, Ke, S^#, Cao H, Zhang C, Deng G, Yang F, Zhou S, Liu P, Guo X, Liu P

Poultry Science

Genome-wide association studies identify susceptibility loci affecting respiratory disease in Chinese Erhualian pigs under natural conditions

Huang X, Huang T, Deng W, Yan G, Qiu H, Huang Y, Ke, S, Hou Y, Zhang Y, Zhang Z, Fang S, Zhou L, Yang B, Ren J, Ai H, Huang L

Animal Genetics

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples

He M, Fang S, Huang X, Zhao Y, Ke, S, Yang H, Li Z, Gao J, Chen C, Huang L

Frontiers in Microbiology