2024 Mitchell, Joshua | Chi, Yuanye | Thapa, Maheshwor | Pang, Zhiqiang | Xia, Jianguo | Li, Shuzhao
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline
bioRxiv, , 2024--02, 2024
2024 Pang, Zhiqiang | Lu, Yao | Zhou, Guangyan | Hui, Fiona | Xu, Lei | Viau, Charles | Spigelman, Aliya F | MacDonald, Patrick E | Wishart, David S | Li, Shuzhao | others
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation
Nucleic Acids Research, , gkae253, 2024
2023 Li, Shuzhao | Siddiqa, Amnah | Thapa, Maheshwor | Chi, Yuanye | Zheng, Shujian
Trackable and scalable LC-MS metabolomics data processing using asari
Nature Communications, 14, 4113, 2023
2023 Li, Shuzhao | Zheng, Shujian
Generalized tree structure to annotate untargeted metabolomics and stable isotope tracing data
Analytical chemistry, 95, 6212--6217, 2023
2023 Siddiqa, Amnah | Wang, Yating | Thapa, Maheshwor | Martin, Dominique E | Cadar, Andreia N | Bartley, Jenna M | Li, Shuzhao
A pilot metabolomic study of drug interaction with the immune response to seasonal influenza vaccination
npj Vaccines, 8, 92, 2023
2022 Lee, Choon-myung | Liu, Ken H | Singer, Grant | Miller, Gary W | Li, Shuzhao | Jones, Dean P | Morgan, Edward T
High-Throughput Production of Diverse Xenobiotic Metabolites with Cytochrome P450--Transduced Huh7 Hepatoma Cell Lines
Drug Metabolism and Disposition, 50, 1182--1189, 2022
2022 Singer, Grant T | Liu, Ken H | Lee, Choon M | Miller, Gary W | Li, Shuzhao | Go, Young-Mi | Jones, Dean P | Morgan, Edward T
Evaluating Co-occurrence as a Criterion for Identification of Undocumented Xenobiotic Exposures in Human Metabolomics
The FASEB Journal, 36, , 2022
2021 Chang HY, Colby SM, Du X, Gomez JD, Helf MJ, Kechris K, Kirkpatrick CR, Li S, Patti GJ, Renslow RS, Subramaniam S, Verma M, Xia J, Young JD.
A Practical Guide to Metabolomics Software Development
Anal Chem, 93, 1921, 2021
2021 Liu, Ken H | Lee, Choon M | Singer, Grant | Bais, Preeti | Castellanos, Francisco | Woodworth, Michael H | Ziegler, Thomas R | Kraft, Colleen S | Miller, Gary W | Li, Shuzhao | others
Large scale enzyme based xenobiotic identification for exposomics
Nature Communications, 12, 5418, 2021
2021 Lee, Choon-myung | Liu, Ken | Singer, Grant | Miller, Gary | Li, Shuzhao | Jones, Dean | Morgan, Edward
Pooling Strategies to Improve Throughput of High Resolution Mass Spectrometry-Based Analysis of Xenobiotic Metabolites Generated from Huh7 Human Hepatoma Cell Lines Transduced with P450 Enzymes
The FASEB Journal, 35, , 2021
2021 Liu, Ken | Lee, Choon-myung | Singer, Grant | Woodworth, Michael | Ziegler, Thomas | Kraft, Colleen | Miller, Gary | Li, Shuzhao | Go, Young-Mi | Morgan, Edward | others
Enzyme-based chemical identification for metabolomics
The FASEB Journal, 35, , 2021
2021 Pang, Zhiqiang | Chong, Jasmine | Zhou, Guangyan | de Lima Morais, David Anderson | Chang, Le | Barrette, Michel | Gauthier, Carol | Jacques, Pierre-{\'Etienne | Li, Shuzhao | Xia, Jianguo
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights
Nucleic acids research, 49, W388--W396, 2021
2021 L|ay, Alan | Bartley, Jenna M | Banerjee, Dishary | Hargis, Geneva | Haynes, Laura | Keshavarzian, Ali | Kuo, Chia-Ling | Kwon, Oh Sung | Li, Sheng | Li, Shuzhao | others
Network topology of biological aging and geroscience-guided approaches to COVID-19
Frontiers in aging, 2, 695218, 2021
2020 Hu, Xin | Li, Shuzhao | Cirillo, Piera | Krigbaum, Nickilou | Tran, ViLinh | Ishikawa, Tomoko | La Merrill, Michele A | Jones, Dean P | Cohn, Barbara
Metabolome wide association study of serum DDT and DDE in pregnancy and early postpartum
Reproductive toxicology, 92, 129--137, 2020
2020 Ge, Yong | Gong, Minghao | Zadeh, Mojgan | Li, Jing | Abbott, Jeffrey R | Li, Wei | Morel, Laurence | Sonon, Roberto | Supekar, Nitin T | Azadi, Parastoo | others
Regulating colonic dendritic cells by commensal glycosylated large surface layer protein A to sustain gut homeostasis against pathogenic inflammation
Mucosal immunology, 13, 34--46, 2020
2020 Li, Shuzhao | Cirillo, Piera | Hu, Xin | Tran, ViLinh | Krigbaum, Nickilou | Yu, Shaojun | Jones, Dean P | Cohn, Barbara
Understanding mixed environmental exposures using metabolomics via a hierarchical community network model in a cohort of California women in 1960’s
Reproductive toxicology, 92, 57--65, 2020
2020 Zhou, Guangyan | Li, Shuzhao | Xia, Jianguo
Network-based approaches for multi-omics integration
Computational methods and data analysis for metabolomics, , 469--487, 2020
2020 Karnovsky, Alla | Li, Shuzhao
Pathway analysis for targeted and untargeted metabolomics
Computational methods and data analysis for metabolomics, , 387--400, 2020
2020 Pittard, W Stephen | Li, Shuzhao
The essential toolbox of data science: Python, R, Git, and Docker
Computational Methods and Data Analysis for Metabolomics, , 265--311, 2020
2020 Pittard, W Stephen | Villaveces, Cecilia “Keeko” | Li, Shuzhao
A Bioinformatics Primer to Data Science, with Examples for Metabolomics
Computational Methods and Data Analysis for Metabolomics, , 245--263, 2020
2020 Hu, Xin | Li, Shuzhao | Cirillo, Piera M | Krigbaum, Nickilou Y | Tran, ViLinh | Jones, Dean P | Cohn, Barbara A
Reprint of “metabolome wide association study of serum poly and perfluoroalkyl substances (PFASs) in pregnancy and early postpartum”
Reproductive Toxicology, 92, 120--128, 2020
2020 Ferranti, Erin P | Frediani, Jennifer K | Mitchell, Rebecca | Fern|es, Jolyn | Li, Shuzhao | Jones, Dean P | Corwin, Elizabeth | Dunlop, Anne L | others
Early pregnancy serum metabolite profiles associated with hypertensive disorders of pregnancy in African American women: a pilot study
Journal of pregnancy, 2020, , 2020
2020 Corwin, Elizabeth | Dunlop, Anne L | Fern|es, Jolyn | Li, Shuzhao | Pearce, Bradley | Jones, Dean P
Metabolites and metabolic pathways associated with glucocorticoid resistance in pregnant African-American women
Comprehensive psychoneuroendocrinology, 1, 100001, 2020
2020 Collins, Jeffrey M | Siddiqa, Amnah | Jones, Dean P | Liu, Ken | Kempker, Russell R | Nizam, Azhar | Shah, N Sarita | Ismail, Nazir | Ouma, Samuel G | Tukvadze, Nestani | others
Tryptophan catabolism reflects disease activity in human tuberculosis
JCI insight, 5, , 2020
2020 Pang, Zhiqiang | Chong, Jasmine | Li, Shuzhao | Xia, Jianguo
MetaboAnalystR 3.0: toward an optimized workflow for global metabolomics
Metabolites, 10, 186, 2020
2020 Goll, Johannes B | Li, Shuzhao | Edwards, James L | Bosinger, Steven E | Jensen, Travis L | Wang, Yating | Hooper, William F | Gelber, Casey E | S|ers, Katherine L | Anderson, Evan J | others
Transcriptomic and metabolic responses to a live-attenuated francisella tularensis vaccine
Vaccines, 8, 412, 2020
2020 Liu, Qin | Walker, Douglas | Uppal, Karan | Liu, Zihe | Ma, Chunyu | Tran, ViLinh | Li, Shuzhao | Jones, Dean P | Yu, Tianwei
Addressing the batch effect issue for LC/MS metabolomics data in data preprocessing
Scientific reports, 10, 13856, 2020
2020 Palermo, Amelia | Huan, Tao | Rinehart, Duane | Rinschen, Markus M | Li, Shuzhao | O'Donnell, Valerie B | Fahy, Eoin | Xue, Jingchuan | Subramaniam, Shankar | Benton, H Paul | others
Cloud-based archived metabolomics data: A resource for in-source fragmentation/annotation, meta-analysis and systems biology
Analytical science advances, 1, 70--80, 2020
2019 Cordy, Regina Joice | Patrapuvich, Rapatbhorn | Lili, Loukia N | Cabrera-Mora, Monica | Chien, Jung-Ting | Tharp, Gregory K | Khadka, Manoj | Meyer, Esmeralda VS | Lapp, Stacey A | Joyner, Chester J | others
Distinct amino acid and lipid perturbations characterize acute versus chronic malaria
JCI insight, 4, , 2019
2019 Taylor Fischer, S | Frederick, Allison B | Tran, ViLinh | Li, Shuzhao | Jones, Dean P | Fridovich-Keil, Judith L
Metabolic perturbations in classic galactosemia beyond the Leloir pathway: insights from an untargeted metabolomic study
Journal of inherited metabolic disease, 42, 254--263, 2019
2019 Khadka, Manoj | Todor, Andrei | Maner-Smith, Kristal M | Colucci, Jennifer K | Tran, ViLinh | Gaul, David A | Anderson, Evan J | Natrajan, Muktha S | Rouphael, Nadine | Mulligan, Mark J | others
The effect of anticoagulants, temperature, and time on the human plasma metabolome and lipidome from healthy donors as determined by liquid chromatography-mass spectrometry
Biomolecules, 9, 200, 2019
2019 Ge, Yong | Gong, Minghao | Colliou, Natacha | Zadeh, Mojgan | Li, Jing | Jones, Dean P | Li, Shuzhao | Mohamadzadeh, Mansour
Neonatal intestinal immune regulation by the commensal bacterium, P. UF1
Mucosal immunology, 12, 434--444, 2019
2019 Hagan, Thomas | Cortese, Mario | Rouphael, Nadine | Boudreau, Carolyn | Linde, Caitlin | Maddur, Mohan S | Das, Jishnu | Wang, Hong | Guthmiller, Jenna | Zheng, Nai-Ying | others
Antibiotics-driven gut microbiome perturbation alters immunity to vaccines in humans
Cell, 178, 1313--1328, 2019
2019 Hu, Xin | Li, Shuzhao | Cirillo, Piera M | Krigbaum, Nickilou Y | Tran, ViLinh | Jones, Dean P | Cohn, Barbara A
Metabolome wide association study of serum poly and perfluoroalkyl substances (PFASs) in pregnancy and early postpartum
Reproductive toxicology, 87, 70--78, 2019
2018 Safo, S|ra E | Li, Shuzhao | Long, Qi
Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information
Biometrics, 74, 300--312, 2018
2018 Chong, Jasmine | Soufan, Othman | Li, Carin | Caraus, Iurie | Li, Shuzhao | Bourque, Guillaume | Wishart, David S | Xia, Jianguo
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
Nucleic acids research, 46, W486--W494, 2018
2018 Gardinassi, Luiz G | Ar{\'evalo-Herrera, Myriam | Herrera, S{\'ocrates | Cordy, Regina J | Tran, ViLinh | Smith, Matthew R | Johnson, Michelle S | Chacko, Balu | Liu, Ken H | Darley-Usmar, Victor M | others
Integrative metabolomics and transcriptomics signatures of clinical tolerance to Plasmodium vivax reveal activation of innate cell immunity and T cell signaling
Redox biology, 17, 158--170, 2018
2018 Walker, Douglas Ian | Kalia, Vrinda | Uppal, Karan | Li, Shuzhao | Miller, Gary W | Jones, Dean
Metabolome Wide Association Study and the Exposome: Linking Exposure to Internal Dose, Biological Response and Disease
ISEE Conference Abstracts, 2018, , 2018
2018 Schwartz, Charles E | Fischer, Taylor | Lili, Loukia | Li, Shuzhao | Tran, ViLinh | Stewart, Kim | Jones, Dean | Sherman, Stephanie | Fridovich-Keil, Judith
METABOLIC PERTURBATIONS IN SECOND-TRIMESTER ARE AMNIOTIC FLUID ASSOCIATED WITH LOW-LEVEL MATERNAL EXPOSURE TO NICOTINE
AMERICAN JOURNAL OF MEDICAL GENETICS PART A, 176, 1498--1499, 2018
2018 Li, Shuzhao
Metabolomics, Complex Exposures, and Multi-Omics Integration
ISEE Conference Abstracts, 2018, , 2018
2018 Li, C | Soufan, O | Chong, J | Xia, J | Bourque, G | Li, S | Caraus, I | Wishart, DS
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
Nucleic Acids Res, 46, W486--W494, 2018
2017 Alvarez, Jessica A | Chong, Elizabeth Y | Walker, Douglas I | Ch|ler, Joshua D | Michalski, Ellen S | Grossmann, Ruth E | Uppal, Karan | Li, Shuzhao | Frediani, Jennifer K | Tirouvanziam, Rabindra | others
Plasma metabolomics in adults with cystic fibrosis during a pulmonary exacerbation: a pilot randomized study of high-dose vitamin D3 administration
Metabolism, 70, 31--41, 2017
2017 Li, Shuzhao | Sullivan, Nicole L | Rouphael, Nadine | Yu, Tianwei | Banton, Sophia | Maddur, Mohan S | McCausl|, Megan | Chiu, Christopher | Canniff, Jennifer | Dubey, Sheri | others
Metabolic phenotypes of response to vaccination in humans
Cell, 169, 862--877, 2017
2017 Myers, Owen D | Sumner, Susan J | Li, Shuzhao | Barnes, Stephen | Du, Xiuxia
One step forward for reducing false positive and false negative compound identifications from mass spectrometry metabolomics data: new algorithms for constructing extracted ion chromatograms and detecting chromatographic peaks
Analytical chemistry, 89, 8696--8703, 2017
2017 Fischer, S Taylor | Lili, Loukia N | Li, Shuzhao | Tran, ViLinh T | Stewart, Kim B | Schwartz, Charles E | Jones, Dean P | Sherman, Stephanie L | Fridovich-Keil, Judith L
Low-level maternal exposure to nicotine associates with significant metabolic perturbations in second-trimester amniotic fluid
Environment international, 107, 227--234, 2017
2017 Sinclair, Charles | Bommakanti, Gayathri | Gardinassi, Luiz | Loebbermann, Jens | Johnson, Matthew Joseph | Hakimpour, Paul | Hagan, Thomas | Benitez, Lydia | Todor, Andrei | Machiah, Deepa | others
mTOR regulates metabolic adaptation of APCs in the lung and controls the outcome of allergic inflammation
Science, 357, 1014--1021, 2017
2017 Gardinassi, Luiz Gustavo | Cordy, Regina Joice | Lacerda, Marcus VG | Salinas, Jorge L | Monteiro, Wuelton M | Melo, Gisely C | Siqueira, Andr{\'e M | Val, Fern|o F | Tran, ViLinh | Jones, Dean P | others
Metabolome-wide association study of peripheral parasitemia in Plasmodium vivax malaria
International Journal of Medical Microbiology, 307, 533--541, 2017
2017 Colliou, Natacha | Ge, Yong | Sahay, Bikash | Gong, Minghao | Zadeh, Mojgan | Owen, Jennifer L | Neu, Josef | Farmerie, William G | Alonzo, Francis | Liu, Ken | others
Commensal Propionibacterium strain UF1 mitigates intestinal inflammation via Th17 cell regulation
The Journal of clinical investigation, 127, 3970--3986, 2017
2017 Gardinassi, Luiz Gustavo | Xia, Jianguo | Safo, S|ra E | Li, Shuzhao
Bioinformatics tools for the interpretation of metabolomics data
Current Pharmacology Reports, 3, 374--383, 2017
2017 Myers, Owen D | Sumner, Susan J | Li, Shuzhao | Barnes, Stephen | Du, Xiuxia
Detailed investigation and comparison of the XCMS and MZmine 2 chromatogram construction and chromatographic peak detection methods for preprocessing mass spectrometry metabolomics data
Analytical Chemistry, 89, 8689--8695, 2017
2017 Banton, Sophia | Luo, Ruiyan | Joice, Regina | Moreno, Alberto | Galinski, Mary R | Jones, Dean P | Li, Shuzhao
PATHWAY GROUP LASSO INTEGRATION OF METABOLOMICS AND TRANSCRIPTOMICS TO CHARACTERIZE MALARIA INFECTION IN RHESUS MACAQUES
AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE, 95, 463--463, 2017
2017 Morris, Claudia R | Ma, Chunyu | Li, Shuzhao | Jones, Dean | Brown, Lou Ann | Machado, Roberto F | Kato, Gregory J | Zhang, Yingze | Nouraie, Seyed Mehdi | Gladwin, Mark T
Biomarker Discovery: Novel Insights into Red Blood Cell Metabolomics in Patients with Sickle Cell Disease at Risk for Early Mortality
Blood, 130, 4772, 2017
2017 Alvarez, Jessica A | Chong, Elizabeth Y | Walker, Douglas I | Ch|ler, Joshua D | Michalski, Ellen S | Grossmann, Ruth E | Uppal, Karan | Li, Shuzhao | Frediani, Jennifer K | Tirouvanziam, Rabindra | others
Corrigendum to “Plasma metabolomics in adults with cystic fibrosis during a pulmonary exacerbation: A pilot randomized study of high-dose vitamin D3 administration”[Metabolism vol. 70, May 2017, pages 31--41]
Metabolism-Clinical and Experimental, 74, 41--42, 2017
2017 Alvarez, Jessica A | Chong, Elizabeth Y | Walker, Douglas I | Ch|ler, Joshua D | Michalski, Ellen S | Grossmann, Ruth E | Uppal, Karan | Li, Shuzhao | Frediani, Jennifer K | Tirouvanziam, Rabindra | others
Plasma metabolomics in adults with cystic fibrosis during a pulmonary exacerbation: A pilot randomized study of high-dose vitamin D-3 administration (vol 70, pg 31, 2017)
METABOLISM-CLINICAL AND EXPERIMENTAL, 74, 41--42, 2017
2016 Li S, Dunlop AL, Jones DP, Corwin EJ.
High-Resolution Metabolomics: Review of the Field and Implications for Nursing Science and the Study of Preterm Birth
Biol Res Nurs, 18, 12--22, 2016
2016 Ravindran R, Loebbermann J, Nakaya HI, Khan N, Ma H, Gama L, Machiah DK, Lawson B, Hakimpour P, Wang YC, Li S, Sharma P, Kaufman RJ, Martinez J, Pulendran B
The amino acid sensor GCN2 controls gut inflammation by inhibiting inflammasome activation
Nature, 531, 523--7, 2016
2016 Cribbs SK, Uppal K, Li S, Jones DP, Huang L, Tipton L, Fitch A, Greenblatt RM, Kingsley L, Guidot DM, Ghedin E, Morris A
Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection
Microbiome, 4, 3, 2016
2016 Jin R, Banton S, Tran VT, Konomi JV, Li S, Jones DP, Vos MB
Amino Acid Metabolism is Altered in Adolescents with Nonalcoholic Fatty Liver Disease-An Untargeted, High Resolution Metabolomics Study
J Pediatr., , , 2016
2016 Uppal, Karan | Tran, ViLinh | Jones, Dean | Li, Shuzhao | Esper, Annette M
High-Resolution Metabolomics Reveals Distinct Pathways In Septic Patients That Developed Acute Respiratory Distress Syndrome
B104. RESPIRATORY FAILURE: LUNG REGIONAL AND TRANSLATIONAL MECHANISMS IN ARDS, , A4407--A4407, 2016
2016 Perry-Walker, Kayla | Walker, Douglas I | Alvarez, Jessica A | Han, Jenny E | Jones, Jennifer L | Hao, Li | Li, Shuzhao | Uppal, Karan | Tran, ViLinh T | Brown, LouAnn | others
Impact of Vitamin D Status and High-dose Vitamin D3 Administration on the Plasma Metabolome in Critically Ill Adults
The FASEB Journal, 30, 271--3, 2016
2016 Ch|ler, Joshua D | Wongtrakool, Cherry | Banton, Sophia A | Li, Shuzhao | Orr, Michael L | Barr, Dana Boyd | Neujahr, David C | Sutliff, Roy L | Go, Young-Mi | Jones, Dean P
Low-dose oral cadmium increases airway reactivity and lung neuronal gene expression in mice
Physiological reports, 4, e12821, 2016
2016 Barnes, Stephen | Benton, H Paul | Casazza, Krista | Cooper, Sara J | Cui, Xiangqin | Du, Xiuxia | Engler, Jeffrey | Kabarowski, Janusz H | Li, Shuzhao | Pathmasiri, Wimal | others
Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future
Journal of mass spectrometry, 51, 535--548, 2016
2016 Barnes, Stephen | Benton, H Paul | Casazza, Krista | Cooper, Sara J | Cui, Xiangqin | Du, Xiuxia | Engler, Jeffrey | Kabarowski, Janusz H | Li, Shuzhao | Pathmasiri, Wimal | others
Training in metabolomics research. I. Designing the experiment, collecting and extracting samples and generating metabolomics data
Journal of Mass Spectrometry, 51, 461--475, 2016
2016 Uppal, Karan | Walker, Douglas I | Liu, Ken | Li, Shuzhao | Go, Young-Mi | Jones, Dean P
Computational metabolomics: a framework for the million metabolome
Chemical research in toxicology, 29, 1956--1975, 2016
2016 Cribbs, SK | Uppal, K | Li, S | Jones, DP | Huang, L | Tipton, L | Fitch, A | Greenblatt, RM | Kingsley, L | Guidot, DM | others
Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection. Microbiome 4: 3
, , , 2016
2015 Li S, Todor A, Luo R
Blood transcriptomics and metabolomics for personalized medicine
Comput Struct Biotechnol J, 14, 1--7, 2015
2015 Smith, Ellen | Grossmann, Ruth | Chong, Elizabeth | Uppal, Karan | Li, Shuzhao | Jones, Dean | Tangpricha, Vin | Ziegler, Thomas | Alvarez, Jessica
Plasma Metabolome-Wide Association Study of Clinical Variables in Hospitalized Adults with Cystic Fibrosis
The FASEB Journal, 29, 745--5, 2015
2015 Rao, Anuradha | Kosters, Astrid | Mells, Jamie | Keller, Bradley T | Yin, Hong | Banton, Sophia | Li, Shuzhao | Jones, Dean P | Wu, Hao | Dawson, Paul | others
Administration of an ileal apical sodium-dependent bile acid transporter inhibitor protects against non-alcoholic fatty liver disease in high fat diet-fed mice
Hepatology, 62, 217A--217A, 2015
2015 Sinclair, Charles | Loebbermann, Jens | Ravindran, Rajesh | Johnson, Matthew | Bommakanti, Gayathri | Li, Shuzhao | Pulendran, Bali
Critical roles for mTOR signaling in DC homeostasis and function (INC6P. 306)
The Journal of Immunology, 194, 192--8, 2015
2015 Li, Shuzhao
Mummichog: pathway and network analysis for metabolomics
, , , 2015
2015 Vos, Miriam B | Jin, Ran | Banton, Sophia | Li, Shuzhao | Jones, Dean P
Discovery of plasma biomarkers for NAFLD using high resolution metabolomics
HEPATOLOGY, 62, 1295A--1295A, 2015
2014 Li, Shuzhao | Rouphael, Nadine | Duraisingham, Sai | Romero-Steiner, S|ra | Presnell, Scott | Davis, Carl | Schmidt, Daniel S | Johnson, Scott E | Milton, Andrea | Rajam, Gowrisankar | others
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines
Nature immunology, 15, 195--204, 2014
2014 Ravindran, Rajesh | Khan, Nooruddin | Nakaya, Helder I | Li, Shuzhao | Loebbermann, Jens | Maddur, Mohan S | Park, Youngja | Jones, Dean P | Chappert, Pascal | Davoust, Jean | others
Vaccine activation of the nutrient sensor GCN2 in dendritic cells enhances antigen presentation
Science, 343, 313--317, 2014
2014 Hoffman, Jessica M | Soltow, Quinlyn A | Li, Shuzhao | Sidik, Alfire | Jones, Dean P | Promislow, Daniel EL
Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, D rosophila melanogaster
Aging Cell, 13, 596--604, 2014
2014 Boube, I | Lotz, JM | Pozhitkov, AE | Li, S | Griffitt, RJ
Identification of genes involved in Taura Syndrome Virus resistance in Litopenaeus vannamei
Journal of aquatic animal health, 26, 137--143, 2014
2014 Xu, Xiaojin | Araki, Koichi | Li, Shuzhao | Han, Jin-Hwan | Ye, Lilin | Tan, Wendy G | Konieczny, Bogumila T | Bruinsma, Monique W | Martinez, Jennifer | Pearce, Erika L | others
Autophagy is essential for effector CD8+ T cell survival and memory formation
Nature immunology, 15, 1152--1161, 2014
2013 Li, Shuzhao | Nakaya, Helder I | Kazmin, Dmitri A | Oh, Jason Z | Pulendran, Bali
Systems biological approaches to measure and understand vaccine immunity in humans
Seminars in immunology, 25, 209--218, 2013
2013 Li, Shuzhao | Park, Youngja | Duraisingham, Sai | Strobel, Frederick H | Khan, Nooruddin | Soltow, Quinlyn A | Jones, Dean P | Pulendran, Bali
Predicting network activity from high throughput metabolomics
PLoS computational biology, 9, e1003123, 2013
2013 Yu, Tianwei | Park, Youngja | Li, Shuzhao | Jones, Dean P
Hybrid feature detection and information accumulation using high-resolution LC--MS metabolomics data
Journal of proteome research, 12, 1419--1427, 2013
2012 Nakaya, Helder I | Li, Shuzhao | Pulendran, Bali
Systems vaccinology: learning to compute the behavior of vaccine induced immunity
Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 4, 193--205, 2012
2012 Roede, James R | Park, Youngja | Li, Shuzhao | Strobel, Frederick H | Jones, Dean P
Detailed mitochondrial phenotyping by high resolution metabolomics
PloS one, 7, e33020, 2012
2012 Wilkinson, Peter | Filali-Mouhim, Abdelali | Li, Shuzhao | Ahlers, Jeffrey | Schatzle, John | Pulendran, Bali | Sekaly, Rafick-Pierre | Cameron, Mark J
An open-ended plea for the development of a global database of HIV vaccine responses
Current Opinion in HIV and AIDS, 7, 10--16, 2012
2011 Nakaya, Helder I | Wrammert, Jens | Lee, Eva K | Racioppi, Luigi | Marie-Kunze, Stephanie | Haining, W Nicholas | Means, Anthony R | Kasturi, Sudhir P | Khan, Nooruddin | Li, Gui-Mei | others
Systems biology of vaccination for seasonal influenza in humans
Nature immunology, 12, 786--795, 2011
2010 Pulendran, Bali | Li, Shuzhao | Nakaya, Helder I
Systems vaccinology
Immunity, 33, 516--529, 2010
2010 Li, Shuzhao | Pozhitkov, Alex|er | Ryan, Rachel A | Manning, Charles S | Brown-Peterson, Nancy | Brouwer, Marius
Constructing a fish metabolic network model
Genome biology, 11, 1--15, 2010
2009 Cornish, E Jean | Hassan, Sabah M | Martin, Joshua D | Li, Shuzhao | Merzdorf, Christa S
A microarray screen for direct targets of Zic1 identifies an aquaporin gene, aqp-3b, expressed in the neural folds
Developmental dynamics: an official publication of the American Association of Anatomists, 238, 1179--1194, 2009
2008 Li, Shuzhao | Pozhitkov, Alex | Brouwer, Marius
A competitive hybridization model predicts probe signal intensity on high density DNA microarrays
Nucleic acids research, 36, 6585--6591, 2008
2006 Li, Shuzhao | Shin, Yongchol | Cho, Ken WY | Merzdorf, Christa S
The Xfeb gene is directly upregulated by Zic1 during early neural development
Developmental dynamics, 235, 2817--2827, 2006
2006 Li, Shuzhao | Cho, Ken W | Merzdorf, Christa
The Xfeb gene is a direct target of zic1 and is expressed in the hindbrain
Developmental Biology, 295, 381--382, 2006
, , ,
Colliou, Natacha | Ge, Yong | Sahay, Bikash | Gong, Minghao | Zadeh, Mojgan | Owen, Jennifer L | Neu, Josef | Farmerie, William G | Alonzo III, Francis | Liu, Ken | others
Supplemental data includes
, , ,
Chong, Jasmine | Soufan, Othman | Li, Carin | Caraus, Iurie | Li, Shuzhao | Bourque, Guillaume | David, S
Wishart, and Jianguo Xia. 2018.“MetaboAnalyst 4.0: Towards More Transparent and Integrative Metabolomics Analysis.”
Nucleic Acids Research, 46, ,
Chong, J | Soufan, O | Li, C | Caraus, I | Li, S | Bourque, G | Wishart, DS | MetaboAnalyst, J Xia
4.0: Towards more transparent and integrative metabolomics analysis., 2018, 46, pp
W486-W494. DOI: https://doi. org/10.1093/nar/gky310, , ,
Pang, Z | Chong, J | Zhou, G | de Lima Morais, DA | Chang, L | Barrette, M | Gauthier, C | Jacques, PE | Li, S | MetaboAnalyst, J Xia
5.0: Narrowing the gap between raw spectra and functional insights., 2021, 49, pp
W388-W396. DOI: https://doi. org/10.1093/nar/gkab382. PMID: https://www. ncbi. nlm. nih. gov/pubmed/34019663, , ,