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The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies.
Published in:
Frontiers in Aging Neuroscience, 2022, v. 14, p. 1, doi. 10.3389/fnagi.2022.875261
By:
- Lubomski, Michal;
- Xu, Xiangnan;
- Holmes, Andrew J.;
- Muller, Samuel;
- Yang, Jean Y. H.;
- Davis, Ryan L.;
- Sue, Carolyn M.
Publication type:
Article
Nutritional Intake and Gut Microbiome Composition Predict Parkinson's Disease.
Published in:
Frontiers in Aging Neuroscience, 2022, v. 14, p. 1, doi. 10.3389/fnagi.2022.881872
By:
- Lubomski, Michal;
- Xu, Xiangnan;
- Holmes, Andrew J.;
- Muller, Samuel;
- Yang, Jean Y. H.;
- Davis, Ryan L.;
- Sue, Carolyn M.
Publication type:
Article
scREMOTE: Using multimodal single cell data to predict regulatory gene relationships and to build a computational cell reprogramming model.
Published in:
NAR Genomics & Bioinformatics, 2022, v. 4, n. 1, p. 1, doi. 10.1093/nargab/lqac023
By:
- Tran, Andy;
- Yang, Pengyi;
- Yang, Jean Y H;
- Ormerod, John T
Publication type:
Article
Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance.
Published in:
eLife, 2018, p. 1, doi. 10.7554/eLife.32111
By:
- Fazakerley, Daniel J.;
- Chaudhuri, Rima;
- Pengyi Yang;
- Maghzal, Ghassan J.;
- Thomas, Kristen C.;
- Krycer, James R.;
- Humphrey, Sean J.;
- Parker, Benjamin L.;
- Fisher-Wellman, Kelsey H.;
- Meoli, Christopher C.;
- Hoffman, Nolan J.;
- Diskin, Ciana;
- Burchfield, James G.;
- Cowley, Mark J.;
- Kaplan, Warren;
- Modrusan, Zora;
- Kolumam, Ganesh;
- Yang, Jean Y. H.;
- Chen, Daniel L.;
- Samocha-Bonet, Dorit
Publication type:
Article
Differential distribution improves gene selection stability and has competitive classification performance for patient survival.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 13, p. 1, doi. 10.1093/nar/gkw444
By:
- Strbenac, Dario;
- Mann, Graham J.;
- Yang, Jean Y. H.;
- Ormerod, John T.
Publication type:
Article
scJoint integrates atlas-scale single-cell RNA-seq and ATAC-seq data with transfer learning.
Published in:
Nature Biotechnology, 2022, v. 40, n. 5, p. 703, doi. 10.1038/s41587-021-01161-6
By:
- Lin, Yingxin;
- Wu, Tung-Yu;
- Wan, Sheng;
- Yang, Jean Y. H.;
- Wong, Wing H.;
- Wang, Y. X. Rachel
Publication type:
Article
Whole genome duplication in oral squamous cell carcinoma in patients younger than 50 years: implications for prognosis and adverse clinicopathological factors.
Published in:
Genes, Chromosomes & Cancer, 2022, v. 61, n. 9, p. 561, doi. 10.1002/gcc.23076
By:
- Satgunaseelan, Laveniya;
- Strbenac, Dario;
- Willet, Cali;
- Chew, Tracy;
- Sadsad, Rosemarie;
- Wykes, James;
- Low, Tsu‐Hui;
- Cooper, Wendy A.;
- Lee, C. Soon;
- Palme, Carsten E.;
- Yang, Jean Y. H.;
- Clark, Jonathan R.;
- Gupta, Ruta
Publication type:
Article
SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data.
Published in:
GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac071
By:
- Zhang, Yunwei;
- Wong, Germaine;
- Mann, Graham;
- Muller, Samuel;
- Yang, Jean Y H
Publication type:
Article
Evaluating stably expressed genes in single cells.
Published in:
GigaScience, 2019, v. 8, n. 9, p. N.PAG, doi. 10.1093/gigascience/giz106
By:
- Lin, Yingxin;
- Ghazanfar, Shila;
- Strbenac, Dario;
- Wang, Andy;
- Patrick, Ellis;
- Lin, David M;
- Speed, Terence;
- Yang, Jean Y H;
- Yang, Pengyi
Publication type:
Article
BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data.
Published in:
Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-023-44560-w
By:
- Fu, Xiaohang;
- Lin, Yingxin;
- Lin, David M.;
- Mechtersheimer, Daniel;
- Wang, Chuhan;
- Ameen, Farhan;
- Ghazanfar, Shila;
- Patrick, Ellis;
- Kim, Jinman;
- Yang, Jean Y. H.
Publication type:
Article
Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39923-2
By:
- Lin, Yingxin;
- Cao, Yue;
- Willie, Elijah;
- Patrick, Ellis;
- Yang, Jean Y. H.
Publication type:
Article
Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02622-0
By:
- Yu, Lijia;
- Cao, Yue;
- Yang, Jean Y. H.;
- Yang, Pengyi
Publication type:
Article
Lipidomics Profiling and Risk of Coronary Artery Disease in the BioHEART-CT Discovery Cohort.
Published in:
Biomolecules (2218-273X), 2023, v. 13, n. 6, p. 917, doi. 10.3390/biom13060917
By:
- Zhu, Dantong;
- Vernon, Stephen T.;
- D'Agostino, Zac;
- Wu, Jingqin;
- Giles, Corey;
- Chan, Adam S.;
- Kott, Katharine A.;
- Gray, Michael P.;
- Gholipour, Alireza;
- Tang, Owen;
- Beyene, Habtamu B.;
- Patrick, Ellis;
- Grieve, Stuart M.;
- Meikle, Peter J.;
- Figtree, Gemma A.;
- Yang, Jean Y. H.
Publication type:
Article
Viral Integration Plays a Minor Role in the Development and Prognostication of Oral Squamous Cell Carcinoma.
Published in:
Cancers, 2022, v. 14, n. 21, p. 5213, doi. 10.3390/cancers14215213
By:
- Satgunaseelan, Laveniya;
- Strbenac, Dario;
- Tadi, Sahithi;
- Nguyen, Kevin;
- Wykes, James;
- Palme, Carsten E.;
- Low, Tsu-Hui;
- Yang, Jean Y. H.;
- Clark, Jonathan R.;
- Gupta, Ruta
Publication type:
Article
Analysis of the Whole-Exome Sequencing of Tumor and Circulating Tumor DNA in Metastatic Melanoma.
Published in:
Cancers, 2019, v. 11, n. 12, p. 1905, doi. 10.3390/cancers11121905
By:
- Diefenbach, Russell J.;
- Lee, Jenny H.;
- Strbenac, Dario;
- Yang, Jean Y. H.;
- Menzies, Alexander M.;
- Carlino, Matteo S.;
- Long, Georgina V.;
- Spillane, Andrew J.;
- Stretch, Jonathan R.;
- Saw, Robyn P. M.;
- Thompson, John F.;
- Ch'ng, Sydney;
- Scolyer, Richard A.;
- Kefford, Richard F.;
- Rizos, Helen
Publication type:
Article
Integrated single cell data analysis reveals cell specific networks and novel coactivation markers.
Published in:
BMC Systems Biology, 2016, v. 10, p. 11, doi. 10.1186/s12918-016-0370-4
By:
- Ghazanfar, Shila;
- Bisogni, Adam J.;
- Ormerod, John T.;
- Lin, David M.;
- Yang, Jean Y. H.
Publication type:
Article
Scalable workflow for characterization of cell-cell communication in COVID-19 patients.
Published in:
PLoS Computational Biology, 2022, v. 18, n. 10, p. 1, doi. 10.1371/journal.pcbi.1010495
By:
- Lin, Yingxin;
- Loo, Lipin;
- Tran, Andy;
- Lin, David M.;
- Moreno, Cesar;
- Hesselson, Daniel;
- Neely, G. Gregory;
- Yang, Jean Y. H.
Publication type:
Article
Oral Squamous Cell Carcinoma in Young Patients Show Higher Rates of EGFR Amplification: Implications for Novel Personalized Therapy.
Published in:
Frontiers in Oncology, 2021, v. 11, p. 1, doi. 10.3389/fonc.2021.750852
By:
- Satgunaseelan, Laveniya;
- Porazinski, Sean;
- Strbenac, Dario;
- Istadi, Aji;
- Willet, Cali;
- Chew, Tracy;
- Sadsad, Rosemarie;
- Palme, Carsten E.;
- Lee, Jenny H.;
- Boyer, Michael;
- Yang, Jean Y. H.;
- Clark, Jonathan R.;
- Pajic, Marina;
- Gupta, Ruta
Publication type:
Article
Genome-wide analysis in Drosophila reveals diet-by-gene interactions and uncovers diet-responsive genes.
Published in:
G3: Genes | Genomes | Genetics, 2021, v. 11, n. 10, p. 1, doi. 10.1093/g3journal/jkab171
By:
- Francis, Deanne;
- Ghazanfar, Shila;
- Havula, Essi;
- Krycer, James R.;
- Strbenac, Dario;
- Senior, Alistair;
- Minard, Annabel Y.;
- Geddes, Thomas;
- Nelson, Marin E.;
- Weiss, Fiona;
- Stöckli, Jacqueline;
- Yang, Jean Y. H.;
- James, David E.
Publication type:
Article
Autoencoder-based cluster ensembles for single-cell RNA-seq data analysis.
Published in:
BMC Bioinformatics, 2019, v. 20, p. 1, doi. 10.1186/s12859-019-3179-5
By:
- Geddes, Thomas A.;
- Taiyun Kim;
- Lihao Nan;
- Burchfield, James G.;
- Yang, Jean Y. H.;
- Dacheng Tao;
- Pengyi Yang
Publication type:
Article
A field guide to cultivating computational biology.
Published in:
PLoS Biology, 2021, v. 19, n. 10, p. 1, doi. 10.1371/journal.pbio.3001419
By:
- Way, Gregory P.;
- Greene, Casey S.;
- Carninci, Piero;
- Carvalho, Benilton S.;
- de Hoon, Michiel;
- Finley, Stacey;
- Gosline, Sara J. C.;
- Lȇ Cao, Kim-Anh;
- Lee, Jerry S. H.;
- Marchionni, Luigi;
- Robine, Nicolas;
- Sindi, Suzanne S.;
- Theis, Fabian J.;
- Yang, Jean Y. H.;
- Carpenter, Anne E.;
- Fertig, Elana J.
Publication type:
Article
scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell RNA sequencing data.
Published in:
Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad062
By:
- Hao, Jie;
- Zou, Jiawei;
- Zhang, Jiaqiang;
- Chen, Ke;
- Wu, Duojiao;
- Cao, Wei;
- Shang, Guoguo;
- Yang, Jean Y H;
- Wong-Lin, KongFatt;
- Sun, Hourong;
- Zhang, Zhen;
- Wang, Xiangdong;
- Chen, Wantao;
- Zou, Xin
Publication type:
Article
NEMoE: a nutrition aware regularized mixture of experts model to identify heterogeneous diet-microbiome-host health interactions.
Published in:
Microbiome, 2023, v. 11, n. 1, p. 1, doi. 10.1186/s40168-023-01475-4
By:
- Xu, Xiangnan;
- Lubomski, Michal;
- Holmes, Andrew J.;
- Sue, Carolyn M.;
- Davis, Ryan L.;
- Muller, Samuel;
- Yang, Jean Y. H.
Publication type:
Article
Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development.
Published in:
BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4342-x
By:
- Xianbin Su;
- Yi Shi;
- Xin Zou;
- Zhao-Ning Lu;
- Gangcai Xie;
- Yang, Jean Y. H.;
- Chong-Chao Wu;
- Xiao-Fang Cui;
- Kun-Yan He;
- Qing Luo;
- Yu-Lan Qu;
- Na Wang;
- Lan Wang;
- Ze-Guang Han
Publication type:
Article
The impact of device-assisted therapies on the gut microbiome in Parkinson's disease.
Published in:
Journal of Neurology, 2022, v. 269, n. 2, p. 780, doi. 10.1007/s00415-021-10657-9
By:
- Lubomski, Michal;
- Xu, Xiangnan;
- Holmes, Andrew J.;
- Yang, Jean Y. H.;
- Sue, Carolyn M.;
- Davis, Ryan L.
Publication type:
Article
Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma.
Published in:
Prostate, 2020, v. 80, n. 6, p. 508, doi. 10.1002/pros.23965
By:
- Su, Xianbin;
- Long, Qi;
- Bo, Juanjie;
- Shi, Yi;
- Zhao, Li‐Nan;
- Lin, Yingxin;
- Luo, Qing;
- Ghazanfar, Shila;
- Zhang, Chao;
- Liu, Qiang;
- Wang, Lan;
- He, Kunyan;
- He, Jian;
- Cui, Xiaofang;
- Yang, Jean Y. H.;
- Han, Ze‐Guang;
- Yang, Guoliang;
- Sha, Jian‐jun
Publication type:
Article
Cross-Platform Omics Prediction procedure: a statistical machine learning framework for wider implementation of precision medicine.
Published in:
NPJ Digital Medicine, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s41746-022-00618-5
By:
- Wang, Kevin Y. X.;
- Pupo, Gulietta M.;
- Tembe, Varsha;
- Patrick, Ellis;
- Strbenac, Dario;
- Schramm, Sarah-Jane;
- Thompson, John F.;
- Scolyer, Richard A.;
- Muller, Samuel;
- Tarr, Garth;
- Mann, Graham J.;
- Yang, Jean Y. H.
Publication type:
Article
Computational approaches for direct cell reprogramming: from the bulk omics era to the single cell era.
Published in:
Briefings in Functional Genomics, 2022, v. 21, n. 4, p. 270, doi. 10.1093/bfgp/elac008
By:
- Tran, Andy;
- Yang, Pengyi;
- Yang, Jean Y H;
- Ormerod, John
Publication type:
Article
Detection and classification of peaks in 5’ cap RNA sequencing data.
Published in:
BMC Genomics, 2013, v. 14, p. 1, doi. 10.1186/1471-2164-14-S5-S9
By:
- Strbenac, Dario;
- Armstrong, Nicola J.;
- Yang, Jean Y. H.
Publication type:
Article
bcGST—an interactive bias-correction method to identify over-represented gene-sets in boutique arrays.
Published in:
Bioinformatics, 2019, v. 35, n. 8, p. 1350, doi. 10.1093/bioinformatics/bty783
By:
- Wang, Kevin Y X;
- Menzies, Alexander M;
- Silva, Ines P;
- Wilmott, James S;
- Yan, Yibing;
- Wongchenko, Matthew;
- Kefford, Richard F;
- Scolyer, Richard A;
- Long, Georgina V;
- Tarr, Garth;
- Mueller, Samuel;
- Yang, Jean Y H
Publication type:
Article
DCARS: differential correlation across ranked samples.
Published in:
Bioinformatics, 2019, v. 35, n. 5, p. 823, doi. 10.1093/bioinformatics/bty698
By:
- Ghazanfar, Shila;
- Strbenac, Dario;
- Ormerod, John T;
- Yang, Jean Y H;
- Patrick, Ellis
Publication type:
Article
Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data.
Published in:
Bioinformatics, 2015, v. 31, n. 17, p. 2822, doi. 10.1093/bioinformatics/btv220
By:
- Patrick, Ellis;
- Buckley, Michael;
- Müller, Samuel;
- Lin, David M.;
- Yang, Jean Y. H.
Publication type:
Article
ClassifyR: an R package for performance assessment of classification with applications to transcriptomics.
Published in:
2015
By:
- Strbenac, Dario;
- Mann, Graham J.;
- Ormerod, John T.;
- Yang, Jean Y. H.
Publication type:
Product Review
Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15726-7
By:
- Lee, Jenny H.;
- Shklovskaya, Elena;
- Lim, Su Yin;
- Carlino, Matteo S.;
- Menzies, Alexander M.;
- Stewart, Ashleigh;
- Pedersen, Bernadette;
- Irvine, Malama;
- Alavi, Sara;
- Yang, Jean Y. H.;
- Strbenac, Dario;
- Saw, Robyn P. M.;
- Thompson, John F.;
- Wilmott, James S.;
- Scolyer, Richard A.;
- Long, Georgina V.;
- Kefford, Richard F.;
- Rizos, Helen
Publication type:
Article
Gene expression allelic imbalance in ovine brown adipose tissue impacts energy homeostasis.
Published in:
PLoS ONE, 2017, v. 12, n. 6, p. 1, doi. 10.1371/journal.pone.0180378
By:
- Ghazanfar, Shila;
- Vuocolo, Tony;
- Morrison, Janna L.;
- Nicholas, Lisa M.;
- McMillen, Isabella C.;
- Yang, Jean Y. H.;
- Buckley, Michael J.;
- Tellam, Ross L.
Publication type:
Article
LC-N2G: a local consistency approach for nutrigenomics data analysis.
Published in:
BMC Bioinformatics, 2020, v. 21, n. 1, p. N.PAG, doi. 10.1186/s12859-020-03861-3
By:
- Xu, Xiangnan;
- Solon-Biet, Samantha M.;
- Senior, Alistair;
- Raubenheimer, David;
- Simpson, Stephen J.;
- Fontana, Luigi;
- Mueller, Samuel;
- Yang, Jean Y. H.
Publication type:
Article

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