Integrating spatially-resolved transcriptomics data across tissues and individuals: challenges and opportunities

Authors: Guo, Boyi, Ling, Wodan, Kwon, Sang Ho, Panwar, Pratibha, Ghazanfar, Shila, Martinowich, Keri, Hicks, Stephanie C.

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/2408.00367

Deep ensemble learning over the microbial phylogenetic tree (DeepEn-Phy)

Authors: Ling, Wodan, Qi, Youran, Hua, Xing, Wu, Michael C.

Source: 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2021 IEEE International Conference on. :470-477 Dec, 2021

Relation: 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

STATISTICAL INFERENCE IN QUANTILE REGRESSION FOR ZERO-INFLATED OUTCOMES

Authors: Ling, Wodan, Cheng, Bin, Wei, Ying, Willey, Joshua Z., Cheung, Ying Kuen

Source: Statistica Sinica, 2022 Jan 01. 32(3), 1411-1433.

Access URL: https://www.jstor.org/stable/27164213

ZERO-INFLATED QUANTILE RANK-SCORE BASED TEST (ZIQRANK) WITH APPLICATION TO SCRNA-SEQ DIFFERENTIAL GENE EXPRESSION ANALYSIS

Authors: Ling, Wodan, Zhang, Wenfei, Cheng, Bin, Wei, Ying

Source: The Annals of Applied Statistics, 2021 Dec 01. 15(4), 1673-1696.

Access URL: https://www.jstor.org/stable/27273904

Integrating Spatially‐Resolved Transcriptomics Data Across Tissues and Individuals: Challenges and Opportunities.

Authors: Guo, Boyi¹ (AUTHOR), Ling, Wodan² (AUTHOR), Kwon, Sang Ho^3,4,5 (AUTHOR), Panwar, Pratibha^6,7,8 (AUTHOR), Ghazanfar, Shila^6,7,8 (AUTHOR) shila.ghazanfar@sydney.edu.au, Martinowich, Keri^3,4,9,10,11 (AUTHOR) keri.martinowich@libd.org, Hicks, Stephanie C.^1,12,13 (AUTHOR) shicks19@jhu.edu

Source: Small Methods. Feb2025, p1. 13p. 11 Illustrations.

ZINQ-L: a zero-inflated quantile approach for differential abundance analysis of longitudinal microbiome data.

Authors: Li, Shuai, Li, Runzhe, Lee, John R., Zhao, Ni, Ling, Wodan

Source: Frontiers in Genetics; 2025, p1-14, 14p

Subject Terms: KIDNEY transplantation, LONGITUDINAL method, FALSE discovery rate, PHENOTYPES, PRICE inflation, SIGNALS & signaling

General Kernel Machine Methods for Multi‐Omics Integration and Genome‐Wide Association Testing With Related Individuals.

Authors: Little, Amarise, Zhao, Ni, Mikhaylova, Anna, Zhang, Angela, Ling, Wodan, Thibord, Florian, Johnson, Andrew D., Raffield, Laura M., Curran, Joanne E., Blangero, John, O'Connell, Jeffrey R., Xu, Huichun, Rotter, Jerome I., Rich, Stephen S., Rice, Kenneth M., Chen, Ming‐Huei, Reiner, Alexander, Kooperberg, Charles, Vu, Thao, Hou, Lifang

Source: Genetic Epidemiology; Feb2025, Vol. 49 Issue 1, p1-17, 17p

Testing microbiome association using integrated quantile regression models

Authors: Wang, Tianying, Ling, Wodan, Plantinga, Anna M, Wu, Michael C, Zhan, Xiang

Source: Bioinformatics. 38(2):419-425

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100138747029.0x000001&indx=1&recIds=ETOCvdc_100138747029.0x000001

Enhanced visualization of microbiome data in repeated measures designs.

Authors: Little, Amarise, Deek, Rebecca A., Zhang, Angela, Zhao, Ni, Ling, Wodan, Wu, Michael C.

Source: Frontiers in Genetics; 2024, p1-13, 13p

Subject Terms: REPEATED measures design, CONFOUNDING variables, RESEARCH personnel, DATA visualization, NUISANCES

SurvBal: compositional microbiome balances for survival outcomes.

Authors: Li, Ying¹, Lee, Teresa², Marin, Kai², Hua, Xing², Srinivasan, Sujatha³, Fredricks, David N^3,4, Lee, John R^5,6, Ling, Wodan¹, wol4002@med.cornell.edu

Source: Bioinformatics; Oct2024, Vol. 40 Issue 10, p1-4, 4p

Accommodating multiple potential normalizations in microbiome associations studies.

Authors: Song, Hoseung¹ (AUTHOR), Ling, Wodan¹ (AUTHOR), Zhao, Ni² (AUTHOR), Plantinga, Anna M.³ (AUTHOR), Broedlow, Courtney A.⁴ (AUTHOR), Klatt, Nichole R.⁴ (AUTHOR), Hensley-McBain, Tiffany⁵ (AUTHOR), Wu, Michael C.¹ (AUTHOR) mcwu@fredhutch.org

Source: BMC Bioinformatics. 1/19/2023, Vol. 24 Issue 1, p1-15. 15p.

Subject Terms: *FALSE positive error, *MICROBIAL communities, *REGRESSION analysis

Factors associated with preventable hospitalizations after hospice live discharge among Medicare patients with Alzheimer's disease and related dementias.

Authors: Zhang, Yongkang, Luth, Elizabeth A., Phongtankuel, Veerawat, Ling, Wodan, Zhang, Manyao, Shao, Hui

Source: Journal of the American Geriatrics Society; Nov2023, Vol. 71 Issue 11, p3631-3635, 5p

Subject Terms: HOSPICE care, ALZHEIMER'S disease, CONFIDENCE intervals, RETROSPECTIVE studies, REGRESSION analysis, DEMENTIA patients, ADVANCE directives (Medical care), HOSPITAL care, DEMENTIA, DESCRIPTIVE statistics, RESEARCH funding, STATISTICAL sampling, DISCHARGE planning, MEDICARE, LONGITUDINAL method, PROPORTIONAL hazards models

Conditional Quantile Inference with Zero-Inflated Outcomes
Joint statistical meetings

Authors: Ling, Wodan, Wei, Ying, Cheng, Bin, Cheung, Ken

Source: JSM proceedings (CD-ROM edition). 2018:344-5

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCCN605173741&indx=1&recIds=ETOCCN605173741

Batch effects removal for microbiome data via conditional quantile regression.

Authors: Ling, Wodan, Lu, Jiuyao, Zhao, Ni, Lulla, Anju, Plantinga, Anna M., Fu, Weijia, Zhang, Angela, Liu, Hongjiao, Song, Hoseung, Li, Zhigang, Chen, Jun, Randolph, Timothy W., Koay, Wei Li A., White, James R., Launer, Lenore J., Fodor, Anthony A., Meyer, Katie A., Wu, Michael C.

Source: Nature Communications; 9/15/2022, Vol. 13 Issue 1, p1-14, 14p

Subject Terms: QUANTILE regression, REGRESSION analysis, EXPERIMENTAL design

Comparison of the Vaginal Microbiota in Postmenopausal Black and White Women.

Authors: Hudson, Patricia L^1,2 (AUTHOR), Ling, Wodan³ (AUTHOR), Wu, Michael C³ (AUTHOR), Hayward, Matthew R⁴ (AUTHOR), Mitchell, Alissa J² (AUTHOR), Larson, Joseph³ (AUTHOR), Guthrie, Katherine A³ (AUTHOR), Reed, Susan D⁵ (AUTHOR), Kwon, Douglas S^4,6 (AUTHOR), Mitchell, Caroline M^1,2 (AUTHOR) caroline.mitchell@mgh.harvard.edu

Source: Journal of Infectious Diseases. Dec2021, Vol. 224 Issue 11, p1945-1949. 5p.

Subject Terms: *WHITE women, *BLACK women, *HUMAN microbiota, *CLINICAL trial registries, *SHOTGUN sequencing

Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ).

Authors: Ling, Wodan, Zhao, Ni, Plantinga, Anna M., Launer, Lenore J., Fodor, Anthony A., Meyer, Katie A., Wu, Michael C.

Source: Microbiome; 9/2/2021, Vol. 9 Issue 1, p1-19, 19p

Subject Terms: TAXONOMY, BACTERIAL diversity, QUANTILES, METAGENOMICS, LOGISTIC regression analysis

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Evaluation of a recommender app for apps for the treatment of depression and anxiety: an analysis of longitudinal user engagement.

Authors: Cheung, Ken¹, yc632@cumc.columbia.edu, Ling, Wodan¹, Karr, Chris J², Weingardt, Kenneth³, Schueller, Stephen M³, Mohr, David C³

Source: Journal of the American Medical Informatics Association; Aug2018, Vol. 25 Issue 8, p955-962, 8p, 1 Diagram, 4 Charts, 3 Graphs