Sparse group principal component analysis via double thresholding with application to multi-cellular programs

Συγγραφείς: Xu, Qi, Lei, Jing, Roeder, Kathryn

Θεματικοί όροι: Methodology, Applications, Computation

Σύνδεσμος πρόσβασης: http://arxiv.org/abs/2602.04178

Shared multicellular injury programs of acute and chronic kidney disease enable mechanistic patient stratification

Συγγραφείς: Fallegger, Robin, Gomez-Ochoa, Sergio A., Boys, Charlotte, Ramirez Flores, Ricardo Omar, Tanevski, Jovan, Pashos, Evanthia, Feliers, Denis, Piper, Mary, Schaub, Jennifer A., Zhou, Zixiang, Mao, Weiguang, Chen, Xi, Sealfon, Rachel S. G., Menon, Rajasree, Nair, Viji, Eddy, Sean, Alakwaa, Fadhl M., Pyle, Laura, Choi, Ye Ji, Bjornstad, Petter, Alpers, Charles E., Bitzer, Markus, Bomback, Andrew S., Caramori, M. Luiza, Demeke, Dawit, Fogo, Agnes B., Herlitz, Leal C., Kiryluk, Krzysztof, Lash, James P., Murugan, Raghavan, O'Toole, John F., Palevsky, Paul M., Parikh, Chirag R., Rosas, Sylvia E., Rosenberg, Avi Z., Sedor, John R., Vazquez, Miguel A., Waikar, Sushrut S., Wilson, F. Perry, Hodgin, Jeffrey B., Barisoni, Laura, Himmelfarb, Jonathan, Jain, Sanjay, Ju, Wenjun, Troyanskaya, Olga G., Kretzler, Matthias, Eadon, Michael T., Saez-Rodriguez, Julio

Συνεισφορές: Medicine, School of Medicine

Πηγή: PMC

Θεματικοί όροι: Acute kidney injury, Chronic kidney disease, Single cell transcriptomics, Multi-cellular programs

Περιγραφή αρχείου: application/pdf

Relation: https://hdl.handle.net/1805/55148

Διαθεσιμότητα: https://hdl.handle.net/1805/55148

Shared multicellular injury programs of acute and chronic kidney disease enable mechanistic patient stratification.

Συγγραφείς: Fallegger R; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany., Gomez-Ochoa SA; Heidelberg University Hospital, Department of General Internal Medicine and Psychosomatics, Heidelberg, Germany., Boys C; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany., Flores ROR; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, U.K., Tanevski J; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany., Pashos E; Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, United States., Feliers D; Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, United States., Piper M; Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, United States., Schaub JA; Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA., Zhou Z; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.; Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA., Mao W; Princeton Precision Health, Princeton University, Princeton, NJ 08544, USA., Chen X; Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA., Sealfon RSG; Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA., Menon R; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Nair V; Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA., Eddy S; Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA., Alakwaa FM; Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA., Pyle L; University of Washington Medicine Diabetes Institute, Seattle, WA 98109, USA., Choi YJ; University of Washington Medicine Diabetes Institute, Seattle, WA 98109, USA., Bjornstad P; University of Washington Medicine Diabetes Institute and Seattle Children's Research Institute, Seattle, WA 98109, USA., Alpers CE; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195., Bitzer M; University of Michigan., Bomback AS; Division of Nephrology, Columbia University Irving Medical Center, New York, NY, USA., Caramori ML; Department of Endocrinology and Metabolism, Cleveland Clinic Foundation, Cleveland, OH, USA.; Department of Internal Medicine, Division of Diabetes, Endocrinology and Metabolism, University of Minnesota, Minneapolis, MN, USA., Demeke D; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA., Fogo AB; Department. Of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA., Herlitz LC; Cleveland Clinic., Kiryluk K; Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University., Lash JP; Department of Medicine, University of Illinois Chicago, Chicago, Illinois., Murugan R; University of Pittsburgh., O'Toole JF; Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic & Department of Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH., Palevsky PM; Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA., Parikh CR; Department of Medicine, Johns Hopkins School of Medicine, Baltimore, US., Rosas SE; Kidney and Hypertension Unit, Joslin Diabetes Center and Harvard Medical School, Boston, MA 02215, USA., Rosenberg AZ; Department of Pathology, Johns Hopkins University School of Medicine Baltimore, MD, USA., Sedor JR; Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic & Department of Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH., Vazquez MA; Nephrology Division, University of Texas Southwestern Medical Center., Waikar SS; Section of Nephrology, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine., Wilson FP; Clinical and Translational Research Accelerator, Department of Medicine, Yale School of Medicine, New Haven, CT., Hodgin JB; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA., Barisoni L; Department of Pathology, Division of AI & Computational Pathology, Department of Medicine, Division of Nephrology, Duke University, Durham, NC, USA., Himmelfarb J; Barbara T. Murphy Division of Nephrology, Samuel Bronfman Department of Medicine, Icahn School of Medicine at Mount Sinai., Jain S; Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA.; Kidney Translational Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA., Ju W; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.; Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA., Troyanskaya OG; Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.; Princeton Precision Health, Princeton University, Princeton, NJ 08544, USA.; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA.; Department of Computer Science, Princeton University, Princeton, NJ 08544, USA., Kretzler M; Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, MI 48109, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.; Co-senior authors: Matthias Kretzler, Michael T. Eadon, Julio Saez-Rodriguez., Eadon MT; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.; Co-senior authors: Matthias Kretzler, Michael T. Eadon, Julio Saez-Rodriguez., Saez-Rodriguez J; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany.; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, U.K.; Co-senior authors: Matthias Kretzler, Michael T. Eadon, Julio Saez-Rodriguez.

Πηγή: MedRxiv : the preprint server for health sciences [medRxiv] 2026 Mar 06. Date of Electronic Publication: 2026 Mar 06.

Τύπος έκδοσης: Journal Article; Preprint

Στοιχεία περιοδικού: Country of Publication: United States NLM ID: 101767986 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: medRxiv Subsets: PubMed not MEDLINE

Cell and tissue mechanics in 3-D organ morphogenesis: Insights from Drosophila pupal retina development

Συγγραφείς: Decker, Jacob R., Altinok, Irmak, Rebay, Ilaria ^⁎

Πηγή: In Developmental Biology August 2026 536:142-154

An exploratory simulation of the optimization of leukocyte transmigration, indicating that barrier routing is governed by context-dependent biochemical cues rather than hardwired programs.

Συγγραφείς: Religa, Piotr, Mickael, Michel-Edwar, Kubick, Norwin, Horbańczuk, Jarosław Olav, Sacharczuk, Mariusz

Πηγή: Frontiers in Immunology; 2026, p1-15, 15p

Θεματικοί όροι: Blood-brain barrier, Lymphocyte subsets, Cell migration, Inflammatory mediators, Sensitivity analysis

Beyond β-Adrenergic Receptor Brake: Compartment-Selective GRK2 Programs from Heart Failure to Cardio-Oncology.

Συγγραφείς: Dotson, Cody Reid, Underwood, Lilly, Sato, Priscila Y.

Πηγή: Kinases & Phosphatases; Sep2026, Vol. 4 Issue 3, p19, 19p

Θεματικοί όροι: G protein-coupled receptor kinases, Cardio-oncology, Beta adrenoceptors, Heart failure, Physiology, Cell communication

Spatial mapping of Ethiopian cutaneous leishmaniasis lesions reveals distinct tissue level immune programs.

Συγγραφείς: Dey, Nidhi S., Pham, Thao-Thy, Dey, Shoumit, Kassa, Mekibib, Mekonnen, Tigist, Fikre, Helina, Monsieurs, Pieter, Consortium, Spatial CL, Pareyn, Myrthe, van Griensven, Johan, Domagalska, Malgorzata, Dujardin, Jean-Claude, Asres, Mezgebu Silamsaw, Woldetensay, Mikias, Kaye, Paul M., Adriaensen, Wim

Πηγή: Frontiers in Immunology; 2026, p1-22, 22p

Θεματικοί όροι: Immunopathology, Immune response, Skin injuries, Ethiopians, RNA sequencing, Cutaneous leishmaniasis, Granuloma, Tissue remodeling

Multi-type branching models to describe cell differentiation programs

Συγγραφείς: Nordon, Robert E. ^{a, ⁎}, Ko, Kap-Hyoun ^a, Odell, Ross ^a, Schroeder, Timm ^b

Πηγή: In Journal of Theoretical Biology 2011 277(1):7-18

Multi-modal comparison of molecular programs driving nurse cell death and clearance in Drosophila melanogaster oogenesis.

Συγγραφείς: Bandyadka, Shruthi^1,2 (AUTHOR), Lebo, Diane P. V.² (AUTHOR), Mondragon, Albert A.^2,3 (AUTHOR), Serizier, Sandy B.^2,3 (AUTHOR), Kwan, Julian⁴ (AUTHOR), Peterson, Jeanne S.² (AUTHOR), Chasse, Alexandra Y.^2,3 (AUTHOR), Jenkins, Victoria² (AUTHOR), Calikyan, Anoush² (AUTHOR), Ortega, Anthony J.² (AUTHOR), Campbell, Joshua D.⁵ (AUTHOR), Emili, Andrew^2,4,6 (AUTHOR), McCall, Kimberly² (AUTHOR) kmccall@bu.edu

Πηγή: PLoS Genetics. 1/3/2025, Vol. 21 Issue 1, p1-32. 32p.

Θεματικοί όροι: *Apoptosis, *Drosophila melanogaster, *Drosophilidae, *Cell death, *Somatic cells

Matrix stiffness may drive multi-cellular crosstalk via YAP signaling in biliary atresia liver fibrosis: a mechanistic review.

Συγγραφείς: Cheng, Jiwen

Πηγή: Frontiers in Cell & Developmental Biology; 2026, p1-12, 12p

Θεματικοί όροι: Extracellular matrix, YAP signaling proteins, Hepatic fibrosis, Bile ducts, Liver cells, Biliary atresia

T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset.

Συγγραφείς: Di Giovenale, Stefano, Lischio, Ottavio, Cortile, Clelia, Corleone, Giacomo, Fanciulli, Maurizio, Bonchi, Francesco, Barozzi, Iros

Πηγή: NAR Genomics & Bioinformatics; Jun2026, Vol. 8 Issue 2, p1-15, 15p

Cell-autonomous timing drives the vertebrate segmentation clock's wave pattern.

Συγγραφείς: Rohde, Laurel A.^1,2, Bercowsky-Rama, Arianne¹, Valentin, Guillaume³, Naganathan, Sundar Ram^1,4, Desai, Ravi A.², Strnad, Petr¹, Soroldoni, Daniele^1,2, Oates, Andrew C.^1,2,4 andrew.oates@epfl.ch

Πηγή: eLife. 12/13/2024, p1-18. 18p.

Θεματικοί όροι: *Segmentation (Biology), *Developmental programs, *Gene expression, *Mesoderm, *Time management

Editorial: Hands-on Training Program.

Συγγραφείς: Kumiko Hayashi

Πηγή: Biophysics & Physicobiology; 2024 Supplement, Vol. 21, p1-10, 10p

Θεματικοί όροι: Life sciences, Grants in aid (Public finance), Nanoscience, Solid state physics, Optical tweezers

Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states

Συγγραφείς: Tianyu Liu, Edward De Brouwer, Tony Kuo, Nathaniel Diamant, Alsu Missarova, Hanchen Wang, Minsheng Hao, Tommaso Biancalani, Hector Corrada Bravo, Gabriele Scalia, Aviv Regev, Graham Heimberg

From mono- to multi-cellular in vitro models: reconstructing colorectal cancer complexity for translational and personalized applications.

Συγγραφείς: Edwards, Gareth Owain, Li Causi, Francesco Saverio, Castagnola, Giorgio, Singh, Shailendra, Amendola, Pier Giorgio

Πηγή: Frontiers in Cell & Developmental Biology; 2026, p1-11, 11p

Θεματικοί όροι: Colorectal cancer, Translational research, Immunological tolerance, Individualized medicine, Microphysiological systems, Tumor microenvironment, Drug development, Cell culture

Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues

Συγγραφείς: Yin Xu, Zurui Huang, Yawei Zhang, Minghui Gong, Zhenghang Wang, Peijin Guo, Feifan Zhang, Jing Yang, Guanghao Liang, Lihui Dong, Renbao Chang, Yu Xia, Haochen Ni, Wenxuan Gong, Boyuan Mei, Yuan Gao, Zhaoqi Liu, Lin Shen, Jian Li, Meng Michelle Xu, Dali Han

Πηγή: Nature Communications.

Θεματικοί όροι: 3. Good health

Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues

Συγγραφείς: Xu, Yin, Huang, Zurui, Zhang, Yawei, Han, Dali

Single‐Cell Mapping Identifies Aging‐Associated Neutrophil Remodeling Across Multiple Organs.

Συγγραφείς: Wang, Yuman, Chang, Teding, Fu, Yangguang, Liang, Guangyu, Liu, Huicheng, Zhang, Le, Yan, Jinhua, Liu, Man, Liu, Anding, Zhang, Cuntai

Πηγή: Aging Cell; Oct2026, Vol. 25 Issue 10, p1-26, 26p

Omics landscapes of hepatic echinococcosis: bulk foundations, emerging single-cell studies, and analytical considerations.

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Πηγή: Frontiers in Immunology; 2026, p1-10, 10p

Θεματικοί όροι: Hepatic echinococcosis, Multiomics, Neovascularization, Cell communication, Inflammation, Immunoregulation, RNA sequencing

Engineering Programmable Material-To-Cell Pathways Via Synthetic Notch Receptors To Spatially Control Cellular Phenotypes In Multi-Cellular Constructs.

Συγγραφείς: Garibyan M, Hoffman T, Makaske T, Do S, March AR, Cho N, Pedroncelli N, Lima RE, Soto J, Jackson B, Khademhosseini A, Li S, McCain M, Morsut L

Πηγή: BioRxiv : the preprint server for biology [bioRxiv] 2023 May 20. Date of Electronic Publication: 2023 May 20.

Τύπος έκδοσης: Preprint; Journal Article

Στοιχεία περιοδικού: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE