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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
HuBMAP (54)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Integrated spatial genomics reveals global architecture of single nuclei. | Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, Shengbao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, Long | Nature | 2021 02 | 33505024 | |
| Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. | McMillen, Josiah C; Fincher, Jarod A; Klein, Dustin R; Spraggins, Jeffrey M; Caprioli, Richard M | Journal of mass spectrometry : JMS. | 2020 Dec; | 33241625 | |
| Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells. | Martin, Kendall; Zhang, Tong; Zhang, Pengfei; Chrisler, William B; Thomas, Fillmore L; Liu, Fen; Liu, Tao; Qian, Wei-Jun; Smith, Richard D; Shi, Tujin | Journal of visualized experiments : JoVE. | 2020 11 06; | 33226031 | |
| Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. | Uzun, Yasin; Wu, Hao; Tan, Kai | Genome research | 2021 Jan | 33219054 | |
| High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. | Liu, Yang; Yang, Mingyu; Deng, Yanxiang; Su, Graham; Enninful, Archibald; Guo, Cindy C; Tebaldi, Toma; Zhang, Di; Kim, Dongjoo; Bai, Zhiliang; Norris, Eileen; Pan, Alisia; Li, Jiatong; Xiao, Yang; Halene, Stephanie; Fan, Rong | Cell. | 2020 Dec 10; | 33188776 | |
| CDKL5: a promising new therapeutic target for acute kidney injury? | de Caestecker, Mark P | American journal of physiology. Renal physiology. | 2020 Oct 19; | 33073588 | |
| Landscape of coordinated immune responses to H1N1 challenge in humans. | Rahil, Zainab; Leylek, Rebecca; Schürch, Christian M; Chen, Han; Bjornson-Hooper, Zach; Christensen, Shannon R; Gherardini, Pier Federico; Bhate, Salil S; Spitzer, Matthew H; Fragiadakis, Gabriela K; Mukherjee, Nilanjan; Kim, Nelson; Jiang, Sizun; Yo, Jennifer; Gaudilliere, Brice; Affrime, Melton; Bock, Bonnie; Hensley, Scott E; Idoyaga, Juliana; Aghaeepour, Nima; Kim, Kenneth; Nolan, Garry P; McIlwain, David R | The Journal of clinical investigation. | 2020 Nov 02; | 33044226 | |
| Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. | Rivera, Emilio S; Djambazova, Katerina V; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of mass spectrometry : JMS. | 2020 Jul 04; | 32955134 | |
| Single-cell metabolic profiling of human cytotoxic T cells. | Hartmann, Felix J; Mrdjen, Dunja; McCaffrey, Erin; Glass, David R; Greenwald, Noah F; Bharadwaj, Anusha; Khair, Zumana; Verberk, Sanne G S; Baranski, Alex; Baskar, Reema; Graf, William; Van Valen, David; Van den Bossche, Jan; Angelo, Michael; Bendall, Sean C | Nature biotechnology. | 2020 Aug 31; | 32868913 | |
| Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. | Schürch, Christian M; Bhate, Salil S; Barlow, Graham L; Phillips, Darci J; Noti, Luca; Zlobec, Inti; Chu, Pauline; Black, Sarah; Demeter, Janos; McIlwain, David R; Kinoshita, Shigemi; Samusik, Nikolay; Goltsev, Yury; Nolan, Garry P | Cell. | 2020 Sep 03; | 32763154 | |
| An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. | Glass, David R; Tsai, Albert G; Oliveria, John Paul; Hartmann, Felix J; Kimmey, Samuel C; Calderon, Ariel A; Borges, Luciene; Glass, Marla C; Wagar, Lisa E; Davis, Mark M; Bendall, Sean C | Immunity. | 2020 Jul 14; | 32668225 | |
| A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. | Keyes, Timothy J; Domizi, Pablo; Lo, Yu-Chen; Nolan, Garry P; Davis, Kara L | Cytometry. Part A : the journal of the International Society for Analytical Cytology. | 2020 08; | 32602650 | |
| Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. | Ji, Andrew L; Rubin, Adam J; Thrane, Kim; Jiang, Sizun; Reynolds, David L; Meyers, Robin M; Guo, Margaret G; George, Benson M; Mollbrink, Annelie; Bergenstråhle, Joseph; Larsson, Ludvig; Bai, Yunhao; Zhu, Bokai; Bhaduri, Aparna; Meyers, Jordan M; Rovira-Clavé, Xavier; Hollmig, S Tyler; Aasi, Sumaira Z; Nolan, Garry P; Lundeberg, Joakim; Khavari, Paul A | Cell. | 2020 Jul 23; | 32579974 | |
| The Importance of Clinical Tissue Imaging. | Spraggins, Jeffrey M; Schwamborn, Kristina; Heeren, Ron M A; Eberlin, Livia S | Clinical mass spectrometry (Del Mar, Calif.). | 2019 Apr; | 32483555 | |
| Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. | Islam, Mirazul; Chen, Bob; Spraggins, Jeffrey M; Kelly, Ryan T; Lau, Ken S | Gastroenterology. | 2020 Aug; | 32417404 | |
| Discovering New Lipidomic Features Using Cell Type Specific Fluorophore Expression to Provide Spatial and Biological Specificity in a Multimodal Workflow with MALDI Imaging Mass Spectrometry. | Jones, Marissa A; Cho, Sung Hoon; Patterson, Nathan Heath; Van de Plas, Raf; Spraggins, Jeffrey M; Boothby, Mark R; Caprioli, Richard M | Analytical chemistry. | 2020 05 19; | 32298091 | |
| Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu, Yan; Zhang, Kun | Nature reviews. Nephrology. | 2020 07; | 32221477 | |
| Multiplexed single-cell morphometry for hematopathology diagnostics. | Tsai, Albert G; Glass, David R; Juntilla, Marisa; Hartmann, Felix J; Oak, Jean S; Fernandez-Pol, Sebastian; Ohgami, Robert S; Bendall, Sean C | Nature medicine. | 2020 03; | 32161403 | |
| RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. | Wei, Christopher Jen-Yue; Zhang, Kun | Genome research. | 2020 Apr; | 32127417 | |
| Integrated molecular imaging technologies for investigation of metals in biological systems: A brief review. | Perry, William J; Weiss, Andy; Van de Plas, Raf; Spraggins, Jeffrey M; Caprioli, Richard M; Skaar, Eric P | Current opinion in chemical biology. | 2020 Apr; | 32087551 | |
| Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-?m spatial resolution. | Piehowski, Paul D; Zhu, Ying; Bramer, Lisa M; Stratton, Kelly G; Zhao, Rui; Orton, Daniel J; Moore, Ronald J; Yuan, Jia; Mitchell, Hugh D; Gao, Yuqian; Webb-Robertson, Bobbie-Jo M; Dey, Sudhansu K; Kelly, Ryan T; Burnum-Johnson, Kristin E | Nature communications. | 2020 Jan 07; | 31911630 | |
| Immune monitoring using mass cytometry and related high-dimensional imaging approaches. | Hartmann, Felix J; Bendall, Sean C | Nature reviews. Rheumatology. | 2020 02; | 31892734 | |
| Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. | Hafemeister, Christoph; Satija, Rahul | Genome biology. | 2019 12 23; | 31870423 | |
| Uncovering Matrix Effects on Lipid Analyses in MALDI Imaging Mass Spectrometry Experiments. | Perry, William J; Patterson, Nathan Heath; Prentice, Boone M; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of mass spectrometry : JMS. | 2019 Dec 20; | 31860760 | |
| Toward a Common Coordinate Framework for the Human Body. | Rood, Jennifer E; Stuart, Tim; Ghazanfar, Shila; Biancalani, Tommaso; Fisher, Eyal; Butler, Andrew; Hupalowska, Anna; Gaffney, Leslie; Mauck, William; Eraslan, Gökçen; Marioni, John C; Regev, Aviv; Satija, Rahul | Cell. | 2019 Dec 12; | 31835027 | |
| High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry. | Yin, Ruichuan; Burnum-Johnson, Kristin E; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Nature protocols. | 2019 12; | 31723300 | |
| High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. | Chen, Song; Lake, Blue B; Zhang, Kun | Nature biotechnology. | 2019 12; | 31611697 | |
| Staphylococcus aureus exhibits heterogeneous siderophore production within the vertebrate host. | Perry, William J; Spraggins, Jeffrey M; Sheldon, Jessica R; Grunenwald, Caroline M; Heinrichs, David E; Cassat, James E; Skaar, Eric P; Caprioli, Richard M | Proceedings of the National Academy of Sciences of the United States of America. | 2019 10 29; | 31611408 | |
| Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. | Verbeeck, Nico; Caprioli, Richard M; Van de Plas, Raf | Mass spectrometry reviews. | 2020 May; | 31602691 | |
| The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. | HuBMAP Consortium | Nature. | 2019 10; | 31597973 | |
| High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry. | Spraggins, Jeffrey M; Djambazova, Katerina V; Rivera, Emilio S; Migas, Lukasz G; Neumann, Elizabeth K; Fuetterer, Arne; Suetering, Juergen; Goedecke, Niels; Ly, Alice; Van de Plas, Raf; Caprioli, Richard M | Analytical chemistry. | 2019 11 19; | 31593446 | |
| High-Parameter Immune Profiling with CyTOF. | Sahaf, Bita; Rahman, Adeeb; Maecker, Holden T; Bendall, Sean C | Methods in molecular biology (Clifton, N.J.). | 2020; | 31502160 | |
| Supervised classification enables rapid annotation of cell atlases. | Pliner, Hannah A; Shendure, Jay; Trapnell, Cole | Nature methods. | 2019 Oct; | 31501545 | |
| A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. | McFaline-Figueroa, José L; Hill, Andrew J; Qiu, Xiaojie; Jackson, Dana; Shendure, Jay; Trapnell, Cole | Nature genetics. | 2019 Sep; | 31477929 | |
| Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. | Saka, Sinem K; Wang, Yu; Kishi, Jocelyn Y; Zhu, Allen; Zeng, Yitian; Xie, Wenxin; Kirli, Koray; Yapp, Clarence; Cicconet, Marcelo; Beliveau, Brian J; Lapan, Sylvain W; Yin, Siyuan; Lin, Millicent; Boyden, Edward S; Kaeser, Pascal S; Pihan, German; Church, George M; Yin, Peng | Nature biotechnology. | 2019 Sep; | 31427819 | |
| A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. | Judd, Audra M; Gutierrez, Danielle B; Moore, Jessica L; Patterson, Nathan Heath; Yang, Junhai; Romer, Carrie E; Norris, Jeremy L; Caprioli, Richard M | Journal of mass spectrometry : JMS. | 2019 Aug; | 31254303 | |
| Two Specific Sulfatide Species Are Dysregulated during Renal Development in a Mouse Model of Alport Syndrome. | Gessel, Megan M; Spraggins, Jeffrey M; Voziyan, Paul A; Abrahamson, Dale R; Caprioli, Richard M; Hudson, Billy G | Lipids. | 2019 06; | 31197846 | |
| Comprehensive Integration of Single-Cell Data. | Stuart, Tim; Butler, Andrew; Hoffman, Paul; Hafemeister, Christoph; Papalexi, Efthymia; Mauck 3rd, William M; Hao, Yuhan; Stoeckius, Marlon; Smibert, Peter; Satija, Rahul | Cell. | 2019 Jun 13; | 31178118 | |
| MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies. | Ryan, Daniel J; Patterson, Nathan Heath; Putnam, Nicole E; Wilde, Aimee D; Weiss, Andy; Perry, William J; Cassat, James E; Skaar, Eric P; Caprioli, Richard M; Spraggins, Jeffrey M | Analytical chemistry. | 2019 06 18; | 31149808 | |
| SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. | Kishi, Jocelyn Y; Lapan, Sylvain W; Beliveau, Brian J; West, Emma R; Zhu, Allen; Sasaki, Hiroshi M; Saka, Sinem K; Wang, Yu; Cepko, Constance L; Yin, Peng | Nature methods. | 2019 Jun; | 31110282 | |
| Visualizing learner engagement, performance, and trajectories to evaluate and optimize online course design. | Ginda, Michael; Richey, Michael C; Cousino, Mark; Börner, Katy | PloS one. | 2019; | 31059546 | |
| Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data. | Lin, Chieh; Bar-Joseph, Ziv | Bioinformatics (Oxford, England). | 2019 Apr 30; | 31038684 | |
| The 2019 mathematical oncology roadmap. | Rockne, Russell C; Hawkins-Daarud, Andrea; Swanson, Kristin R; Sluka, James P; Glazier, James A; Macklin, Paul; Hormuth, David A; Jarrett, Angela M; Lima, Ernesto A B F; Tinsley Oden, J; Biros, George; Yankeelov, Thomas E; Curtius, Kit; Al Bakir, Ibrahim; Wodarz, Dominik; Komarova, Natalia; Aparicio, Luis; Bordyuh, Mykola; Rabadan, Raul; Finley, Stacey D; Enderling, Heiko; Caudell, Jimmy; Moros, Eduardo G; Anderson, Alexander R A; Gatenby, Robert A; Kaznatcheev, Artem; Jeavons, Peter; Krishnan, Nikhil; Pelesko, Julia; Wadhwa, Raoul R; Yoon, Nara; Nichol, Daniel; Marusyk, Andriy; Hinczewski, Michael; Scott, Jacob G | Physical biology. | 2019 Jun 19; | 30991381 | |
| Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. | Prentice, Boone M; Hart, Nathaniel J; Phillips, Neil; Haliyur, Rachana; Judd, Audra; Armandala, Radhika; Spraggins, Jeffrey M; Lowe, Cindy L; Boyd, Kelli L; Stein, Roland W; Wright, Christopher V; Norris, Jeremy L; Powers, Alvin C; Brissova, Marcela; Caprioli, Richard M | Diabetologia. | 2019 06; | 30955045 | |
| Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Eng, Chee-Huat Linus; Lawson, Michael; Zhu, Qian; Dries, Ruben; Koulena, Noushin; Takei, Yodai; Yun, Jina; Cronin, Christopher; Karp, Christoph; Yuan, Guo-Cheng; Cai, Long | Nature. | 2019 Apr; | 30911168 | |
| Multiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry. | Prentice, Boone M; McMillen, Josiah C; Caprioli, Richard M | International journal of mass spectrometry. | 2019 Mar; | 30906202 | |
| Cell lineage inference from SNP and scRNA-Seq data. | Ding, Jun; Lin, Chieh; Bar-Joseph, Ziv | Nucleic acids research. | 2019 Jun 04; | 30820578 | |
| The single-cell transcriptional landscape of mammalian organogenesis. | Cao, Junyue; Spielmann, Malte; Qiu, Xiaojie; Huang, Xingfan; Ibrahim, Daniel M; Hill, Andrew J; Zhang, Fan; Mundlos, Stefan; Christiansen, Lena; Steemers, Frank J; Trapnell, Cole; Shendure, Jay | Nature. | 2019 02; | 30787437 | |
| Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data. | Rashid, Sabrina; Shah, Sohrab; Bar-Joseph, Ziv; Pandya, Ravi | Bioinformatics (Oxford, England). | 2019 Feb 15; | 30768159 | |
| Data visualization literacy: Definitions, conceptual frameworks, exercises, and assessments. | Börner, Katy; Bueckle, Andreas; Ginda, Michael | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Feb 05; | 30718386 | |
| Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. | Stoeckius, Marlon; Zheng, Shiwei; Houck-Loomis, Brian; Hao, Stephanie; Yeung, Bertrand Z; Mauck 3rd, William M; Smibert, Peter; Satija, Rahul | Genome biology. | 2018 12 19; | 30567574 | |
| Forecasting innovations in science, technology, and education. | Börner, Katy; Rouse, William B; Trunfio, Paul; Stanley, H Eugene | Proceedings of the National Academy of Sciences of the United States of America. | 2018 12 11; | 30530683 | |
| Protein identification strategies in MALDI imaging mass spectrometry: a brief review. | Ryan, Daniel J; Spraggins, Jeffrey M; Caprioli, Richard M | Current opinion in chemical biology. | 2019 02; | 30476689 | |
| Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. | Zhu, Qian; Shah, Sheel; Dries, Ruben; Cai, Long; Yuan, Guo-Cheng | Nature biotechnology. | 2018 Oct 29; | 30371680 |