HuBMAP (52)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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 MJournal 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, TujinJournal of visualized experiments : JoVE.2020 11 06;33226031
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, RongCell.2020 Dec 10;33188776
CDKL5: a promising new therapeutic target for acute kidney injury?de Caestecker, Mark PAmerican 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 RThe 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 MJournal 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 CNature 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 PCell.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 CImmunity.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 LCytometry. 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 ACell.2020 Jul 23;32579974
The Importance of Clinical Tissue Imaging.Spraggins, Jeffrey M; Schwamborn, Kristina; Heeren, Ron M A; Eberlin, Livia SClinical 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 SGastroenterology.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 MAnalytical chemistry.2020 05 19;32298091
Tools for the analysis of high-dimensional single-cell RNA sequencing data.Wu, Yan; Zhang, KunNature 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 CNature medicine.2020 03;32161403
RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells.Wei, Christopher Jen-Yue; Zhang, KunGenome 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 PCurrent 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 ENature communications.2020 Jan 07;31911630
Immune monitoring using mass cytometry and related high-dimensional imaging approaches.Hartmann, Felix J; Bendall, Sean CNature reviews. Rheumatology.2020 02;31892734
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.Hafemeister, Christoph; Satija, RahulGenome 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 MJournal 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, RahulCell.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, JuliaNature protocols.2019 12;31723300
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell.Chen, Song; Lake, Blue B; Zhang, KunNature 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 MProceedings 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, RafMass spectrometry reviews.2020 May;31602691
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.HuBMAP ConsortiumNature.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 MAnalytical chemistry.2019 11 19;31593446
High-Parameter Immune Profiling with CyTOF.Sahaf, Bita; Rahman, Adeeb; Maecker, Holden T; Bendall, Sean CMethods in molecular biology (Clifton, N.J.).2020;31502160
Supervised classification enables rapid annotation of cell atlases.Pliner, Hannah A; Shendure, Jay; Trapnell, ColeNature 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, ColeNature 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, PengNature 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 MJournal 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 GLipids.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, RahulCell.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 MAnalytical 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, PengNature 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, KatyPloS one.2019;31059546
Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data.Lin, Chieh; Bar-Joseph, ZivBioinformatics (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 GPhysical 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 MDiabetologia.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, LongNature.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 MInternational journal of mass spectrometry.2019 Mar;30906202
Cell lineage inference from SNP and scRNA-Seq data.Ding, Jun; Lin, Chieh; Bar-Joseph, ZivNucleic 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, JayNature.2019 02;30787437
Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data.Rashid, Sabrina; Shah, Sohrab; Bar-Joseph, Ziv; Pandya, RaviBioinformatics (Oxford, England).2019 Feb 15;30768159
Data visualization literacy: Definitions, conceptual frameworks, exercises, and assessments.Börner, Katy; Bueckle, Andreas; Ginda, MichaelProceedings 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, RahulGenome biology.2018 12 19;30567574
Forecasting innovations in science, technology, and education.Börner, Katy; Rouse, William B; Trunfio, Paul; Stanley, H EugeneProceedings 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 MCurrent 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-ChengNature biotechnology.2018 Oct 29;30371680