Publications Search by Program
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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 (78)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Embryo-scale, single-cell spatial transcriptomics. | Srivatsan, Sanjay R; Regier, Mary C; Barkan, Eliza; Franks, Jennifer M; Packer, Jonathan S; Grosjean, Parker; Duran, Madeleine; Saxton, Sarah; Ladd, Jon J; Spielmann, Malte; Lois, Carlos; Lampe, Paul D; Shendure, Jay; Stevens, Kelly R; Trapnell, Cole | Science (New York, N.Y.) | 2021 07 02 | 34210887 | |
| The emerging landscape of single-molecule protein sequencing technologies. | Alfaro, Javier Antonio; Bohländer, Peggy; Dai, Mingjie; Filius, Mike; Howard, Cecil J; van Kooten, Xander F; Ohayon, Shilo; Pomorski, Adam; Schmid, Sonja; Aksimentiev, Aleksei; Anslyn, Eric V; Bedran, Georges; Cao, Chan; Chinappi, Mauro; Coyaud, Etienne; Dekker, Cees; Dittmar, Gunnar; Drachman, Nicholas; Eelkema, Rienk; Goodlett, David; Hentz, Sébastien; Kalathiya, Umesh; Kelleher, Neil L; Kelly, Ryan T; Kelman, Zvi; Kim, Sung Hyun; Kuster, Bernhard; Rodriguez-Larrea, David; Lindsay, Stuart; Maglia, Giovanni; Marcotte, Edward M; Marino, John P; Masselon, Christophe; Mayer, Michael; Samaras, Patroklos; Sarthak, Kumar; Sepiashvili, Lusia; Stein, Derek; Wanunu, Meni; Wilhelm, Mathias; Yin, Peng; Meller, Amit; Joo, Chirlmin | Nature methods | 2021 Jun | 34099939 | |
| Multiomics Imaging Using High-Energy Water Gas Cluster Ion Beam Secondary Ion Mass Spectrometry [(H2O)n-GCIB-SIMS] of Frozen-Hydrated Cells and Tissue. | Tian, Hua; Sheraz Née Rabbani, Sadia; Vickerman, John C; Winograd, Nicholas | Analytical chemistry | 2021 06 08 | 34038090 | |
| Pancreas Optical Clearing and 3-D Microscopy in Health and Diabetes. | Campbell-Thompson, Martha; Tang, Shiue-Cheng | Frontiers in endocrinology | 2021 | 33981285 | |
| CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data. | Hu, Yuxuan; Peng, Tao; Gao, Lin; Tan, Kai | Science advances | 2021 Apr | 33853780 | |
| Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. | Gerbasi, Vincent R; Melani, Rafael D; Abbatiello, Susan E; Belford, Michael W; Huguet, Romain; McGee, John P; Dayhoff, Dawson; Thomas, Paul M; Kelleher, Neil L | Analytical chemistry | 2021 04 27 | 33844503 | |
| Islet sympathetic innervation and islet neuropathology in patients with type 1 diabetes. | Campbell-Thompson, Martha; Butterworth, Elizabeth A; Boatwright, J Lucas; Nair, Malavika A; Nasif, Lith H; Nasif, Kamal; Revell, Andy Y; Riva, Alberto; Mathews, Clayton E; Gerling, Ivan C; Schatz, Desmond A; Atkinson, Mark A | Scientific reports | 2021 Mar 22 | 33753784 | |
| Advances in Proximity Ligation in situ Hybridization (PLISH). | Nagendran, Monica; Andruska, Adam M; Harbury, Pehr B; Desai, Tushar J | Bio-protocol | 2020 Nov 05 | 33659462 | |
| Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics. | Tsai, Chia-Feng; Zhang, Pengfei; Scholten, David; Martin, Kendall; Wang, Yi-Ting; Zhao, Rui; Chrisler, William B; Patel, Dhwani B; Dou, Maowei; Jia, Yuzhi; Reduzzi, Carolina; Liu, Xia; Moore, Ronald J; Burnum-Johnson, Kristin E; Lin, Miao-Hsia; Hsu, Chuan-Chih; Jacobs, Jon M; Kagan, Jacob; Srivastava, Sudhir; Rodland, Karin D; Steven Wiley, H; Qian, Wei-Jun; Smith, Richard D; Zhu, Ying; Cristofanilli, Massimo; Liu, Tao; Liu, Huiping; Shi, Tujin | Communications biology | 2021 Mar 01 | 33649493 | |
| Spatial Segmentation of Mass Spectrometry Imaging Data by Combining Multivariate Clustering and Univariate Thresholding. | Hu, Hang; Yin, Ruichuan; Brown, Hilary M; Laskin, Julia | Analytical chemistry | 2021 02 23 | 33570915 | |
| Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. | Kennedy-Darling, Julia; Bhate, Salil S; Hickey, John W; Black, Sarah; Barlow, Graham L; Vazquez, Gustavo; Venkataraaman, Vishal G; Samusik, Nikolay; Goltsev, Yury; Schürch, Christian M; Nolan, Garry P | European journal of immunology | 2021 May | 33548142 | |
| 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 | |
| Quantitative Mass Spectrometry Imaging of Biological Systems. | Unsihuay, Daisy; Mesa Sanchez, Daniela; Laskin, Julia | Annual review of physical chemistry | 2021 Apr 20 | 33441032 | |
| RIPK3-mediated inflammation is a conserved β cell response to ER stress. | Yang, Bingyuan; Maddison, Lisette A; Zaborska, Karolina E; Dai, Chunhua; Yin, Linlin; Tang, Zihan; Zang, Liqing; Jacobson, David A; Powers, Alvin C; Chen, Wenbiao | Science advances | 2020 Dec | 33355143 | |
| 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 | |
| Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. | Salahudeen, Ameen A; Choi, Shannon S; Rustagi, Arjun; Zhu, Junjie; van Unen, Vincent; de la O, Sean M; Flynn, Ryan A; Margalef-Català, Mar; Santos, António J M; Ju, Jihang; Batish, Arpit; Usui, Tatsuya; Zheng, Grace X Y; Edwards, Caitlin E; Wagar, Lisa E; Luca, Vincent; Anchang, Benedict; Nagendran, Monica; Nguyen, Khanh; Hart, Daniel J; Terry, Jessica M; Belgrader, Phillip; Ziraldo, Solongo B; Mikkelsen, Tarjei S; Harbury, Pehr B; Glenn, Jeffrey S; Garcia, K Christopher; Davis, Mark M; Baric, Ralph S; Sabatti, Chiara; Amieva, Manuel R; Blish, Catherine A; Desai, Tushar J; Kuo, Calvin J | Nature | 2020 12 | 33238290 | |
| 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 | |
| Guidelines for reporting single-cell RNA-seq experiments. | Füllgrabe, Anja; George, Nancy; Green, Matthew; Nejad, Parisa; Aronow, Bruce; Fexova, Silvie Korena; Fischer, Clay; Freeberg, Mallory Ann; Huerta, Laura; Morrison, Norman; Scheuermann, Richard H; Taylor, Deanne; Vasilevsky, Nicole; Clarke, Laura; Gehlenborg, Nils; Kent, Jim; Marioni, John; Teichmann, Sarah; Brazma, Alvis; Papatheodorou, Irene | Nature biotechnology | 2020 12 | 33188371 | |
| 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 | |
| Changes to Zonular Tension Alters the Subcellular Distribution of AQP5 in Regions of Influx and Efflux of Water in the Rat Lens. | Petrova, Rosica S; Bavana, Nandini; Zhao, Rusin; Schey, Kevin L; Donaldson, Paul J | Investigative ophthalmology & visual science | 2020 09 01 | 32945844 | |
| Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. | Zhou, Xin X; Bracken, Colton J; Zhang, Kaihua; Zhou, Jie; Mou, Yun; Wang, Lei; Cheng, Yifan; Leung, Kevin K; Wells, James A | Journal of the American Chemical Society | 2020 10 14 | 32924468 | |
| The impact of air transport availability on research collaboration: A case study of four universities. | Ploszaj, Adam; Yan, Xiaoran; Börner, Katy | PloS one | 2020 | 32886681 | |
| 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 Microfluidic Probe for Mass Spectrometry Imaging of Biological Samples*. | Li, Xiangtang; Yin, Ruichuan; Hu, Hang; Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Angewandte Chemie (International ed. in English) | 2020 12 07 | 32743957 | |
| Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures. | Salahudeen, Ameen A; Choi, Shannon S; Rustagi, Arjun; Zhu, Junjie; de la O, Sean M; Flynn, Ryan A; Margalef-Català, Mar; Santos, António J M; Ju, Jihang; Batish, Arpit; van Unen, Vincent; Usui, Tatsuya; Zheng, Grace X Y; Edwards, Caitlin E; Wagar, Lisa E; Luca, Vincent; Anchang, Benedict; Nagendran, Monica; Nguyen, Khanh; Hart, Daniel J; Terry, Jessica M; Belgrader, Phillip; Ziraldo, Solongo B; Mikkelsen, Tarjei S; Harbury, Pehr B; Glenn, Jeffrey S; Garcia, K Christopher; Davis, Mark M; Baric, Ralph S; Sabatti, Chiara; Amieva, Manuel R; Blish, Catherine A; Desai, Tushar J; Kuo, Calvin J | bioRxiv : the preprint server for biology | 2020 Jul 27 | 32743583 | |
| Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. | Shafin, Kishwar; Pesout, Trevor; Lorig-Roach, Ryan; Haukness, Marina; Olsen, Hugh E; Bosworth, Colleen; Armstrong, Joel; Tigyi, Kristof; Maurer, Nicholas; Koren, Sergey; Sedlazeck, Fritz J; Marschall, Tobias; Mayes, Simon; Costa, Vania; Zook, Justin M; Liu, Kelvin J; Kilburn, Duncan; Sorensen, Melanie; Munson, Katy M; Vollger, Mitchell R; Monlong, Jean; Garrison, Erik; Eichler, Evan E; Salama, Sofie; Haussler, David; Green, Richard E; Akeson, Mark; Phillippy, Adam; Miga, Karen H; Carnevali, Paolo; Jain, Miten; Paten, Benedict | Nature biotechnology. | 2020 09; | 32686750 | |
| Localization of the lens intermediate filament switch by imaging mass spectrometry. | Wang, Zhen; Ryan, Daniel J; Schey, Kevin L | Experimental eye research | 2020 09 | 32682822 | |
| 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 | |
| Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High-Resolution Imaging Mass Spectrometry. | Anderson, David M G; Messinger, Jeffrey D; Patterson, Nathan H; Rivera, Emilio S; Kotnala, Ankita; Spraggins, Jeffrey M; Caprioli, Richard M; Curcio, Christine A; Schey, Kevin L | Journal of the American Society for Mass Spectrometry | 2020 Dec 02 | 32628476 | |
| 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 | |
| Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. | Rodriques, Samuel G; Stickels, Robert R; Goeva, Aleksandrina; Martin, Carly A; Murray, Evan; Vanderburg, Charles R; Welch, Joshua; Chen, Linlin M; Chen, Fei; Macosko, Evan Z | Science (New York, N.Y.). | 2019 03 29; | 30923225 | |
| 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 |