The Human BioMolecular Atlas Program (HuBMAP)
The Human BioMolecular Atlas Program (HuBMAP)
Program Publications
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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.
| Title | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| 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. | 30371680 | 2018 Oct 29; |
| 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. | 30476689 | 2019 02; |
| 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. | 30530683 | 2018 12 11; |
| 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. | 30567574 | 2018 12 19; |
| 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. | 30718386 | 2019 Feb 05; |
| Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data. | Rashid, Sabrina; Shah, Sohrab; Bar-Joseph, Ziv; Pandya, Ravi | Bioinformatics (Oxford, England). | 30768159 | 2019 Feb 15; |
| 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. | 30787437 | 2019 02; |
| Cell lineage inference from SNP and scRNA-Seq data. | Ding, Jun; Lin, Chieh; Bar-Joseph, Ziv | Nucleic acids research. | 30820578 | 2019 Jun 04; |
| 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. | 30906202 | 2019 Mar; |
| 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. | 30911168 | 2019 Apr; |
| 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.). | 30923225 | 2019 03 29; |
| 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. | 30955045 | 2019 06; |
| 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. | 30991381 | 2019 Jun 19; |
| Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data. | Lin, Chieh; Bar-Joseph, Ziv | Bioinformatics (Oxford, England). | 31038684 | 2019 Apr 30; |
| Visualizing learner engagement, performance, and trajectories to evaluate and optimize online course design. | Ginda, Michael; Richey, Michael C; Cousino, Mark; Börner, Katy | PloS one. | 31059546 | 2019; |
| 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. | 31110282 | 2019 Jun; |
| 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. | 31149808 | 2019 06 18; |
| 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. | 31178118 | 2019 Jun 13; |
| 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. | 31197846 | 2019 06; |
| 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. | 31254303 | 2019 Aug; |
| 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. | 31427819 | 2019 Sep; |
| 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. | 31477929 | 2019 Sep; |
| Supervised classification enables rapid annotation of cell atlases. | Pliner, Hannah A; Shendure, Jay; Trapnell, Cole | Nature methods. | 31501545 | 2019 Oct; |
| High-Parameter Immune Profiling with CyTOF. | Sahaf, Bita; Rahman, Adeeb; Maecker, Holden T; Bendall, Sean C | Methods in molecular biology (Clifton, N.J.). | 31502160 | 2020; |
| 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. | 31593446 | 2019 11 19; |
| The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. | HuBMAP Consortium | Nature. | 31597973 | 2019 10; |
| Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. | Verbeeck, Nico; Caprioli, Richard M; Van de Plas, Raf | Mass spectrometry reviews. | 31602691 | 2020 May; |
| 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. | 31611408 | 2019 10 29; |
| High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. | Chen, Song; Lake, Blue B; Zhang, Kun | Nature biotechnology. | 31611697 | 2019 12; |
| 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. | 31723300 | 2019 12; |
| Deep learning for inferring gene relationships from single-cell expression data. | Yuan, Ye; Bar-Joseph, Ziv | Proceedings of the National Academy of Sciences of the United States of America | 31822622 | 2019 Dec 10 |
| 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. | 31835027 | 2019 Dec 12; |
| 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. | 31860760 | 2019 Dec 20; |
| Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. | Hafemeister, Christoph; Satija, Rahul | Genome biology. | 31870423 | 2019 12 23; |
| Immune monitoring using mass cytometry and related high-dimensional imaging approaches. | Hartmann, Felix J; Bendall, Sean C | Nature reviews. Rheumatology. | 31892734 | 2020 02; |
| 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. | 31911630 | 2020 Jan 07; |
| Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. | Hurley, Killian; Ding, Jun; Villacorta-Martin, Carlos; Herriges, Michael J; Jacob, Anjali; Vedaie, Marall; Alysandratos, Konstantinos D; Sun, Yuliang L; Lin, Chieh; Werder, Rhiannon B; Huang, Jessie; Wilson, Andrew A; Mithal, Aditya; Mostoslavsky, Gustavo; Oglesby, Irene; Caballero, Ignacio S; Guttentag, Susan H; Ahangari, Farida; Kaminski, Naftali; Rodriguez-Fraticelli, Alejo; Camargo, Fernando; Bar-Joseph, Ziv; Kotton, Darrell N | Cell stem cell | 32004478 | 2020 04 02 |
| Inferring TF activation order in time series scRNA-Seq studies. | Lin, Chieh; Ding, Jun; Bar-Joseph, Ziv | PLoS computational biology | 32069291 | 2020 02 |
| 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. | 32087551 | 2020 Apr; |
| RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. | Wei, Christopher Jen-Yue; Zhang, Kun | Genome research. | 32127417 | 2020 Apr; |
| 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. | 32161403 | 2020 03; |
| Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu, Yan; Zhang, Kun | Nature reviews. Nephrology. | 32221477 | 2020 07; |
| 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. | 32298091 | 2020 05 19; |
| 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. | 32417404 | 2020 Aug; |
| The Importance of Clinical Tissue Imaging. | Spraggins, Jeffrey M; Schwamborn, Kristina; Heeren, Ron M A; Eberlin, Livia S | Clinical mass spectrometry (Del Mar, Calif.). | 32483555 | 2019 Apr; |
| Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data. | Zafar, Hamim; Lin, Chieh; Bar-Joseph, Ziv | Nature communications | 32546686 | 2020 Jun 16 |
| 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. | 32579974 | 2020 Jul 23; |
| 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. | 32602650 | 2020 08; |
| 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 | 32628476 | 2020 Dec 02 |
| 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. | 32668225 | 2020 Jul 14; |
| Localization of the lens intermediate filament switch by imaging mass spectrometry. | Wang, Zhen; Ryan, Daniel J; Schey, Kevin L | Experimental eye research | 32682822 | 2020 09 |
| 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. | 32686750 | 2020 09; |
| 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 | 32743583 | 2020 Jul 27 |
| 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) | 32743957 | 2020 12 07 |
| 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. | 32763154 | 2020 Sep 03; |
| Tetraspanin-7 regulation of L-type voltage-dependent calcium channels controls pancreatic β-cell insulin secretion. | Dickerson, Matthew T; Dadi, Prasanna K; Butterworth, Regan B; Nakhe, Arya Y; Graff, Sarah M; Zaborska, Karolina E; Schaub, Charles M; Jacobson, David A | The Journal of physiology | 32790176 | 2020 Nov |
| 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. | 32868913 | 2020 Aug 31; |
| Identifying signaling genes in spatial single-cell expression data. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 32886099 | 2021 05 17 |
| Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. | Neumann, Elizabeth K; Djambazova, Katerina V; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of the American Society for Mass Spectrometry | 32886506 | 2020 Dec 02 |
| The impact of air transport availability on research collaboration: A case study of four universities. | Ploszaj, Adam; Yan, Xiaoran; Börner, Katy | PloS one | 32886681 | 2020 |
| 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 | 32924468 | 2020 10 14 |
| 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 | 32945844 | 2020 09 01 |
| 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. | 32955134 | 2020 Jul 04; |
| A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling. | Lekschas, Fritz; Zhou, Xinyi; Chen, Wei; Gehlenborg, Nils; Bach, Benjamin; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics | 33026994 | 2021 02 |
| 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. | 33044226 | 2020 Nov 02; |
| CDKL5: a promising new therapeutic target for acute kidney injury? | de Caestecker, Mark P | American journal of physiology. Renal physiology. | 33073588 | 2020 Oct 19; |
| Iterative point set registration for aligning scRNA-seq data. | Alavi, Amir; Bar-Joseph, Ziv | PLoS computational biology | 33108369 | 2020 10 |
| 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 | 33188371 | 2020 12 |
| 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. | 33188776 | 2020 Dec 10; |
| A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project. | El-Achkar, Tarek M; Eadon, Michael T; Menon, Rajasree; Lake, Blue B; Sigdel, Tara K; Alexandrov, Theodore; Parikh, Samir; Zhang, Guanshi; Dobi, Dejan; Dunn, Kenneth W; Otto, Edgar A; Anderton, Christopher R; Carson, Jonas M; Luo, Jinghui; Park, Chris; Hamidi, Habib; Zhou, Jian; Hoover, Paul; Schroeder, Andrew; Joanes, Marianinha; Azeloglu, Evren U; Sealfon, Rachel; Winfree, Seth; Steck, Becky; He, Yongqun; D'Agati, Vivette; Iyengar, Ravi; Troyanskaya, Olga G; Barisoni, Laura; Gaut, Joseph; Zhang, Kun; Laszik, Zoltan; Rovin, Brad H; Dagher, Pierre C; Sharma, Kumar; Sarwal, Minnie M; Hodgin, Jeffrey B; Alpers, Charles E; Kretzler, Matthias; Jain, Sanjay | Physiological genomics | 33197228 | 2021 Jan 01 |
| Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. | Uzun, Yasin; Wu, Hao; Tan, Kai | Genome research | 33219054 | 2021 Jan |
| 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. | 33226031 | 2020 11 06; |
| 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 | 33238290 | 2020 12 |
| 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. | 33241625 | 2020 Dec; |
| GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data. | Yuan, Ye; Bar-Joseph, Ziv | Genome biology | 33303016 | 2020 Dec 10 |
| 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 | 33355143 | 2020 Dec |
| Phase identification for dynamic CT enhancements with generative adversarial network. | Tang, Yucheng; Gao, Riqiang; Lee, Ho Hin; Chen, Yunqiang; Gao, Dashan; Bermudez, Camilo; Bao, Shunxing; Huo, Yuankai; Savoie, Brent V; Landman, Bennett A | Medical physics | 33410167 | 2021 Mar |
| Quantitative Mass Spectrometry Imaging of Biological Systems. | Unsihuay, Daisy; Mesa Sanchez, Daniela; Laskin, Julia | Annual review of physical chemistry | 33441032 | 2021 Apr 20 |
| Supervised Adversarial Alignment of Single-Cell RNA-seq Data. | Ge, Songwei; Wang, Haohan; Alavi, Amir; Xing, Eric; Bar-Joseph, Ziv | Journal of computational biology : a journal of computational molecular cell biology | 33470876 | 2021 05 |
| 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 | 33505024 | 2021 02 |
| 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 | 33548142 | 2021 May |
| Body Part Regression With Self-Supervision. | Tang, Yucheng; Gao, Riqiang; Han, Shizhong; Chen, Yunqiang; Gao, Dashan; Nath, Vishwesh; Bermudez, Camilo; Savona, Michael R; Bao, Shunxing; Lyu, Ilwoo; Huo, Yuankai; Landman, Bennett A | IEEE transactions on medical imaging | 33560981 | 2021 May |
| 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 | 33570915 | 2021 02 23 |
| 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 | 33649493 | 2021 Mar 01 |
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| Ductal Carcinoma In Situ of Breast: From Molecular Etiology to Therapeutic Management. | Hophan, Shelby Lynn; Odnokoz, Olena; Liu, Huiping; Luo, Yuan; Khan, Seema; Gradishar, William; Zhou, Zhuan; Badve, Sunil; Torres, Mylin A; Wan, Yong | Endocrinology | 35245349 | 2022 Apr 01 |
| Limited extent and consequences of pancreatic SARS-CoV-2 infection. | van der Heide, Verena; Jangra, Sonia; Cohen, Phillip; Rathnasinghe, Raveen; Aslam, Sadaf; Aydillo, Teresa; Geanon, Daniel; Handler, Diana; Kelley, Geoffrey; Lee, Brian; Rahman, Adeeb; Dawson, Travis; Qi, Jingjing; D'Souza, Darwin; Kim-Schulze, Seunghee; Panzer, Julia K; Caicedo, Alejandro; Kusmartseva, Irina; Posgai, Amanda L; Atkinson, Mark A; Albrecht, Randy A; García-Sastre, Adolfo; Rosenberg, Brad R; Schotsaert, Michael; Homann, Dirk | Cell reports | 35247306 | 2022 Feb 21 |
| TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data. | Li, Dongshunyi; Velazquez, Jeremy J; Ding, Jun; Hislop, Joshua; Ebrahimkhani, Mo R; Bar-Joseph, Ziv | Genome biology | 35255944 | 2022 Mar 07 |
| MITI minimum information guidelines for highly multiplexed tissue images. | Schapiro, Denis; Yapp, Clarence; Sokolov, Artem; Reynolds, Sheila M; Chen, Yu-An; Sudar, Damir; Xie, Yubin; Muhlich, Jeremy; Arias-Camison, Raquel; Arena, Sarah; Taylor, Adam J; Nikolov, Milen; Tyler, Madison; Lin, Jia-Ren; Burlingame, Erik A; Human Tumor Atlas Network; Chang, Young H; Farhi, Samouil L; Thorsson, Vésteinn; Venkatamohan, Nithya; Drewes, Julia L; Pe'er, Dana; Gutman, David A; Herrmann, Markus D; Gehlenborg, Nils; Bankhead, Peter; Roland, Joseph T; Herndon, John M; Snyder, Michael P; Angelo, Michael; Nolan, Garry; Swedlow, Jason R; Schultz, Nikolaus; Merrick, Daniel T; Mazzili, Sarah A; Cerami, Ethan; Rodig, Scott J; Santagata, Sandro; Sorger, Peter K | Nature methods | 35277708 | 2022 03 |
| Clinical Implementation and Initial Experience With a 1.5 Tesla MR-Linac for MR-Guided Radiation Therapy for Gynecologic Cancer: An R-IDEAL Stage 1 and 2a First in Humans Feasibility Study of New Technology Implementation. | Lakomy, David S; Yang, Jinzhong; Vedam, Sastry; Wang, Jihong; Lee, Belinda; Sobremonte, Angela; Castillo, Pamela; Hughes, Neil; Mohammedsaid, Mustefa; Jhingran, Anuja; Klopp, Ann H; Choi, Seungtaek; Fuller, C David; Lin, Lilie L | Practical radiation oncology | 35278717 | 2022 Jul-Aug |
| Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. | LeDuc, Richard D; Deutsch, Eric W; Binz, Pierre-Alain; Fellers, Ryan T; Cesnik, Anthony J; Klein, Joshua A; Van Den Bossche, Tim; Gabriels, Ralf; Yalavarthi, Arshika; Perez-Riverol, Yasset; Carver, Jeremy; Bittremieux, Wout; Kawano, Shin; Pullman, Benjamin; Bandeira, Nuno; Kelleher, Neil L; Thomas, Paul M; Vizcaíno, Juan Antonio | Journal of proteome research | 35290070 | 2022 Apr 01 |
| Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. | Zhang, Bingjie; Srivastava, Avi; Mimitou, Eleni; Stuart, Tim; Raimondi, Ivan; Hao, Yuhan; Smibert, Peter; Satija, Rahul | Nature biotechnology | 35332340 | 2022 Aug |
| Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation. | Menon, Rajasree; Bomback, Andrew S; Lake, Blue B; Stutzke, Christy; Grewenow, Stephanie M; Menez, Steven; D'Agati, Vivette D; Jain, Sanjay; Kidney Precision Medicine Project | Kidney international | 35339536 | 2022 Jun |
| Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments. | Richardson, Luke T; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M; Solouki, Touradj | Analytical chemistry | 35344335 | 2022 04 12 |
| Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. | Goenka, Sneha D; Gorzynski, John E; Shafin, Kishwar; Fisk, Dianna G; Pesout, Trevor; Jensen, Tanner D; Monlong, Jean; Chang, Pi-Chuan; Baid, Gunjan; Bernstein, Jonathan A; Christle, Jeffrey W; Dalton, Karen P; Garalde, Daniel R; Grove, Megan E; Guillory, Joseph; Kolesnikov, Alexey; Nattestad, Maria; Ruzhnikov, Maura R Z; Samadi, Mehrzad; Sethia, Ankit; Spiteri, Elizabeth; Wright, Christopher J; Xiong, Katherine; Zhu, Tong; Jain, Miten; Sedlazeck, Fritz J; Carroll, Andrew; Paten, Benedict; Ashley, Euan A | Nature biotechnology | 35347328 | 2022 Jul |
| Reproducible, high-dimensional imaging in archival human tissue by multiplexed ion beam imaging by time-of-flight (MIBI-TOF). | Liu, Candace C; Bosse, Marc; Kong, Alex; Kagel, Adam; Kinders, Robert; Hewitt, Stephen M; Varma, Sushama; van de Rijn, Matt; Nowak, Stanisław H; Bendall, Sean C; Angelo, Michael | Laboratory investigation; a journal of technical methods and pathology | 35351966 | 2022 07 |
| Complete genomic and epigenetic maps of human centromeres. | Altemose, Nicolas; Logsdon, Glennis A; Bzikadze, Andrey V; Sidhwani, Pragya; Langley, Sasha A; Caldas, Gina V; Hoyt, Savannah J; Uralsky, Lev; Ryabov, Fedor D; Shew, Colin J; Sauria, Michael E G; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A; Dvorkina, Tatiana; Kunyavskaya, Olga; Vollger, Mitchell R; Rhie, Arang; McCartney, Ann M; Asri, Mobin; Lorig-Roach, Ryan; Shafin, Kishwar; Lucas, Julian K; Aganezov, Sergey; Olson, Daniel; de Lima, Leonardo Gomes; Potapova, Tamara; Hartley, Gabrielle A; Haukness, Marina; Kerpedjiev, Peter; Gusev, Fedor; Tigyi, Kristof; Brooks, Shelise; Young, Alice; Nurk, Sergey; Koren, Sergey; Salama, Sofie R; Paten, Benedict; Rogaev, Evgeny I; Streets, Aaron; Karpen, Gary H; Dernburg, Abby F; Sullivan, Beth A; Straight, Aaron F; Wheeler, Travis J; Gerton, Jennifer L; Eichler, Evan E; Phillippy, Adam M; Timp, Winston; Dennis, Megan Y; O'Neill, Rachel J; Zook, Justin M; Schatz, Michael C; Pevzner, Pavel A; Diekhans, Mark; Langley, Charles H; Alexandrov, Ivan A; Miga, Karen H | Science (New York, N.Y.) | 35357911 | 2022 04 |
| A complete reference genome improves analysis of human genetic variation. | Aganezov, Sergey; Yan, Stephanie M; Soto, Daniela C; Kirsche, Melanie; Zarate, Samantha; Avdeyev, Pavel; Taylor, Dylan J; Shafin, Kishwar; Shumate, Alaina; Xiao, Chunlin; Wagner, Justin; McDaniel, Jennifer; Olson, Nathan D; Sauria, Michael E G; Vollger, Mitchell R; Rhie, Arang; Meredith, Melissa; Martin, Skylar; Lee, Joyce; Koren, Sergey; Rosenfeld, Jeffrey A; Paten, Benedict; Layer, Ryan; Chin, Chen-Shan; Sedlazeck, Fritz J; Hansen, Nancy F; Miller, Danny E; Phillippy, Adam M; Miga, Karen H; McCoy, Rajiv C; Dennis, Megan Y; Zook, Justin M; Schatz, Michael C | Science (New York, N.Y.) | 35357935 | 2022 04 |
| Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. | Mc Cartney, Ann M; Shafin, Kishwar; Alonge, Michael; Bzikadze, Andrey V; Formenti, Giulio; Fungtammasan, Arkarachai; Howe, Kerstin; Jain, Chirag; Koren, Sergey; Logsdon, Glennis A; Miga, Karen H; Mikheenko, Alla; Paten, Benedict; Shumate, Alaina; Soto, Daniela C; Sović, Ivan; Wood, Jonathan M D; Zook, Justin M; Phillippy, Adam M; Rhie, Arang | Nature methods | 35361931 | 2022 06 |
| Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. | Formenti, Giulio; Rhie, Arang; Walenz, Brian P; Thibaud-Nissen, Françoise; Shafin, Kishwar; Koren, Sergey; Myers, Eugene W; Jarvis, Erich D; Phillippy, Adam M | Nature methods | 35361932 | 2022 06 |
| Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping. | Fan, Rong; Liu, Yang; DiStasio, Marcello; Su, Graham; Asashima, Hiromitsu; Enninful, Archibald; Qin, Xiaoyu; Deng, Yanxiang; Bordignon, Pino; Cassano, Marco; Tomayko, Mary; Xu, Mina; Halene, Stephanie; Craft, Joseph; Hafler, David | Research square | 35378748 | 2022 Mar 30 |
| Analyzing Spatial Transcriptomics Data Using Giotto. | Del Rossi, Natalie; Chen, Jiaji G; Yuan, Guo-Cheng; Dries, Ruben | Current protocols | 35384407 | 2022 Apr |
| Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. | Bailey, Andrew D; Talkish, Jason; Ding, Hongxu; Igel, Haller; Duran, Alejandra; Mantripragada, Shreya; Paten, Benedict; Ares, Manuel | eLife | 35384842 | 2022 Apr 06 |
| Cell Trafficking at the Intersection of the Tumor-Immune Compartments. | Du, Wenxuan; Nair, Praful; Johnston, Adrian; Wu, Pei-Hsun; Wirtz, Denis | Annual review of biomedical engineering | 35385679 | 2022 Jun 06 |
| Mapping the Proteoform Landscape of Five Human Tissues. | Drown, Bryon S; Jooß, Kevin; Melani, Rafael D; Lloyd-Jones, Cameron; Camarillo, Jeannie M; Kelleher, Neil L | Journal of proteome research | 35413190 | 2022 05 06 |
| Interactive single-cell data analysis using Cellar. | Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, Ziv | Nature communications | 35422041 | 2022 04 14 |
| Membrane marker selection for segmenting single cell spatial proteomics data. | Dayao, Monica T; Brusko, Maigan; Wasserfall, Clive; Bar-Joseph, Ziv | Nature communications | 35422106 | 2022 04 14 |
| A single-cell regulatory map of postnatal lung alveologenesis in humans and mice. | Duong, Thu Elizabeth; Wu, Yan; Sos, Brandon Chin; Dong, Weixiu; Limaye, Siddharth; Rivier, Lauraine H; Myers, Greg; Hagood, James S; Zhang, Kun | Cell genomics | 35434692 | 2022 Mar 09 |
| Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets. | Glass, Marla C; Glass, David R; Oliveria, John-Paul; Mbiribindi, Berenice; Esquivel, Carlos O; Krams, Sheri M; Bendall, Sean C; Martinez, Olivia M | Cell reports | 35443184 | 2022 04 19 |
| Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. | Yang, Manxi; Hu, Hang; Su, Pei; Thomas, Paul M; Camarillo, Jeannie M; Greer, Joseph B; Early, Bryan P; Fellers, Ryan T; Kelleher, Neil L; Laskin, Julia | Angewandte Chemie (International ed. in English) | 35446460 | 2022 07 18 |
| Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. | Baskar, Reema; Chen, Amy F; Favaro, Patricia; Reynolds, Warren; Mueller, Fabian; Borges, Luciene; Jiang, Sizun; Park, Hyun Shin; Kool, Eric T; Greenleaf, William J; Bendall, Sean C | Cell reports methods | 35463156 | 2022 Mar 28 |
| Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. | Andreasson, Johan O L; Gotrik, Michael R; Wu, Michelle J; Wayment-Steele, Hannah K; Kladwang, Wipapat; Portela, Fernando; Wellington-Oguri, Roger; Eterna Participants; Das, Rhiju; Greenleaf, William J | Proceedings of the National Academy of Sciences of the United States of America | 35471911 | 2022 05 03 |
| Computational tools for analyzing single-cell data in pluripotent cell differentiation studies. | Ding, Jun; Alavi, Amir; Ebrahimkhani, Mo R; Bar-Joseph, Ziv | Cell reports methods | 35474899 | 2021 Oct 25 |
| A complete pedigree-based graph workflow for rare candidate variant analysis. | Markello, Charles; Huang, Charles; Rodriguez, Alex; Carroll, Andrew; Chang, Pi-Chuan; Eizenga, Jordan; Markello, Thomas; Haussler, David; Paten, Benedict | Genome research | 35483961 | 2022 May |
| NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. | Chen, Amy F; Parks, Benjamin; Kathiria, Arwa S; Ober-Reynolds, Benjamin; Goronzy, Jorg J; Greenleaf, William J | Nature methods | 35501385 | 2022 05 |
| Unilateral Radiation Therapy for Tonsillar Cancer: Treatment Outcomes in the Era of Human Papillomavirus, Positron-Emission Tomography, and Intensity Modulated Radiation Therapy. | Taku, Nicolette; Chronowski, Gregory; Brandon Gunn, G; Morrison, William H; Gross, Neil D; Moreno, Amy C; Ferrarotto, Renata; Frank, Steven J; Fuller, C David; Goepfert, Ryan P; Phan, Jack; Lai, Stephen Y; Reddy, Jay P; Rosenthal, David I; Garden, Adam S | International journal of radiation oncology, biology, physics | 35504500 | 2022 Aug 01 |
| PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. | Chen, Xu; Calandrelli, Riccardo; Girardini, John; Yan, Zhangming; Tan, Zhiqun; Xu, Xiangmin; Hiniker, Annie; Zhong, Sheng | Cell metabolism | 35508105 | 2022 05 03 |
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| Deep learning identification of stiffness markers in breast cancer. | Sneider, Alexandra; Kiemen, Ashley; Kim, Joo Ho; Wu, Pei-Hsun; Habibi, Mehran; White, Marissa; Phillip, Jude M; Gu, Luo; Wirtz, Denis | Biomaterials | 35537336 | 2022 06 |
| Epigenetic Regulation of Heart-ECHS. | Gan, Lu; Pei, Liming | JACC. Basic to translational science | 35540104 | 2022 Apr |
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| New Views of Old Proteins: Clarifying the Enigmatic Proteome. | Burnum-Johnson, Kristin E; Conrads, Thomas P; Drake, Richard R; Herr, Amy E; Iyengar, Ravi; Kelly, Ryan T; Lundberg, Emma; MacCoss, Michael J; Naba, Alexandra; Nolan, Garry P; Pevzner, Pavel A; Rodland, Karin D; Sechi, Salvatore; Slavov, Nikolai; Spraggins, Jeffrey M; Van Eyk, Jennifer E; Vidal, Marc; Vogel, Christine; Walt, David R; Kelleher, Neil L | Molecular & cellular proteomics : MCP | 35654359 | 2022 Jul |
| A reference tissue atlas for the human kidney. | Hansen, Jens; Sealfon, Rachel; Menon, Rajasree; Eadon, Michael T; Lake, Blue B; Steck, Becky; Anjani, Kavya; Parikh, Samir; Sigdel, Tara K; Zhang, Guanshi; Velickovic, Dusan; Barwinska, Daria; Alexandrov, Theodore; Dobi, Dejan; Rashmi, Priyanka; Otto, Edgar A; Rivera, Miguel; Rose, Michael P; Anderton, Christopher R; Shapiro, John P; Pamreddy, Annapurna; Winfree, Seth; Xiong, Yuguang; He, Yongqun; de Boer, Ian H; Hodgin, Jeffrey B; Barisoni, Laura; Naik, Abhijit S; Sharma, Kumar; Sarwal, Minnie M; Zhang, Kun; Himmelfarb, Jonathan; Rovin, Brad; El-Achkar, Tarek M; Laszik, Zoltan; He, John Cijiang; Dagher, Pierre C; Valerius, M Todd; Jain, Sanjay; Satlin, Lisa M; Troyanskaya, Olga G; Kretzler, Matthias; Iyengar, Ravi; Azeloglu, Evren U; Kidney Precision Medicine Project | Science advances | 35675394 | 2022 Jun 10 |
| Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. | Becker, Winston R; Nevins, Stephanie A; Chen, Derek C; Chiu, Roxanne; Horning, Aaron M; Guha, Tuhin K; Laquindanum, Rozelle; Mills, Meredith; Chaib, Hassan; Ladabaum, Uri; Longacre, Teri; Shen, Jeanne; Esplin, Edward D; Kundaje, Anshul; Ford, James M; Curtis, Christina; Snyder, Michael P; Greenleaf, William J | Nature genetics | 35726067 | 2022 Jul |
| Unsupervised cell functional annotation for single-cell RNA-seq. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Genome research | 35764397 | 2022 Jun 28 |
| High-Throughput Nano-DESI Mass Spectrometry Imaging of Biological Tissues Using an Integrated Microfluidic Probe. | Li, Xiangtang; Hu, Hang; Yin, Ruichuan; Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Analytical chemistry | 35770488 | 2022 07 12 |
| scSTEM: clustering pseudotime ordered single-cell data. | Song, Qi; Wang, Jingtao; Bar-Joseph, Ziv | Genome biology | 35799304 | 2022 07 07 |
| Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications. | Stockwell, Brent R | Cell | 35803244 | 2022 07 07 |
| Hanging drop sample preparation improves sensitivity of spatial proteomics. | Kwon, Yumi; Piehowski, Paul D; Zhao, Rui; Sontag, Ryan L; Moore, Ronald J; Burnum-Johnson, Kristin E; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T; Zhu, Ying | Lab on a chip | 35838077 | 2022 Jul 26 |
| Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. | Sharman, Kavya; Patterson, Nathan Heath; Weiss, Andy; Neumann, Elizabeth K; Guiberson, Emma R; Ryan, Daniel J; Gutierrez, Danielle B; Spraggins, Jeffrey M; Van de Plas, Raf; Skaar, Eric P; Caprioli, Richard M | Journal of proteome research | 35849531 | 2023 May 05 |
| Overcoming Selection Bias In Synthetic Lethality Prediction. | Seale, Colm; Tepeli, Yasin; Gonçalves, Joana P | Bioinformatics (Oxford, England) | 35876858 | 2022 Jul 25 |
| Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. | Su, Pei; McGee, John P; Durbin, Kenneth R; Hollas, Michael A R; Yang, Manxi; Neumann, Elizabeth K; Allen, Jamie L; Drown, Bryon S; Butun, Fatma Ayaloglu; Greer, Joseph B; Early, Bryan P; Fellers, Ryan T; Spraggins, Jeffrey M; Laskin, Julia; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L | Science advances | 35947651 | 2022 Aug 12 |
| Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation. | Schachner, Luis F; Soye, Benjamin Des; Ro, Soo; Kenney, Grace E; Ives, Ashley N; Su, Taojunfeng; Goo, Young Ah; Jewett, Michael C; Rosenzweig, Amy C; Kelleher, Neil L | ACS chemical biology | 35951581 | 2022 Aug 11 |
| Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. | Ozonoff, Al; Schaenman, Joanna; Jayavelu, Naresh Doni; Milliren, Carly E; Calfee, Carolyn S; Cairns, Charles B; Kraft, Monica; Baden, Lindsey R; Shaw, Albert C; Krammer, Florian; van Bakel, Harm; Esserman, Denise A; Liu, Shanshan; Sesma, Ana Fernandez; Simon, Viviana; Hafler, David A; Montgomery, Ruth R; Kleinstein, Steven H; Levy, Ofer; Bime, Christian; Haddad, Elias K; Erle, David J; Pulendran, Bali; Nadeau, Kari C; Davis, Mark M; Hough, Catherine L; Messer, William B; Higuita, Nelson I Agudelo; Metcalf, Jordan P; Atkinson, Mark A; Brakenridge, Scott C; Corry, David; Kheradmand, Farrah; Ehrlich, Lauren I R; Melamed, Esther; McComsey, Grace A; Sekaly, Rafick; Diray-Arce, Joann; Peters, Bjoern; Augustine, Alison D; Reed, Elaine F; Altman, Matthew C; Becker, Patrice M; Rouphael, Nadine; IMPACC study group members | EBioMedicine | 35952496 | 2022 Sep |
| Spatial profiling of chromatin accessibility in mouse and human tissues. | Deng, Yanxiang; Bartosovic, Marek; Ma, Sai; Zhang, Di; Kukanja, Petra; Xiao, Yang; Su, Graham; Liu, Yang; Qin, Xiaoyu; Rosoklija, Gorazd B; Dwork, Andrew J; Mann, J John; Xu, Mina L; Halene, Stephanie; Craft, Joseph E; Leong, Kam W; Boldrini, Maura; Castelo-Branco, Gonçalo; Fan, Rong | Nature | 35978191 | 2022 09 |
| UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Journal of computational biology : a journal of computational molecular cell biology | 36036832 | 2022 Nov |
| Pharmacological inhibition and reversal of pancreatic acinar ductal metaplasia. | da Silva, Lais; Jiang, Jinmai; Perkins, Corey; Atanasova, Kalina Rosenova; Bray, Julie K; Bulut, Gamze; Azevedo-Pouly, Ana; Campbell-Thompson, Martha; Yang, Xiaozhi; Hakimjavadi, Hesamedin; Chamala, Srikar; Ratnayake, Ranjala; Gharaibeh, Raad Z; Li, Chenglong; Luesch, Hendrik; Schmittgen, Thomas D | Cell death discovery | 36055991 | 2022 Sep 02 |
| Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection. | Zemaitis, Kevin J; Veličković, Dušan; Kew, William; Fort, Kyle L; Reinhardt-Szyba, Maria; Pamreddy, Annapurna; Ding, Yanli; Kaushik, Dharam; Sharma, Kumar; Makarov, Alexander A; Zhou, Mowei; Paša-Tolić, Ljiljana | Analytical chemistry | 36067026 | 2022 09 20 |
| Incidence Trends of New-Onset Diabetes in Children and Adolescents Before and During the COVID-19 Pandemic: Findings From Florida. | Guo, Yi; Bian, Jiang; Chen, Aokun; Wang, Fei; Posgai, Amanda L; Schatz, Desmond A; Shenkman, Elizabeth A; Atkinson, Mark A | Diabetes | 36094294 | 2022 Dec 01 |
| CINS: Cell Interaction Network inference from Single cell expression data. | Yuan, Ye; Cosme Jr, Carlos; Adams, Taylor Sterling; Schupp, Jonas; Sakamoto, Koji; Xylourgidis, Nikos; Ruffalo, Matthew; Li, Jiachen; Kaminski, Naftali; Bar-Joseph, Ziv | PLoS computational biology | 36095011 | 2022 09 |
| Polyphony: An Interactive Transfer Learning Framework for Single-Cell Data Analysis. | Cheng, Furui; Keller, Mark S; Qu, Huamin; Gehlenborg, Nils; Wang, Qianwen | IEEE transactions on visualization and computer graphics | 36155452 | 2022 Sep 26 |
| GBZ file format for pangenome graphs. | Sirén, Jouni; Paten, Benedict | Bioinformatics (Oxford, England) | 36179091 | 2022 Nov 15 |
| Anatomic nomenclature and 3-dimensional regional model of the human ovary: call for a new paradigm. | O'Neill, Kathleen E; Maher, Jacqueline Y; Laronda, Monica M; Duncan, Francesca E; LeDuc, Richard D; Lujan, Marla E; Oktay, Kutluk H; Pouch, Alison M; Segars, James H; Tsui, Elizabeth L; Zelinski, Mary B; Halvorson, Lisa M; Gomez-Lobo, Veronica | American journal of obstetrics and gynecology | 36191605 | 2023 Mar |
| The expanding vistas of spatial transcriptomics. | Tian, Luyi; Chen, Fei; Macosko, Evan Z | Nature biotechnology | 36192637 | 2022 Oct 03 |
| Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. | Ramos, Erika K; Tsai, Chia-Feng; Jia, Yuzhi; Cao, Yue; Manu, Megan; Taftaf, Rokana; Hoffmann, Andrew D; El-Shennawy, Lamiaa; Gritsenko, Marina A; Adorno-Cruz, Valery; Schuster, Emma J; Scholten, David; Patel, Dhwani; Liu, Xia; Patel, Priyam; Wray, Brian; Zhang, Youbin; Zhang, Shanshan; Moore, Ronald J; Mathews, Jeremy V; Schipma, Matthew J; Liu, Tao; Tokars, Valerie L; Cristofanilli, Massimo; Shi, Tujin; Shen, Yang; Dashzeveg, Nurmaa K; Liu, Huiping | eLife | 36193887 | 2022 Oct 04 |
| A Parallelization Strategy for the Time Efficient Analysis of Thousands of LC/MS Runs in High-Performance Computing Environment. | van Zalm, Patrick; Viodé, Arthur; Smolen, Kinga; Fatou, Benoit; Hayati, Arash Nemati; Schlaffner, Christoph N; Levy, Ofer; Steen, Judith; Steen, Hanno | Journal of proteome research | 36201825 | 2022 Nov 04 |
| Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program. | Shapira, Suzanne N; Naji, Ali; Atkinson, Mark A; Powers, Alvin C; Kaestner, Klaus H | Cell metabolism | 36206763 | 2022 Sep 30 |
| Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. | Kishi, Jocelyn Y; Liu, Ninning; West, Emma R; Sheng, Kuanwei; Jordanides, Jack J; Serrata, Matthew; Cepko, Constance L; Saka, Sinem K; Yin, Peng | Nature methods | 36216958 | 2022 Nov |
| Spatial epitope barcoding reveals clonal tumor patch behaviors. | Rovira-Clavé, Xavier; Drainas, Alexandros P; Jiang, Sizun; Bai, Yunhao; Baron, Maya; Zhu, Bokai; Dallas, Alec E; Lee, Myung Chang; Chu, Theresa P; Holzem, Alessandra; Ayyagari, Ramya; Bhattacharya, Debadrita; McCaffrey, Erin F; Greenwald, Noah F; Markovic | Cancer cell | 36240778 | 2022 Nov 14 |
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| Gestationally dependent immune organization at the maternal-fetal interface. | Moore, Amber R; Vivanco Gonzalez, Nora; Plummer, Katherine A; Mitchel, Olivia R; Kaur, Harleen; Rivera, Moises; Collica, Brian; Goldston, Mako; Filiz, Ferda; Angelo, Michael; Palmer, Theo D; Bendall, Sean C | Cell reports | 36384130 | 2022 Nov 15 |
| MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. | Shao, Xinhao; Gomez, Clarissa D; Kapoor, Nandini; Considine, James M; Grams, Christopher; Gao, Yu Tom; Naba, Alexandra | Nucleic acids research | 36399478 | 2022 Nov 18 |
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| An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue. | Lukowski, Jessica K; Olson, Heather; Velickovic, Marija; Wang, Juan; Kyle, Jennifer E; Kim, Young-Mo; Williams, Sarah M; Zhu, Ying; Huyck, Heidi L; McGraw, Matthew D; Poole, Cory; Rogers, Lisa; Misra, Ravi; Alexandrov, Theodore; Ansong, Charles; Pryhuber, Gloria S; Clair, Geremy; Adkins, Joshua N; Carson, James P; Anderton, Christopher R | Frontiers in molecular biosciences | 36465564 | 2022 |
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| Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. | Stuart, Tim; Hao, Stephanie; Zhang, Bingjie; Mekerishvili, Levan; Landau, Dan A; Maniatis, Silas; Satija, Rahul; Raimondi, Ivan | Nature biotechnology | 36536150 | 2023 Jun |
| Senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus. | Swahn, Hannah; Li, Kun; Duffy, Tomas; Olmer, Merissa; D'Lima, Darryl D; Mondala, Tony S; Natarajan, Padmaja; Head, Steven R; Lotz, Martin K | Annals of the rheumatic diseases | 36564153 | 2023 Mar |
| Machine-learning based investigation of prognostic indicators for oncological outcome of pancreatic ductal adenocarcinoma. | Chang, Jeremy; Liu, Yanan; Saey, Stephanie A; Chang, Kevin C; Shrader, Hannah R; Steckly, Kelsey L; Rajput, Maheen; Sonka, Milan; Chan, Carlos H F | Frontiers in oncology | 36568148 | 2022 |
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| A Multicompartmental Diffusion Model for Improved Assessment of Whole-Body Diffusion-weighted Imaging Data and Evaluation of Prostate Cancer Bone Metastases. | Conlin, Christopher C; Feng, Christine H; Digma, Leonardino A; Rodríguez-Soto, Ana E; Kuperman, Joshua M; Rakow-Penner, Rebecca; Karow, David S; White, Nathan S; Seibert, Tyler M; Hahn, Michael E; Dale, Anders M | Radiology. Imaging cancer | 36705559 | 2023 Jan |
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| Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. | Jain, Yashvardhan; Godwin, Leah L; Joshi, Sripad; Mandarapu, Shriya; Le, Trang; Lindskog, Cecilia; Lundberg, Emma; Börner, Katy | bioRxiv : the preprint server for biology | 36711953 | 2023 Jan 06 |
| Multimodal characterization of antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. | Zhang, Bingjie; Upadhyay, Rabi; Hao, Yuhan; Samanovic, Marie I; Herati, Ramin S; Blair, John; Axelrad, Jordan; Mulligan, Mark J; Littman, Dan R; Satija, Rahul | bioRxiv : the preprint server for biology | 36747786 | 2023 Jan 24 |
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| Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. | Yang, Manxi; Unsihuay, Daisy; Hu, Hang; Nguele Meke, Frederick; Qu, Zihan; Zhang, Zhong-Yin; Laskin, Julia | Analytical chemistry | 36917636 | 2023 Mar 28 |
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| Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics. | Robinson, Makeda L; Glass, David R; Duran, Veronica; Agudelo Rojas, Olga Lucia; Sanz, Ana Maria; Consuegra, Monika; Sahoo, Malaya Kumar; Hartmann, Felix J; Bosse, Marc; Gelvez, Rosa Margarita; Bueno, Nathalia; Pinsky, Benjamin A; Montoya, Jose G; Maecker, Holden; Estupiñan Cardenas, Maria Isabel; Villar Centeno, Luis Angel; Garrido, Elsa Marina Rojas; Rosso, Fernando; Bendall, Sean C; Einav, Shirit | Science advances | 36961888 | 2023 Mar 24 |
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| Multiomic Analysis and CRISPR Perturbation Screens Identify Endothelial Cell Programs and Novel Therapeutic Targets for Coronary Artery Disease. | Gupta, Rajat M; Schnitzler, Gavin R; Fang, Shi; Lee-Kim, Vivian S; Barry, Aurelie | Arteriosclerosis, thrombosis, and vascular biology | 36994731 | 2023 May |
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| Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids. | Bagheri, Pegah; Hoang, Khang; Kuo, Chan-Yu; Trivedi, Hetvi; Jang, Hongje; Shi, Lingyan | Journal of visualized experiments : JoVE | 37246865 | 2023 May 12 |
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| Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer. | Dashzeveg, Nurmaa K; Jia, Yuzhi; Zhang, Youbin; Gerratana, Lorenzo; Patel, Priyam; Shajahan, Asif; Dandar, Tsogbadrakh; Ramos, Erika K; Almubarak, Hannah F; Adorno-Cruz, Valery; Taftaf, Rokana; Schuster, Emma J; Scholten, David; Sokolowski, Michael T; Reduzzi, Carolina; El-Shennawy, Lamiaa; Hoffmann, Andrew D; Manai, Maroua; Zhang, Qiang; D'Amico, Paolo; Azadi, Parastoo; Colley, Karen J; Platanias, Leonidas C; Shah, Ami N; Gradishar, William J; Cristofanilli, Massimo; Muller, William A; Cobb, Brian A; Liu, Huiping | Cancer discovery | 37272843 | 2023 Jun 05 |
| The technological landscape and applications of single-cell multi-omics. | Baysoy, Alev; Bai, Zhiliang; Satija, Rahul; Fan, Rong | Nature reviews. Molecular cell biology | 37280296 | 2023 Oct |
| An integrated cell atlas of the lung in health and disease. | Sikkema, Lisa; Ramírez-Suástegui, Ciro; Strobl, Daniel C; Gillett, Tessa E; Zappia, Luke; Madissoon, Elo; Markov, Nikolay S; Zaragosi, Laure-Emmanuelle; Ji, Yuge; Ansari, Meshal; Arguel, Marie-Jeanne; Apperloo, Leonie; Banchero, Martin; Bécavin, Christophe; Berg, Marijn; Chichelnitskiy, Evgeny; Chung, Mei-I; Collin, Antoine; Gay, Aurore C A; Gote-Schniering, Janine; Hooshiar Kashani, Baharak; Inecik, Kemal; Jain, Manu; Kapellos, Theodore S; Kole, Tessa M; Leroy, Sylvie; Mayr, Christoph H; Oliver, Amanda J; von Papen, Michael; Peter, Lance; Taylor, Chase J; Walzthoeni, Thomas; Xu, Chuan; Bui, Linh T; De Donno, Carlo; Dony, Leander; Faiz, Alen; Guo, Minzhe; Gutierrez, Austin J; Heumos, Lukas; Huang, Ni; Ibarra, Ignacio L; Jackson, Nathan D; Kadur Lakshminarasimha Murthy, Preetish; Lotfollahi, Mohammad; Tabib, Tracy; Talavera-López, Carlos; Travaglini, Kyle J; Wilbrey-Clark, Anna; Worlock, Kaylee B; Yoshida, Masahiro; Lung Biological Network Consortium; van den Berge, Maarten; Bossé, Yohan; Desai, Tushar J; Eickelberg, Oliver; Kaminski, Naftali; Krasnow, Mark A; Lafyatis, Robert; Nikolic, Marko Z; Powell, Joseph E; Rajagopal, Jayaraj; Rojas, Mauricio; Rozenblatt-Rosen, Orit; Seibold, Max A; Sheppard, Dean; Shepherd, Douglas P; Sin, Don D; Timens, Wim; Tsankov, Alexander M; Whitsett, Jeffrey; Xu, Yan; Banovich, Nicholas E; Barbry, Pascal; Duong, Thu Elizabeth; Falk, Christine S; Meyer, Kerstin B; Kropski, Jonathan A; Pe'er, Dana; Schiller, Herbert B; Tata, Purushothama Rao; Schultze, Joachim L; Teichmann, Sara A; Misharin, Alexander V; Nawijn, Martijn C; Luecken, Malte D; Theis, Fabian J | Nature medicine | 37291214 | 2023 Jun |
| Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. | Ginley, Brandon; Lucarelli, Nicholas; Zee, Jarcy; Jain, Sanjay; Han, Seung Sook; Rodrigues, Luis; Ozrazgat-Baslanti, Tezcan; Wong, Michelle L; Nadkarni, Girish; Jen, Kuang-Yu; Sarder, Pinaki | bioRxiv : the preprint server for biology | 37292965 | 2023 May 18 |
| Tissue Mass Spectrometry: How Solid Is Our Future? | Unsihuay, Daisy; Phipps, William S; Paulovich, Amanda G; Chapman, Jessica R; Ducret, Axel; Eberlin, Livia S; Spraggins, Jeffrey M; Goodwin, Richard J A | Clinical chemistry | 37293883 | 2023 Jul 05 |
| Ex Vivo OCT-Based Multimodal Imaging of Human Donor Eyes for Research into Age-Related Macular Degeneration. | Messinger, Jeffrey D; Brinkmann, Max; Kimble, James A; Berlin, Andreas; Freund, K Bailey; Grossman, Gregory H; Ach, Thomas; Curcio, Christine A | Journal of visualized experiments : JoVE | 37306417 | 2023 May 26 |
| Semantic-Aware Contrastive Learning for Multi-Object Medical Image Segmentation. | Lee, Ho Hin; Tang, Yucheng; Yang, Qi; Yu, Xin; Cai, Leon Y; Remedios, Lucas W; Bao, Shunxing; Landman, Bennett A; Huo, Yuankai | IEEE journal of biomedical and health informatics | 37310834 | 2023 Sep |
| Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. | Diray-Arce, Joann; Fourati, Slim; Doni Jayavelu, Naresh; Patel, Ravi; Maguire, Cole; Chang, Ana C; Dandekar, Ravi; Qi, Jingjing; Lee, Brian H; van Zalm, Patrick; Schroeder, Andrew; Chen, Ernie; Konstorum, Anna; Brito, Anderson; Gygi, Jeremy P; Kho, Alvin; Chen, Jing; Pawar, Shrikant; Gonzalez-Reiche, Ana Silvia; Hoch, Annmarie; Milliren, Carly E; Overton, James A; Westendorf, Kerstin; IMPACC Network; Cairns, Charles B; Rouphael, Nadine; Bosinger, Steven E; Kim-Schulze, Seunghee; Krammer, Florian; Rosen, Lindsey; Grubaugh, Nathan D; van Bakel, Harm; Wilson, Michael; Rajan, Jayant; Steen, Hanno; Eckalbar, Walter; Cotsapas, Chris; Langelier, Charles R; Levy, Ofer; Altman, Matthew C; Maecker, Holden; Montgomery, Ruth R; Haddad, Elias K; Sekaly, Rafick P; Esserman, Denise; Ozonoff, Al; Becker, Patrice M; Augustine, Alison D; Guan, Leying; Peters, Bjoern; Kleinstein, Steven H | Cell reports. Medicine | 37327781 | 2023 Jun 20 |
| Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence. | Gosline, Sara J C; Veličković, Marija; Pino, James C; Day, Le Z; Attah, Isaac K; Swensen, Adam C; Danna, Vincent; Posso, Camilo; Rodland, Karin D; Chen, Jing; Matthews, Clayton E; Campbell-Thompson, Martha; Laskin, Julia; Burnum-Johnson, Kristin; Zhu, Ying; Piehowski, Paul D | Molecular & cellular proteomics : MCP | 37328065 | 2023 Aug |
| Surgical management of lymphedema: Does a microsurgeon's bias exist? | Friedman, Rosie; Ismail Aly, Mohamed Eldardiri; Singhal, Dhruv | Microsurgery | 37339916 | 2023 Sep |
| Proteome Landscapes of Human Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma. | Yi, Xiao; Zhu, Jiang; Liu, Wei; Peng, Li; Lu, Cong; Sun, Ping; Huang, Lingling; Nie, Xiu; Huang, Shi'ang; Guo, Tiannan; Zhu, Yi | Molecular & cellular proteomics : MCP | 37353004 | 2023 Aug |
| Potential and risks of artificial intelligence models: Common in medicine practice and special in pediatric urology. | Wen, Yi; Di, Huajie | Journal of pediatric urology | 37355343 | 2023 Oct |
| Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. | Dayao, Monica T; Trevino, Alexandro; Kim, Honesty; Ruffalo, Matthew; D'Angio, H Blaize; Preska, Ryan; Duvvuri, Umamaheswar; Mayer, Aaron T; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 37387167 | 2023 Jun 30 |
| IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. | Haslund-Gourley, Benjamin; Woloszcuk, Kyra; Hou, Jintong; Connors, Jennifer; Cusimano, Gina; Bell, Mathew; Taramangalam, Bhavani; Fourati, Slim; Mege, Nathan; Bernui, Mariana; Altman, Matthew; Krammer, Florian; van Bakel, Harm; Maecker, Holden; Wigdahl, Brian; Cairns, Charles; Haddad, Elias; Comunale, Mary | Research square | 37398192 | 2023 Jun 02 |
| SCS: cell segmentation for high-resolution spatial transcriptomics. | Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv | bioRxiv : the preprint server for biology | 37398213 | 2023 Jun 16 |
| Ubiquitin-specific peptidase 22 controls integrin-dependent cancer cell stemness and metastasis. | Liu, Kun; Gao, Qiong; Jia, Yuzhi; Wei, Juncheng; Chaudhuri, Shuvam; Wang, Shengnan; Tang, Amy; Mani, Nikita; Iyer, Radhika; Cheng, Yang; Gao, Beixue; Lu, Weiyuan; Sun, Zhaolin; Liu, Huiping; Fang, Deyu | Research square | 37398311 | 2023 Jun 16 |
| Spatial proteomics reveals human microglial states shaped by anatomy and neuropathology. | Mrdjen, Dunja; Amouzgar, Meelad; Cannon, Bryan; Liu, Candace; Spence, Angie; McCaffrey, Erin; Bharadwaj, Anusha; Tebaykin, Dmitry; Bukhari, Syed; Hartmann, Felix J; Kagel, Adam; Vijayaragavan, Kausalia; Oliveria, John Paul; Yakabi, Koya; Serrano, Geidy E; Corrada, Maria M; Kawas, Claudia H; Camacho, Christine; Bosse, Marc; Tibshirani, Robert; Beach, Thomas G; Angelo, Michael; Montine, Thomas; Bendall, Sean C | Research square | 37398389 | 2023 Jun 02 |
| Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering. | Hislop, Joshua; Alavi, Amir; Song, Qi; Schoenberger, Rayna; Kamyar, Keshavarz F; LeGraw, Ryan; Velazquez, Jeremy; Mokhtari, Tahere; Taheri, Mohammad Nasser; Rytel, Matthew; de Sousa Lopes, Susana M Chuva; Watkins, Simon; Stolz, Donna; Kiani, Samira; Sozen, Berna; Bar-Joseph, Ziv; Ebrahimkhani, Mo R | bioRxiv : the preprint server for biology | 37398391 | 2023 Jul 24 |
| Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain. | Luo, Zhifei; Wen, Xingzhao; Zhao, Wenxin; Nguyen, Tri C; Wan, Xueyi; Richard, John Lalith Charles; Zhong, Sheng | bioRxiv : the preprint server for biology | 37425846 | 2023 Jun 28 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support. | Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E; Gault, David; Ghosh, Satrajit S; Gold, Ilan; Halchenko, Yaroslav O; Hartley, Matthew; Horsfall, Dave; Keller, Mark S; Kittisopikul, Mark; Kovacs, Gabor; Küpcü Yoldaş, Aybüke; Kyoda, Koji; le Tournoulx de la Villegeorges, Albane; Li, Tong; Liberali, Prisca; Lindner, Dominik; Linkert, Melissa; Lüthi, Joel; Maitin-Shepard, Jeremy; Manz, Trevor; Marconato, Luca; McCormick, Matthew; Lange, Merlin; Mohamed, Khaled; Moore, William; Norlin, Nils; Ouyang, Wei; Özdemir, Bugra; Palla, Giovanni; Pape, Constantin; Pelkmans, Lucas; Pietzsch, Tobias; Preibisch, Stephan; Prete, Martin; Rzepka, Norman; Samee, Sameeul; Schaub, Nicholas; Sidky, Hythem; Solak, Ahmet Can; Stirling, David R; Striebel, Jonathan; Tischer, Christian; Toloudis, Daniel; Virshup, Isaac; Walczysko, Petr; Watson, Alan M; Weisbart, Erin; Wong, Frances; Yamauchi, Kevin A; Bayraktar, Omer; Cimini, Beth A; Gehlenborg, Nils; Haniffa, Muzlifah; Hotaling, Nathan; Onami, Shuichi; Royer, Loic A; Saalfeld, Stephan; Stegle, Oliver; Theis, Fabian J; Swedlow, Jason R | Histochemistry and cell biology | 37428210 | 2023 Sep |
| SCS: cell segmentation for high-resolution spatial transcriptomics. | Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv | Nature methods | 37429992 | 2023 Aug |
| Nanospray Desorption Electrospray Ionization (Nano-DESI) Mass Spectrometry Imaging with High Ion Mobility Resolution. | Jiang, Li-Xue; Hernly, Emerson; Hu, Hang; Hilger, Ryan T; Neuweger, Heiko; Yang, Manxi; Laskin, Julia | Journal of the American Society for Mass Spectrometry | 37463098 | 2023 Aug 02 |
| Unsupervised Registration Refinement for Generating Unbiased Eye Atlas. | Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Yang, Qi; Xu, Xin; Schey, Kevin L; Spraggins, Jeffrey M; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 37465097 | 2023 Feb |
| A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. | Canela, Victor Hugo; Bowen, William S; Ferreira, Ricardo Melo; Syed, Farooq; Lingeman, James E; Sabo, Angela R; Barwinska, Daria; Winfree, Seth; Lake, Blue B; Cheng, Ying-Hua; Gaut, Joseph P; Ferkowicz, Michael; LaFavers, Kaice A; Zhang, Kun; Coe, Fredric L; Worcester, Elaine; Kidney Precision Medicine Project; Jain, Sanjay; Eadon, Michael T; Williams Jr, James C; El-Achkar, Tarek M | Nature communications | 37468493 | 2023 Jul 19 |
| Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature. | Boppana, Avinash; Lee, Sujin; Malhotra, Rajeev; Halushka, Marc; Gustilo, Katherine S; Quardokus, Ellen M; Herr 2nd, Bruce W; Börner, Katy; Weber, Griffin M | Scientific data | 37468503 | 2023 Jul 19 |
| Segmentation of human functional tissue units in support of a Human Reference Atlas. | Jain, Yashvardhan; Godwin, Leah L; Ju, Yingnan; Sood, Naveksha; Quardokus, Ellen M; Bueckle, Andreas; Longacre, Teri; Horning, Aaron; Lin, Yiing; Esplin, Edward D; Hickey, John W; Snyder, Michael P; Patterson, Nathan Heath; Spraggins, Jeffrey M; Börner, Katy | Communications biology | 37468557 | 2023 Jul 19 |
| An atlas of healthy and injured cell states and niches in the human kidney. | Lake, Blue B; Menon, Rajasree; Winfree, Seth; Hu, Qiwen; Melo Ferreira, Ricardo; Kalhor, Kian; Barwinska, Daria; Otto, Edgar A; Ferkowicz, Michael; Diep, Dinh; Plongthongkum, Nongluk; Knoten, Amanda; Urata, Sarah; Mariani, Laura H; Naik, Abhijit S; Eddy, Sean; Zhang, Bo; Wu, Yan; Salamon, Diane; Williams, James C; Wang, Xin; Balderrama, Karol S; Hoover, Paul J; Murray, Evan; Marshall, Jamie L; Noel, Teia; Vijayan, Anitha; Hartman, Austin; Chen, Fei; Waikar, Sushrut S; Rosas, Sylvia E; Wilson, Francis P; Palevsky, Paul M; Kiryluk, Krzysztof; Sedor, John R; Toto, Robert D; Parikh, Chirag R; Kim, Eric H; Satija, Rahul; Greka, Anna; Macosko, Evan Z; Kharchenko, Peter V; Gaut, Joseph P; Hodgin, Jeffrey B; KPMP Consortium; Eadon, Michael T; Dagher, Pierre C; El-Achkar, Tarek M; Zhang, Kun; Kretzler, Matthias; Jain, Sanjay | Nature | 37468583 | 2023 Jul |
| Organization of the human intestine at single-cell resolution. | Hickey, John W; Becker, Winston R; Nevins, Stephanie A; Horning, Aaron; Perez, Almudena Espin; Zhu, Chenchen; Zhu, Bokai; Wei, Bei; Chiu, Roxanne; Chen, Derek C; Cotter, Daniel L; Esplin, Edward D; Weimer, Annika K; Caraccio, Chiara; Venkataraaman, Vishal; Schürch, Christian M; Black, Sarah; Brbić, Maria; Cao, Kaidi; Chen, Shuxiao; Zhang, Weiruo; Monte, Emma; Zhang, Nancy R; Ma, Zongming; Leskovec, Jure; Zhang, Zhengyan; Lin, Shin; Longacre, Teri; Plevritis, Sylvia K; Lin, Yiing; Nolan, Garry P; Greenleaf, William J; Snyder, Michael | Nature | 37468586 | 2023 Jul |
| Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging. | Quardokus, Ellen M; Saunders, Diane C; McDonough, Elizabeth; Hickey, John W; Werlein, Christopher; Surrette, Christine; Rajbhandari, Presha; Casals, Anna Martinez; Tian, Hua; Lowery, Lisa; Neumann, Elizabeth K; Björklund, Frida; Neelakantan, Taruna V; Croteau, Josh; Wiblin, Anne E; Fisher, Jeremy; Livengood, April J; Dowell, Karen G; Silverstein, Jonathan C; Spraggins, Jeffrey M; Pryhuber, Gloria S; Deutsch, Gail; Ginty, Fiona; Nolan, Garry P; Melov, Simon; Jonigk, Danny; Caldwell, Michael A; Vlachos, Ioannis S; Muller, Werner; Gehlenborg, Nils; Stockwell, Brent R; Lundberg, Emma; Snyder, Michael P; Germain, Ronald N; Camarillo, Jeannie M; Kelleher, Neil L; Börner, Katy; Radtke, Andrea J | Nature methods | 37468619 | 2023 Aug |
| KRAS(G12D) drives lepidic adenocarcinoma through stem-cell reprogramming. | Juul, Nicholas H; Yoon, Jung-Ki; Martinez, Marina C; Rishi, Neha; Kazadaeva, Yana I; Morri, Maurizio; Neff, Norma F; Trope, Winston L; Shrager, Joseph B; Sinha, Rahul; Desai, Tushar J | Nature | 37468622 | 2023 Jul |
| Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). | Jain, Sanjay; Pei, Liming; Spraggins, Jeffrey M; Angelo, Michael; Carson, James P; Gehlenborg, Nils; Ginty, Fiona; Gonçalves, Joana P; Hagood, James S; Hickey, John W; Kelleher, Neil L; Laurent, Louise C; Lin, Shin; Lin, Yiing; Liu, Huiping; Naba, Alexandra; Nakayasu, Ernesto S; Qian, Wei-Jun; Radtke, Andrea; Robson, Paul; Stockwell, Brent R; Van de Plas, Raf; Vlachos, Ioannis S; Zhou, Mowei; HuBMAP Consortium; Börner, Katy; Snyder, Michael P | Nature cell biology | 37468756 | 2023 Aug |
| 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging. | Ghose, Soumya; Ju, Yingnan; McDonough, Elizabeth; Ho, Jonhan; Karunamurthy, Arivarasan; Chadwick, Chrystal; Cho, Sanghee; Rose, Rachel; Corwin, Alex; Surrette, Christine; Martinez, Jessica; Williams, Eric; Sood, Anup; Al-Kofahi, Yousef; Falo Jr, Louis D; Börner, Katy; Ginty, Fiona | Communications biology | 37468758 | 2023 Jul 19 |
| Non-Linear Lymphatic Anatomy in Breast Cancer Patients Prior to Axillary Lymph Node Dissection: A Risk Factor For Lymphedema Development. | Kinney, JacqueLyn R; Friedman, Rosie; Kim, Erin; Tillotson, Elizabeth; Shillue, Kathy; Lee, Bernard T; Singhal, Dhruv | Journal of mammary gland biology and neoplasia | 37480365 | 2023 Jul 22 |
| Editorial: Global excellence in inflammatory diseases: North America 2021. | Kusner, Linda L; Misra, Ravi S; Lucas, Rudolf | Frontiers in immunology | 37483602 | 2023 |
| Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases. | Ober-Reynolds, Benjamin; Wang, Chen; Ko, Justin M; Rios, Eon J; Aasi, Sumaira Z; Davis, Mark M; Oro, Anthony E; Greenleaf, William J | Nature genetics | 37500727 | 2023 Aug |
| Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. | Jain, Yashvardhan; Godwin, Leah L; Joshi, Sripad; Mandarapu, Shriya; Le, Trang; Lindskog, Cecilia; Lundberg, Emma; Börner, Katy | Nature communications | 37537179 | 2023 Aug 03 |
| Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms. | Petrov, Petar B; Considine, James M; Izzi, Valerio; Naba, Alexandra | Journal of cell science | 37555624 | 2023 Sep 01 |
| Systematic Sampling of the Female Reproductive System for Molecular Characterization. | Fisher, Stephen A; Grijalva, Marielena; Guo, Rong; Johnston, Sarah A; Laurent, Louise C; Nguyen, Hieu; Renz, John; Rosario, Jean G; Rudich, Steven; Gregory, Brian D; Kim, Junhyong; O'Neill, Kathleen | Current protocols | 37584588 | 2023 Aug |
| Segmentation quality assessment by automated detection of erroneous surface regions in medical images. | Zaman, Fahim Ahmed; Zhang, Lichun; Zhang, Honghai; Sonka, Milan; Wu, Xiaodong | Computers in biology and medicine | 37591161 | 2023 Sep |
| Edematous Dermal Thickening on Magnetic Resonance Imaging as a Biomarker for Lymphatic Surgical Outcomes. | Kinney, JacqueLyn R; Babapour, Sara; Kim, Erin; Friedman, Rosie; Singhal, Dhruv; Lee, Bernard T; Tsai, Leo L | Medicina (Kaunas, Lithuania) | 37629659 | 2023 Jul 26 |
| Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. | Kalhor, Kian; Chen, Chien-Ju; Lee, Ho Suk; Cai, Matthew; Nafisi, Mahsa; Que, Richard; Palmer, Carter; Yuan, Yixu; Zhang, Yida; Song, Jinghui; Knoten, Amanda; Lake, Blue B; Gaut, Joseph P; Keene, Dirk; Lein, Ed; Kharchenko, Peter V; Chun, Jerold; Jain, Sanjay; Fan, Jian-Bing; Zhang, Kun | bioRxiv : the preprint server for biology | 37645998 | 2023 Aug 19 |
| Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. | Favaro, Patricia; Glass, David R; Borges, Luciene; Baskar, Reema; Reynolds, Warren; Ho, Daniel; Bruce, Trevor; Tebaykin, Dmitry; Scanlon, Vanessa M; Shestopalov, Ilya; Bendall, Sean C | bioRxiv : the preprint server for biology | 37693547 | 2023 Aug 30 |
| Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. | Aman, Andrew J; Saunders, Lauren M; Carr, August A; Srivatasan, Sanjay; Eberhard, Colten; Carrington, Blake; Watkins-Chow, Dawn; Pavan, William J; Trapnell, Cole; Parichy, David M | eLife | 37695017 | 2023 Sep 11 |
| Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. | Kolmogorov, Mikhail; Billingsley, Kimberley J; Mastoras, Mira; Meredith, Melissa; Monlong, Jean; Lorig-Roach, Ryan; Asri, Mobin; Alvarez Jerez, Pilar; Malik, Laksh; Dewan, Ramita; Reed, Xylena; Genner, Rylee M; Daida, Kensuke; Behera, Sairam; Shafin, Kishwar; Pesout, Trevor; Prabakaran, Jeshuwin; Carnevali, Paolo; Yang, Jianzhi; Rhie, Arang; Scholz, Sonja W; Traynor, Bryan J; Miga, Karen H; Jain, Miten; Timp, Winston; Phillippy, Adam M; Chaisson, Mark; Sedlazeck, Fritz J; Blauwendraat, Cornelis; Paten, Benedict | Nature methods | 37710018 | 2023 Oct |
| Early cancer detection by SERS spectroscopy and machine learning. | Shi, Lingyan; Li, Yajuan; Li, Zhi | Light, science & applications | 37714845 | 2023 Sep 15 |
| Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection. | Zhang, Bingjie; Upadhyay, Rabi; Hao, Yuhan; Samanovic, Marie I; Herati, Ramin S; Blair, John D; Axelrad, Jordan; Mulligan, Mark J; Littman, Dan R; Satija, Rahul | Nature immunology | 37735591 | 2023 Oct |
| Local read haplotagging enables accurate long-read small variant calling. | Kolesnikov, Alexey; Cook, Daniel; Nattestad, Maria; McNulty, Brandy; Gorzynski, John; Goenka, Sneha; Ashley, Euan A; Jain, Miten; Miga, Karen H; Paten, Benedict; Chang, Pi-Chuan; Carroll, Andrew; Shafin, Kishwar | bioRxiv : the preprint server for biology | 37745389 | 2023 Sep 12 |
| Navigating the kidney organoid: insights into assessment and enhancement of nephron function. | Tabibzadeh, Nahid; Satlin, Lisa M; Jain, Sanjay; Morizane, Ryuji | American journal of physiology. Renal physiology | 37767571 | 2023 Dec 01 |
| Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope using the Tile/SED/Array Interface. | Piyadasa, Hadeesha; Oberlton, Benjamin; Kong, Alex; Camacho Fullaway, Christine; Reddy Varra, Sricharan; Sowers, Cameron; Tsai, Albert G | Journal of visualized experiments : JoVE | 37782085 | 2023 Sep 15 |
| A monolithic microfluidic probe for ambient mass spectrometry imaging of biological tissues. | Jiang, Li-Xue; Polack, Matthias; Li, Xiangtang; Yang, Manxi; Belder, Detlev; Laskin, Julia | Lab on a chip | 37782224 | 2023 Oct 24 |
| Mechano-induced homotypic patterned domain formation by monocytes. | Wirtz, Denis; Du, Wenxuan; Zhu, Jingyi; Wu, Yufei; Kiemen, Ashley; Wan, Zeqi; Hanna, Eban; Sun, Sean | Research square | 37790337 | 2023 Sep 22 |
| The Role of Endothelial Cells in Atherosclerosis: Insights from Genetic Association Studies. | Pepin, Mark E; Gupta, Rajat | The American journal of pathology | 37827214 | 2023 Oct 10 |
| High-resolution integrated microfluidic probe for mass spectrometry imaging of biological tissues. | Li, Xiangtang; Hu, Hang; Laskin, Julia | Analytica chimica acta | 37827646 | 2023 Oct 23 |
| Automated imaging and identification of proteoforms directly from ovarian cancer tissue. | McGee, John P; Su, Pei; Durbin, Kenneth R; Hollas, Michael A R; Bateman, Nicholas W; Maxwell, G Larry; Conrads, Thomas P; Fellers, Ryan T; Melani, Rafael D; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L | Nature communications | 37838706 | 2023 Oct 14 |
| Functional Tissue Units in the Human Reference Atlas. | Bidanta, Supriya; Börner, Katy; Herr 2nd, Bruce W; Nagy, Marcell; Gustilo, Katherine S; Bajema, Rachel; Maier, Libby; Molontay, Roland; Weber, Griffin | bioRxiv : the preprint server for biology | 37905079 | 2023 Oct 26 |
| Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia. | Tan, Kai; Xu, Jason; Chen, Changya; Vincent, Tiffaney; Pölönen, Petri; Hu, Jianzhong; Yoshimura, Satoshi; Yu, Wenbao; Sussman, Jonathan; Chen, Chia-Hui; Li, Elizabeth; Diorio, Caroline; Shraim, Rawan; Newman, Haley; Uppuluri, Lahari; Li, Alexander; Chen, Gregory; Bandyopadhyay, Shovik; Wu, David; Ding, Yang-Yang; Xu, Jessica; Lim, Tristan; Hsu, Miles; Thadi, Anusha; Ahn, Kyung Jin; Wu, Chi-Yun; Peng, Jacqueline; Sun, Yusha; Wang, Alice; Mehta, Rushabh; Frank, David; Meyer, Lauren; Loh, Mignon; Raetz, Elizabeth; Chen, Zhiguo; Wood, Brent; Devidas, Meenakshi; Dunsmore, Kimberly; Winter, Stuart; Chang, Ti-Cheng; Wu, Gang; Pounds, Stanley; Zhang, Nancy; Carroll, William; Hunger, Stephen; Bernt, Kathrin; Yang, Jun; Mullighan, Charles; Teachey, David | Research square | 37961674 | 2023 Oct 30 |
| Dimension-agnostic and granularity-based spatially variable gene identification using BSP. | Wang, Juexin; Li, Jinpu; Kramer, Skyler T; Su, Li; Chang, Yuzhou; Xu, Chunhui; Eadon, Michael T; Kiryluk, Krzysztof; Ma, Qin; Xu, Dong | Nature communications | 37963892 | 2023 Nov 14 |
| Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. | Lucarelli, Nicholas; Ginley, Brandon; Zee, Jarcy; Mimar, Sayat; Paul, Anindya S; Jain, Sanjay; Han, Seung Seok; Rodrigues, Luis; Ozrazgat-Baslanti, Tezcan; Wong, Michelle L; Nadkarni, Girish; Clapp, William L; Jen, Kuang-Yu; Sarder, Pinaki | Kidney360 | 37966063 | 2023 Dec 01 |
| Multimodal imaging of metabolic activities for distinguishing subtypes of breast cancer. | Li, Zhi; Nguyen, Chloe; Jang, Hongje; Hoang, David; Min, SoeSu; Ackerstaff, Ellen; Koutcher, Jason A; Shi, Lingyan | Biomedical optics express | 38021123 | 2023 Nov 01 |
| Human mobility networks reveal increased segregation in large cities. | Nilforoshan, Hamed; Looi, Wenli; Pierson, Emma; Villanueva, Blanca; Fishman, Nic; Chen, Yiling; Sholar, John; Redbird, Beth; Grusky, David; Leskovec, Jure | Nature | 38030732 | 2023 Dec |
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| Advances in Imaging Mass Spectrometry for Biomedical and Clinical Research. | Djambazova, Katerina V; van Ardenne, Jacqueline M; Spraggins, Jeffrey M | Trends in analytical chemistry : TRAC | 38045023 | 2023 Dec |
| A Foundation Model for Cell Segmentation. | Israel, Uriah; Marks, Markus; Dilip, Rohit; Li, Qilin; Schwartz, Morgan; Pradhan, Elora; Pao, Edward; Li, Shenyi; Pearson-Goulart, Alexander; Perona, Pietro; Gkioxari, Georgia; Barnowski, Ross; Yue, Yisong; Van Valen, David | bioRxiv : the preprint server for biology | 38045277 | 2023 Nov 20 |
| DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples. | Wang, Qianwen; L'Yi, Sehi; Gehlenborg, Nils | Proceedings of the SIGCHI conference on human factors in computing systems. CHI Conference | 38074525 | 2023 Apr |
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| Modelling post-implantation human development to yolk sac blood emergence. | Hislop, Joshua; Song, Qi; Keshavarz F, Kamyar; Alavi, Amir; Schoenberger, Rayna; LeGraw, Ryan; Velazquez, Jeremy J; Mokhtari, Tahere; Taheri, Mohammad Naser; Rytel, Matthew; Chuva de Sousa Lopes, Susana M; Watkins, Simon; Stolz, Donna; Kiani, Samira; Soze | Nature | 38092041 | 2024 Feb |
| Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. | Russell, Andrew J C; Weir, Jackson A; Nadaf, Naeem M; Shabet, Matthew; Kumar, Vipin; Kambhampati, Sandeep; Raichur, Ruth; Marrero, Giovanni J; Liu, Sophia; Balderrama, Karol S; Vanderburg, Charles R; Shanmugam, Vignesh; Tian, Luyi; Iorgulescu, J Bryan; Yoon, Charles H; Wu, Catherine J; Macosko, Evan Z; Chen, Fei | Nature | 38093010 | 2024 Jan |
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| Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy. | Hickey, John W; Agmon, Eran; Horowitz, Nina; Lamore, Matthew; Sunwoo, John; Covert, Markus; Nolan, Garry P | bioRxiv : the preprint server for biology | 38106218 | 2023 Dec 08 |
| Discussion: Commercial Insurance Rates and Coding for Lymphedema Procedures: The Current State of Confusion and Need for Consensus. | Friedman, Rosie; Lee, Bernard T; Chatterjee, Abhishek; Singhal, Dhruv | Plastic and reconstructive surgery | 38127452 | 2024 Jan 01 |
| Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels. | Hong, Fan; Kishi, Jocelyn Y; Delgado, Ryan N; Jeong, Jiyoun; Saka, Sinem K; Su, Hanquan; Cepko, Constance L; Yin, Peng | Nature methods | 38151595 | 2024 Feb |
| Engineering self-propelled tumor-infiltrating CAR T cells using synthetic velocity receptors. | Johnston, Adrian C; Alicea, Gretchen M; Lee, Cameron C; Patel, Payal V; Hanna, Eban A; Vaz, Eduarda; Forjaz, André; Wan, Zeqi; Nair, Praful R; Lim, Yeongseo; Chen, Tina; Du, Wenxuan; Kim, Dongjoo; Nichakawade, Tushar D; Rebecca, Vito W; Bonifant, Challice L; Fan, Rong; Kiemen, Ashley L; Wu, Pei-Hsun; Wirtz, Denis | bioRxiv : the preprint server for biology | 38168186 | 2024 Mar 26 |
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| Lysolipids are prominent in subretinal drusenoid deposits, a high-risk phenotype in age-related macular degeneration. | Anderson, David M G; Kotnala, Ankita; Migas, Lukasz G; Patterson, Nathan Heath; Tideman, Léonore; Cao, Dongfeng; Adhikari, Bibek; Messinger, Jeffrey D; Ach, Thomas; Tortorella, Sara; Van de Plas, Raf; Curcio, Christine A; Schey, Kevin L | Frontiers in ophthalmology | 38186747 | 2023 |
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| Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes. | Hu, Yuxuan; Rong, Jiazhen; Xu, Yafei; Xie, Runzhi; Peng, Jacqueline; Gao, Lin; Tan, Kai | Nature methods | 38191930 | 2024 Jan 08 |
| IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. | Haslund-Gourley, Benjamin S; Woloszczuk, Kyra; Hou, Jintong; Connors, Jennifer; Cusimano, Gina; Bell, Mathew; Taramangalam, Bhavani; Fourati, Slim; Mege, Nathan; Bernui, Mariana; Altman, Matthew C; Krammer, Florian; van Bakel, Harm; IMPACC Network; Maecker, Holden T; Rouphael, Nadine; Diray-Arce, Joann; Wigdahl, Brian; Kutzler, Michele A; Cairns, Charles B; Haddad, Elias K; Comunale, Mary Ann | Nature communications | 38195739 | 2024 Jan 09 |
| Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients. | Langelier, Charles; Pickering, Harry; Schaenman, Joanna; Phan, Hoang; Maguire, Cole; Tsitsiklis, Alexandra; Rouphael, Nadine; Higuita, Nelson; Atkinson, Mark; Breckenridge, Scott; Fung, Monica; Messer, William; IMPACC Network; Salehi-Rad, Ramin; Altman, M | Research square | 38196658 | 2023 Dec 20 |
| The chromatin landscape of healthy and injured cell types in the human kidney. | Gisch, Debora L; Brennan, Michelle; Lake, Blue B; Basta, Jeannine; Keller, Mark S; Melo Ferreira, Ricardo; Akilesh, Shreeram; Ghag, Reetika; Lu, Charles; Cheng, Ying-Hua; Collins, Kimberly S; Parikh, Samir V; Rovin, Brad H; Robbins, Lynn; Stout, Lisa; Conklin, Kimberly Y; Diep, Dinh; Zhang, Bo; Knoten, Amanda; Barwinska, Daria; Asghari, Mahla; Sabo, Angela R; Ferkowicz, Michael J; Sutton, Timothy A; Kelly, Katherine J; De Boer, Ian H; Rosas, Sylvia E; Kiryluk, Krzysztof; Hodgin, Jeffrey B; Alakwaa, Fadhl; Winfree, Seth; Jefferson, Nichole; Türkmen, Aydın; Gaut, Joseph P; Gehlenborg, Nils; Phillips, Carrie L; El-Achkar, Tarek M; Dagher, Pierre C; Hato, Takashi; Zhang, Kun; Himmelfarb, Jonathan; Kretzler, Matthias; Mollah, Shamim; Kidney Precision Medicine Project (KPMP); Jain, Sanjay; Rauchman, Michael; Eadon, Michael T | Nature communications | 38199997 | 2024 Jan 10 |
| Toward a common standard for data and specimen provenance in life sciences. | Wittner, Rudolf; Holub, Petr; Mascia, Cecilia; Frexia, Francesca; Müller, Heimo; Plass, Markus; Allocca, Clare; Betsou, Fay; Burdett, Tony; Cancio, Ibon; Chapman, Adriane; Chapman, Martin; Courtot, Mélanie; Curcin, Vasa; Eder, Johann; Elliot, Mark; Exter, Katrina; Goble, Carole; Golebiewski, Martin; Kisler, Bron; Kremer, Andreas; Leo, Simone; Lin-Gibson, Sheng; Marsano, Anna; Mattavelli, Marco; Moore, Josh; Nakae, Hiroki; Perseil, Isabelle; Salman, Ayat; Sluka, James; Soiland-Reyes, Stian; Strambio-De-Castillia, Caterina; Sussman, Michael; Swedlow, Jason R; Zatloukal, Kurt; Geiger, Jörg | Learning health systems | 38249839 | 2024 Jan |
| Lymphatic Microsurgical Preventative Healing Approach for the Primary Prevention of Lymphedema: A 4-Year Follow-Up. | Friedman, Rosie; Johnson, Anna Rose; Brunelle, Cheryl L; Chang, David W; Coriddi, Michelle; Dayan, Joseph H; Mehrara, Babak J; Skoracki, Roman; Taghian, Alphonse G; Singhal, Dhruv | Plastic and reconstructive surgery | 38266142 | 2024 Feb 01 |
| Super-Resolution Stimulated Raman Scattering Microscopy with Graphical User Interface-Supported A-PoD. | Jang, Hongje; Li, Yajuan; Wu, Shuang; Shi, Lingyan | Current protocols | 38270527 | 2024 Jan |
| Gene panel selection for targeted spatial transcriptomics. | Zhang, Yida; Petukhov, Viktor; Biederstedt, Evan; Que, Richard; Zhang, Kun; Kharchenko, Peter V | Genome biology | 38273415 | 2024 Jan 25 |
| Expanding the coverage of spatial proteomics: a machine learning approach. | Sun, Huangqingbo; Li, Jiayi; Murphy, Robert F | Bioinformatics (Oxford, England) | 38310340 | 2024 Feb 01 |
| Convergence of coronary artery disease genes onto endothelial cell programs. | Schnitzler, Gavin R; Kang, Helen; Fang, Shi; Angom, Ramcharan S; Lee-Kim, Vivian S; Ma, X Rosa; Zhou, Ronghao; Zeng, Tony; Guo, Katherine; Taylor, Martin S; Vellarikkal, Shamsudheen K; Barry, Aurelie E; Sias-Garcia, Oscar; Bloemendal, Alex; Munson, Glen; Guckelberger, Philine; Nguyen, Tung H; Bergman, Drew T; Hinshaw, Stephen; Cheng, Nathan; Cleary, Brian; Aragam, Krishna; Lander, Eric S; Finucane, Hilary K; Mukhopadhyay, Debabrata; Gupta, Rajat M; Engreitz, Jesse M | Nature | 38326615 | 2024 Feb |
| Far-red chemigenetic biosensors for multi-dimensional and super-resolved kinase activity imaging. | Frei, Michelle S; Sanchez, Samantha A; Liu, Longwei; Schneider, Falk; Wang, Zichen; Hakozaki, Hiroyuki; Li, Yajuan; Lyons, Anne C; Rohm, Theresa V; Olefsky, Jerrold M; Shi, Lingyan; Schöneberg, Johannes; Fraser, Scott E; Mehta, Sohum; Wang, Yingxiao; Zhang, Jin | bioRxiv : the preprint server for biology | 38370804 | 2024 Feb 11 |
| Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. | Bai, Zhiliang; Zhang, Dingyao; Gao, Yan; Tao, Bo; Bao, Shuozhen; Enninful, Archibald; Zhang, Daiwei; Su, Graham; Tian, Xiaolong; Zhang, Ningning; Xiao, Yang; Liu, Yang; Gerstein, Mark; Li, Mingyao; Xing, Yi; Lu, Jun; Xu, Mina L; Fan, Rong | bioRxiv : the preprint server for biology | 38370833 | 2024 Feb 08 |
| vSPACE: Exploring Virtual Spatial Representation of Articular Chondrocytes at the Single-Cell Level. | Zhang, Chenyu; Wang, Honglin; Hong, Seung-Hyun; Olmer, Merissa; Swahn, Hannah; Lotz, Martin K; Maye, Peter; Rowe, David; Shin, Dong-Guk | bioRxiv : the preprint server for biology | 38370845 | 2024 Feb 10 |
| Multi-molecular hyperspectral PRM-SRS microscopy. | Zhang, Wenxu; Li, Yajuan; Fung, Anthony A; Li, Zhi; Jang, Hongje; Zha, Honghao; Chen, Xiaoping; Gao, Fangyuan; Wu, Jane Y; Sheng, Huaxin; Yao, Junjie; Skowronska-Krawczyk, Dorota; Jain, Sanjay; Shi, Lingyan | Nature communications | 38383552 | 2024 Feb 21 |
| Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology. | Van Phan, Hoang; Tsitsiklis, Alexandra; Maguire, Cole P; Haddad, Elias K; Becker, Patrice M; Kim-Schulze, Seunghee; Lee, Brian; Chen, Jing; Hoch, Annmarie; Pickering, Harry; Van Zalm, Patrick; Altman, Matthew C; Augustine, Alison D; Calfee, Carolyn S; Bosinger, Steve; Cairns, Charles; Eckalbar, Walter; Guan, Leying; Jayavelu, Naresh Doni; Kleinstein, Steven H; Krammer, Florian; Maecker, Holden T; Ozonoff, Al; Peters, Bjoern; Rouphael, Nadine; IMPACC Network; Montgomery, Ruth R; Reed, Elaine; Schaenman, Joanna; Steen, Hanno; Levy, Ofer; Diray-Arce, Joann; Langelier, Charles R | medRxiv : the preprint server for health sciences | 38405760 | 2024 Feb 13 |
| Spatial top-down proteomics for the functional characterization of human kidney. | Zemaitis, Kevin J; Fulcher, James M; Kumar, Rashmi; Degnan, David J; Lewis, Logan A; Liao, Yen-Chen; Veličković, Marija; Williams, Sarah M; Moore, Ronald J; Bramer, Lisa M; Veličković, Dušan; Zhu, Ying; Zhou, Mowei; Paša-Tolić, Ljiljana | bioRxiv : the preprint server for biology | 38405958 | 2024 Feb 13 |
| A Panoramic View of Cell Population Dynamics in Mammalian Aging. | Zhang, Zehao; Schaefer, Chloe; Jiang, Weirong; Lu, Ziyu; Lee, Jasper; Sziraki, Andras; Abdulraouf, Abdulraouf; Wick, Brittney; Haeussler, Maximilian; Li, Zhuoyan; Molla, Gesmira; Satija, Rahul; Zhou, Wei; Cao, Junyue | bioRxiv : the preprint server for biology | 38496474 | 2024 Mar 05 |
| Predicting drug outcome of population via clinical knowledge graph. | Brbić, Maria; Yasunaga, Michihiro; Agarwal, Prabhat; Leskovec, Jure | medRxiv : the preprint server for health sciences | 38496488 | 2024 Mar 08 |
| Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. | Kwon, Yumi; Woo, Jongmin; Yu, Fengchao; Williams, Sarah M; Markillie, Lye Meng; Moore, Ronald J; Nakayasu, Ernesto S; Chen, Jing; Campbell-Thompson, Martha; Mathews, Clayton E; Nesvizhskii, Alexey I; Qia, Wei-Jun; Zhu, Ying | bioRxiv : the preprint server for biology | 38496682 | 2024 Mar 04 |
| Mapping human tissues with highly multiplexed RNA in situ hybridization. | Kalhor, Kian; Chen, Chien-Ju; Lee, Ho Suk; Cai, Matthew; Nafisi, Mahsa; Que, Richard; Palmer, Carter R; Yuan, Yixu; Zhang, Yida; Li, Xuwen; Song, Jinghui; Knoten, Amanda; Lake, Blue B; Gaut, Joseph P; Keene, C Dirk; Lein, Ed; Kharchenko, Peter V; Chun, Jerold; Jain, Sanjay; Fan, Jian-Bing; Zhang, Kun | Nature communications | 38509069 | 2024 Mar 20 |
| 3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation. | Chen, Haoran; Murphy, Robert F | bioRxiv : the preprint server for biology | 38559093 | 2024 Mar 12 |
| Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging. | Bandyopadhyay, Shovik; Duffy, Michael; Ahn, Kyung Jin; Pang, Minxing; Smith, David; Duncan, Gwendolyn; Sussman, Jonathan; Zhang, Iris; Huang, Jeffrey; Lin, Yulieh; Xiong, Barbara; Imtiaz, Tamjid; Chen, Chia-Hui; Thadi, Anusha; Chen, Changya; Xu, Jason; Reichart, Melissa; Pillai, Vinodh; Snaith, Oraine; Oldridge, Derek; Bhattacharyya, Siddharth; Maillard, Ivan; Carroll, Martin; Nelson, Charles; Qin, Ling; Tan, Kai | bioRxiv : the preprint server for biology | 38559168 | 2024 Mar 16 |
| Blind Polarization Demultiplexing of Shaped QAM Signals Assisted by Temporal Correlations. | Bajaj, Vinod; Van de Plas, Raf; Wahls, Sander | Journal of lightwave technology : a joint IEEE/OSA publication | 38586243 | 2024 Jan 15 |
