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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
HuBMAP (111)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma. | Phillips, Darci; Matusiak, Magdalena; Gutierrez, Belén Rivero; Bhate, Salil S; Barlow, Graham L; Jiang, Sizun; Demeter, Janos; Smythe, Kimberly S; Pierce, Robert H; Fling, Steven P; Ramchurren, Nirasha; Cheever, Martin A; Goltsev, Yury; West, Robert B; Khodadoust, Michael S; Kim, Youn H; Schürch, Christian M; Nolan, Garry P | Nature communications | 2021 Nov 18 | 34795254 | |
| Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. | Shafin, Kishwar; Pesout, Trevor; Chang, Pi-Chuan; Nattestad, Maria; Kolesnikov, Alexey; Goel, Sidharth; Baid, Gunjan; Kolmogorov, Mikhail; Eizenga, Jordan M; Miga, Karen H; Carnevali, Paolo; Jain, Miten; Carroll, Andrew; Paten, Benedict | Nature methods | 2021 Nov | 34725481 | |
| Deep Learning Approach for Dynamic Sparse Sampling for High-Throughput Mass Spectrometry Imaging. | Helminiak, David; Hu, Hang; Laskin, Julia; Ye, Dong Hye | IS&T International Symposium on Electronic Imaging | 2021 | 34722959 | |
| Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. | Biancalani, Tommaso; Scalia, Gabriele; Buffoni, Lorenzo; Avasthi, Raghav; Lu, Ziqing; Sanger, Aman; Tokcan, Neriman; Vanderburg, Charles R; Segerstolpe, Åsa; Zhang, Meng; Avraham-Davidi, Inbal; Vickovic, Sanja; Nitzan, Mor; Ma, Sai; Subramanian, Ayshwarya; Lipinski, Michal; Buenrostro, Jason; Brown, Nik Bear; Fanelli, Duccio; Zhuang, Xiaowei; Macosko, Evan Z; Regev, Aviv | Nature methods | 2021 Nov | 34711971 | |
| 3D virtual reality vs. 2D desktop registration user interface comparison. | Bueckle, Andreas; Buehling, Kilian; Shih, Patrick C; Börner, Katy | PloS one | 2021 | 34705835 | |
| RAP-NET: COARSE-TO-FINE MULTI-ORGAN SEGMENTATION WITH SINGLE RANDOM ANATOMICAL PRIOR. | Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Abramson, Richard G; Huo, Yuankai; Landman, Bennett A | Proceedings. IEEE International Symposium on Biomedical Imaging | 2021 Apr | 34667487 | |
| Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2). | Plongthongkum, Nongluk; Diep, Dinh; Chen, Song; Lake, Blue B; Zhang, Kun | Nature protocols | 2021 11 | 34650278 | |
| A Pilot Study of Urine Proteomics in Covid-19-associated Acute Kidney Injury. | Ye, Yinyin; Swensen, Adam C; Wang, Yang; Kaushal, Madhurima; Salamon, Diane; Knoten, Amanda; Nicora, Carrie D; Marks, Laura; Gaut, Joseph P; Vijayan, Anitha; Orton, Daniel J; Mudd, Philip A; Parikh, Chirag R; Qian, Wei-Jun; O'Halloran, Jane A; Piehowski, Paul D; Jain, Sanjay | Kidney international reports | 2021 Oct 07 | 34642644 | |
| rPAC: Route based pathway analysis for cohorts of gene expression data sets. | Joshi, Pujan; Basso, Brent; Wang, Honglin; Hong, Seung-Hyun; Giardina, Charles; Shin, Dong-Guk | Methods (San Diego, Calif.) | 2021 Oct 07 | 34628030 | |
| In-depth triacylglycerol profiling using MS3 Q-Trap mass spectrometry. | Cabruja, Matias; Priotti, Josefina; Domizi, Pablo; Papsdorf, Katharina; Kroetz, Deanna L; Brunet, Anne; Contrepois, Kévin; Snyder, Michael P | Analytica chimica acta | 2021 Nov 01 | 34625255 | |
| Highly multiplexed immunofluorescence of the human kidney using co-detection by indexing. | Neumann, Elizabeth K; Patterson, Nathan Heath; Rivera, Emilio S; Allen, Jamie L; Brewer, Maya; deCaestecker, Mark P; Caprioli, Richard M; Fogo, Agnes B; Spraggins, Jeffrey M | Kidney international | 2021 Oct 05 | 34619231 | |
| Advances in spatial transcriptomic data analysis. | Dries, Ruben; Chen, Jiaji; Del Rossi, Natalie; Khan, Mohammed Muzamil; Sistig, Adriana; Yuan, Guo-Cheng | Genome research | 2021 Oct | 34599004 | |
| Renal Cortex, Medulla and Pelvicaliceal System Segmentation on Arterial Phase CT Images with Random Patch-based Networks. | Tang, Yucheng; Gao, Riqiang; Lee, Ho Hin; Xu, Zhoubing; Savoie, Brent V; Bao, Shunxing; Huo, Yuankai; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Spraggins, Jeffrey; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 2021 | 34531632 | |
| Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data. | Hickey, John W; Tan, Yuqi; Nolan, Garry P; Goltsev, Yury | Frontiers in immunology | 2021 | 34484237 | |
| α-Cyano-4-hydroxycinnamic Acid and Tri-Potassium Citrate Salt Pre-Coated Silicon Nanopost Array Provides Enhanced Lipid Detection for High Spatial Resolution MALDI Imaging Mass Spectrometry. | Dufresne, Martin; Fincher, Jarod A; Patterson, Nathan Heath; Schey, Kevin L; Norris, Jeremy L; Caprioli, Richard M; Spraggins, Jeffrey M | Analytical chemistry | 2021 09 14 | 34449196 | |
| Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study. | IMPACC Manuscript Writing Team; IMPACC Network Steering Committee | Science immunology | 2021 08 10 | 34376480 | |
| Construction of a Multi-Phase Contrast Computed Tomography Kidney Atlas. | Lee, Ho Hin; Tang, Yucheng; Xu, Kaiwen; Bao, Shunxing; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Heinrich, Mattias; Spraggins, Jeffrey M; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 2021 | 34354322 | |
| Community-wide hackathons to identify central themes in single-cell multi-omics. | Lê Cao, Kim-Anh; Abadi, Al J; Davis-Marcisak, Emily F; Hsu, Lauren; Arora, Arshi; Coullomb, Alexis; Deshpande, Atul; Feng, Yuzhou; Jeganathan, Pratheepa; Loth, Melanie; Meng, Chen; Mu, Wancen; Pancaldi, Vera; Sankaran, Kris; Righelli, Dario; Singh, Amrit; Sodicoff, Joshua S; Stein-O'Brien, Genevieve L; Subramanian, Ayshwarya; Welch, Joshua D; You, Yue; Argelaguet, Ricard; Carey, Vincent J; Dries, Ruben; Greene, Casey S; Holmes, Susan; Love, Michael I; Ritchie, Matthew E; Yuan, Guo-Cheng; Culhane, Aedin C; Fertig, Elana | Genome biology | 2021 08 05 | 34353350 | |
| Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. | Alseekh, Saleh; Aharoni, Asaph; Brotman, Yariv; Contrepois, Kévin; D'Auria, John; Ewald, Jan; C Ewald, Jennifer; Fraser, Paul D; Giavalisco, Patrick; Hall, Robert D; Heinemann, Matthias; Link, Hannes; Luo, Jie; Neumann, Steffen; Nielsen, Jens; Perez de Souza, Leonardo; Saito, Kazuki; Sauer, Uwe; Schroeder, Frank C; Schuster, Stefan; Siuzdak, Gary; Skirycz, Aleksandra; Sumner, Lloyd W; Snyder, Michael P; Tang, Huiru; Tohge, Takayuki; Wang, Yulan; Wen, Weiwei; Wu, Si; Xu, Guowang; Zamboni, Nicola; Fernie, Alisdair R | Nature methods | 2021 07 | 34239102 | |
| CODEX multiplexed tissue imaging with DNA-conjugated antibodies. | Black, Sarah; Phillips, Darci; Hickey, John W; Kennedy-Darling, Julia; Venkataraaman, Vishal G; Samusik, Nikolay; Goltsev, Yury; Schürch, Christian M; Nolan, Garry P | Nature protocols | 2021 08 | 34215862 | |
| Embryo-scale, single-cell spatial transcriptomics. | Srivatsan, Sanjay R; Regier, Mary C; Barkan, Eliza; Franks, Jennifer M; Packer, Jonathan S; Grosjean, Parker; Duran, Madeleine; Saxton, Sarah; Ladd, Jon J; Spielmann, Malte; Lois, Carlos; Lampe, Paul D; Shendure, Jay; Stevens, Kelly R; Trapnell, Cole | Science (New York, N.Y.) | 2021 07 02 | 34210887 | |
| The emerging landscape of single-molecule protein sequencing technologies. | Alfaro, Javier Antonio; Bohländer, Peggy; Dai, Mingjie; Filius, Mike; Howard, Cecil J; van Kooten, Xander F; Ohayon, Shilo; Pomorski, Adam; Schmid, Sonja; Aksimentiev, Aleksei; Anslyn, Eric V; Bedran, Georges; Cao, Chan; Chinappi, Mauro; Coyaud, Etienne; Dekker, Cees; Dittmar, Gunnar; Drachman, Nicholas; Eelkema, Rienk; Goodlett, David; Hentz, Sébastien; Kalathiya, Umesh; Kelleher, Neil L; Kelly, Ryan T; Kelman, Zvi; Kim, Sung Hyun; Kuster, Bernhard; Rodriguez-Larrea, David; Lindsay, Stuart; Maglia, Giovanni; Marcotte, Edward M; Marino, John P; Masselon, Christophe; Mayer, Michael; Samaras, Patroklos; Sarthak, Kumar; Sepiashvili, Lusia; Stein, Derek; Wanunu, Meni; Wilhelm, Mathias; Yin, Peng; Meller, Amit; Joo, Chirlmin | Nature methods | 2021 Jun | 34099939 | |
| Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging. | Phillips, Darci; Schürch, Christian M; Khodadoust, Michael S; Kim, Youn H; Nolan, Garry P; Jiang, Sizun | Frontiers in immunology | 2021 | 34093591 | |
| Integrated analysis of multimodal single-cell data. | Hao, Yuhan; Hao, Stephanie; Andersen-Nissen, Erica; Mauck 3rd, William M; Zheng, Shiwei; Butler, Andrew; Lee, Maddie J; Wilk, Aaron J; Darby, Charlotte; Zager, Michael; Hoffman, Paul; Stoeckius, Marlon; Papalexi, Efthymia; Mimitou, Eleni P; Jain, Jaison; Srivastava, Avi; Stuart, Tim; Fleming, Lamar M; Yeung, Bertrand; Rogers, Angela J; McElrath, Juliana M; Blish, Catherine A; Gottardo, Raphael; Smibert, Peter; Satija, Rahul | Cell | 2021 06 24 | 34062119 | |
| New Interface for Faster Proteoform Analysis: Immunoprecipitation Coupled with SampleStream-Mass Spectrometry. | Santos Seckler, Henrique Dos; Park, Hae-Min; Lloyd-Jones, Cameron M; Melani, Rafael D; Camarillo, Jeannie M; Wilkins, John T; Compton, Philip D; Kelleher, Neil L | Journal of the American Society for Mass Spectrometry | 2021 Jul 07 | 34043341 | |
| Multiomics Imaging Using High-Energy Water Gas Cluster Ion Beam Secondary Ion Mass Spectrometry [(H2O)n-GCIB-SIMS] of Frozen-Hydrated Cells and Tissue. | Tian, Hua; Sheraz Née Rabbani, Sadia; Vickerman, John C; Winograd, Nicholas | Analytical chemistry | 2021 06 08 | 34038090 | |
| Pancreas Optical Clearing and 3-D Microscopy in Health and Diabetes. | Campbell-Thompson, Martha; Tang, Shiue-Cheng | Frontiers in endocrinology | 2021 | 33981285 | |
| SpatialDWLS: accurate deconvolution of spatial transcriptomic data. | Dong, Rui; Yuan, Guo-Cheng | Genome biology | 2021 05 10 | 33971932 | |
| Deep learning of gene relationships from single cell time-course expression data. | Yuan, Ye; Bar-Joseph, Ziv | Briefings in bioinformatics | 2021 09 02 | 33876191 | |
| CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data. | Hu, Yuxuan; Peng, Tao; Gao, Lin; Tan, Kai | Science advances | 2021 Apr | 33853780 | |
| Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. | Gerbasi, Vincent R; Melani, Rafael D; Abbatiello, Susan E; Belford, Michael W; Huguet, Romain; McGee, John P; Dayhoff, Dawson; Thomas, Paul M; Kelleher, Neil L | Analytical chemistry | 2021 04 27 | 33844503 | |
| Islet sympathetic innervation and islet neuropathology in patients with type 1 diabetes. | Campbell-Thompson, Martha; Butterworth, Elizabeth A; Boatwright, J Lucas; Nair, Malavika A; Nasif, Lith H; Nasif, Kamal; Revell, Andy Y; Riva, Alberto; Mathews, Clayton E; Gerling, Ivan C; Schatz, Desmond A; Atkinson, Mark A | Scientific reports | 2021 Mar 22 | 33753784 | |
| Giotto: a toolbox for integrative analysis and visualization of spatial expression data. | Dries, Ruben; Zhu, Qian; Dong, Rui; Eng, Chee-Huat Linus; Li, Huipeng; Liu, Kan; Fu, Yuntian; Zhao, Tianxiao; Sarkar, Arpan; Bao, Feng; George, Rani E; Pierson, Nico; Cai, Long; Yuan, Guo-Cheng | Genome biology | 2021 Mar 08 | 33685491 | |
| Advances in Proximity Ligation in situ Hybridization (PLISH). | Nagendran, Monica; Andruska, Adam M; Harbury, Pehr B; Desai, Tushar J | Bio-protocol | 2020 Nov 05 | 33659462 | |
| Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics. | Tsai, Chia-Feng; Zhang, Pengfei; Scholten, David; Martin, Kendall; Wang, Yi-Ting; Zhao, Rui; Chrisler, William B; Patel, Dhwani B; Dou, Maowei; Jia, Yuzhi; Reduzzi, Carolina; Liu, Xia; Moore, Ronald J; Burnum-Johnson, Kristin E; Lin, Miao-Hsia; Hsu, Chuan-Chih; Jacobs, Jon M; Kagan, Jacob; Srivastava, Sudhir; Rodland, Karin D; Steven Wiley, H; Qian, Wei-Jun; Smith, Richard D; Zhu, Ying; Cristofanilli, Massimo; Liu, Tao; Liu, Huiping; Shi, Tujin | Communications biology | 2021 Mar 01 | 33649493 | |
| Spatial Segmentation of Mass Spectrometry Imaging Data by Combining Multivariate Clustering and Univariate Thresholding. | Hu, Hang; Yin, Ruichuan; Brown, Hilary M; Laskin, Julia | Analytical chemistry | 2021 02 23 | 33570915 | |
| Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. | Kennedy-Darling, Julia; Bhate, Salil S; Hickey, John W; Black, Sarah; Barlow, Graham L; Vazquez, Gustavo; Venkataraaman, Vishal G; Samusik, Nikolay; Goltsev, Yury; Schürch, Christian M; Nolan, Garry P | European journal of immunology | 2021 May | 33548142 | |
| Integrated spatial genomics reveals global architecture of single nuclei. | Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, Shengbao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, Long | Nature | 2021 02 | 33505024 | |
| 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 | 2021 05 | 33470876 | |
| Quantitative Mass Spectrometry Imaging of Biological Systems. | Unsihuay, Daisy; Mesa Sanchez, Daniela; Laskin, Julia | Annual review of physical chemistry | 2021 Apr 20 | 33441032 | |
| RIPK3-mediated inflammation is a conserved β cell response to ER stress. | Yang, Bingyuan; Maddison, Lisette A; Zaborska, Karolina E; Dai, Chunhua; Yin, Linlin; Tang, Zihan; Zang, Liqing; Jacobson, David A; Powers, Alvin C; Chen, Wenbiao | Science advances | 2020 Dec | 33355143 | |
| Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. | McMillen, Josiah C; Fincher, Jarod A; Klein, Dustin R; Spraggins, Jeffrey M; Caprioli, Richard M | Journal of mass spectrometry : JMS. | 2020 Dec; | 33241625 | |
| Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. | Salahudeen, Ameen A; Choi, Shannon S; Rustagi, Arjun; Zhu, Junjie; van Unen, Vincent; de la O, Sean M; Flynn, Ryan A; Margalef-Català, Mar; Santos, António J M; Ju, Jihang; Batish, Arpit; Usui, Tatsuya; Zheng, Grace X Y; Edwards, Caitlin E; Wagar, Lisa E; Luca, Vincent; Anchang, Benedict; Nagendran, Monica; Nguyen, Khanh; Hart, Daniel J; Terry, Jessica M; Belgrader, Phillip; Ziraldo, Solongo B; Mikkelsen, Tarjei S; Harbury, Pehr B; Glenn, Jeffrey S; Garcia, K Christopher; Davis, Mark M; Baric, Ralph S; Sabatti, Chiara; Amieva, Manuel R; Blish, Catherine A; Desai, Tushar J; Kuo, Calvin J | Nature | 2020 12 | 33238290 | |
| Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells. | Martin, Kendall; Zhang, Tong; Zhang, Pengfei; Chrisler, William B; Thomas, Fillmore L; Liu, Fen; Liu, Tao; Qian, Wei-Jun; Smith, Richard D; Shi, Tujin | Journal of visualized experiments : JoVE. | 2020 11 06; | 33226031 | |
| Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. | Uzun, Yasin; Wu, Hao; Tan, Kai | Genome research | 2021 Jan | 33219054 | |
| High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. | Liu, Yang; Yang, Mingyu; Deng, Yanxiang; Su, Graham; Enninful, Archibald; Guo, Cindy C; Tebaldi, Toma; Zhang, Di; Kim, Dongjoo; Bai, Zhiliang; Norris, Eileen; Pan, Alisia; Li, Jiatong; Xiao, Yang; Halene, Stephanie; Fan, Rong | Cell. | 2020 Dec 10; | 33188776 | |
| Guidelines for reporting single-cell RNA-seq experiments. | Füllgrabe, Anja; George, Nancy; Green, Matthew; Nejad, Parisa; Aronow, Bruce; Fexova, Silvie Korena; Fischer, Clay; Freeberg, Mallory Ann; Huerta, Laura; Morrison, Norman; Scheuermann, Richard H; Taylor, Deanne; Vasilevsky, Nicole; Clarke, Laura; Gehlenborg, Nils; Kent, Jim; Marioni, John; Teichmann, Sarah; Brazma, Alvis; Papatheodorou, Irene | Nature biotechnology | 2020 12 | 33188371 | |
| Iterative point set registration for aligning scRNA-seq data. | Alavi, Amir; Bar-Joseph, Ziv | PLoS computational biology | 2020 10 | 33108369 | |
| CDKL5: a promising new therapeutic target for acute kidney injury? | de Caestecker, Mark P | American journal of physiology. Renal physiology. | 2020 Oct 19; | 33073588 | |
| Landscape of coordinated immune responses to H1N1 challenge in humans. | Rahil, Zainab; Leylek, Rebecca; Schürch, Christian M; Chen, Han; Bjornson-Hooper, Zach; Christensen, Shannon R; Gherardini, Pier Federico; Bhate, Salil S; Spitzer, Matthew H; Fragiadakis, Gabriela K; Mukherjee, Nilanjan; Kim, Nelson; Jiang, Sizun; Yo, Jennifer; Gaudilliere, Brice; Affrime, Melton; Bock, Bonnie; Hensley, Scott E; Idoyaga, Juliana; Aghaeepour, Nima; Kim, Kenneth; Nolan, Garry P; McIlwain, David R | The Journal of clinical investigation. | 2020 Nov 02; | 33044226 | |
| 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 | 2021 02 | 33026994 | |
| Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. | Rivera, Emilio S; Djambazova, Katerina V; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of mass spectrometry : JMS. | 2020 Jul 04; | 32955134 | |
| Changes to Zonular Tension Alters the Subcellular Distribution of AQP5 in Regions of Influx and Efflux of Water in the Rat Lens. | Petrova, Rosica S; Bavana, Nandini; Zhao, Rusin; Schey, Kevin L; Donaldson, Paul J | Investigative ophthalmology & visual science | 2020 09 01 | 32945844 | |
| Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. | Zhou, Xin X; Bracken, Colton J; Zhang, Kaihua; Zhou, Jie; Mou, Yun; Wang, Lei; Cheng, Yifan; Leung, Kevin K; Wells, James A | Journal of the American Chemical Society | 2020 10 14 | 32924468 | |
| The impact of air transport availability on research collaboration: A case study of four universities. | Ploszaj, Adam; Yan, Xiaoran; Börner, Katy | PloS one | 2020 | 32886681 | |
| Identifying signaling genes in spatial single-cell expression data. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 2021 05 17 | 32886099 | |
| Single-cell metabolic profiling of human cytotoxic T cells. | Hartmann, Felix J; Mrdjen, Dunja; McCaffrey, Erin; Glass, David R; Greenwald, Noah F; Bharadwaj, Anusha; Khair, Zumana; Verberk, Sanne G S; Baranski, Alex; Baskar, Reema; Graf, William; Van Valen, David; Van den Bossche, Jan; Angelo, Michael; Bendall, Sean C | Nature biotechnology. | 2020 Aug 31; | 32868913 | |
| Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. | Schürch, Christian M; Bhate, Salil S; Barlow, Graham L; Phillips, Darci J; Noti, Luca; Zlobec, Inti; Chu, Pauline; Black, Sarah; Demeter, Janos; McIlwain, David R; Kinoshita, Shigemi; Samusik, Nikolay; Goltsev, Yury; Nolan, Garry P | Cell. | 2020 Sep 03; | 32763154 | |
| An Integrated Microfluidic Probe for Mass Spectrometry Imaging of Biological Samples*. | Li, Xiangtang; Yin, Ruichuan; Hu, Hang; Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Angewandte Chemie (International ed. in English) | 2020 12 07 | 32743957 | |
| Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures. | Salahudeen, Ameen A; Choi, Shannon S; Rustagi, Arjun; Zhu, Junjie; de la O, Sean M; Flynn, Ryan A; Margalef-Català, Mar; Santos, António J M; Ju, Jihang; Batish, Arpit; van Unen, Vincent; Usui, Tatsuya; Zheng, Grace X Y; Edwards, Caitlin E; Wagar, Lisa E; Luca, Vincent; Anchang, Benedict; Nagendran, Monica; Nguyen, Khanh; Hart, Daniel J; Terry, Jessica M; Belgrader, Phillip; Ziraldo, Solongo B; Mikkelsen, Tarjei S; Harbury, Pehr B; Glenn, Jeffrey S; Garcia, K Christopher; Davis, Mark M; Baric, Ralph S; Sabatti, Chiara; Amieva, Manuel R; Blish, Catherine A; Desai, Tushar J; Kuo, Calvin J | bioRxiv : the preprint server for biology | 2020 Jul 27 | 32743583 | |
| Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. | Shafin, Kishwar; Pesout, Trevor; Lorig-Roach, Ryan; Haukness, Marina; Olsen, Hugh E; Bosworth, Colleen; Armstrong, Joel; Tigyi, Kristof; Maurer, Nicholas; Koren, Sergey; Sedlazeck, Fritz J; Marschall, Tobias; Mayes, Simon; Costa, Vania; Zook, Justin M; Liu, Kelvin J; Kilburn, Duncan; Sorensen, Melanie; Munson, Katy M; Vollger, Mitchell R; Monlong, Jean; Garrison, Erik; Eichler, Evan E; Salama, Sofie; Haussler, David; Green, Richard E; Akeson, Mark; Phillippy, Adam; Miga, Karen H; Carnevali, Paolo; Jain, Miten; Paten, Benedict | Nature biotechnology. | 2020 09; | 32686750 | |
| Localization of the lens intermediate filament switch by imaging mass spectrometry. | Wang, Zhen; Ryan, Daniel J; Schey, Kevin L | Experimental eye research | 2020 09 | 32682822 | |
| An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. | Glass, David R; Tsai, Albert G; Oliveria, John Paul; Hartmann, Felix J; Kimmey, Samuel C; Calderon, Ariel A; Borges, Luciene; Glass, Marla C; Wagar, Lisa E; Davis, Mark M; Bendall, Sean C | Immunity. | 2020 Jul 14; | 32668225 | |
| Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High-Resolution Imaging Mass Spectrometry. | Anderson, David M G; Messinger, Jeffrey D; Patterson, Nathan H; Rivera, Emilio S; Kotnala, Ankita; Spraggins, Jeffrey M; Caprioli, Richard M; Curcio, Christine A; Schey, Kevin L | Journal of the American Society for Mass Spectrometry | 2020 Dec 02 | 32628476 | |
| A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. | Keyes, Timothy J; Domizi, Pablo; Lo, Yu-Chen; Nolan, Garry P; Davis, Kara L | Cytometry. Part A : the journal of the International Society for Analytical Cytology. | 2020 08; | 32602650 | |
| Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. | Ji, Andrew L; Rubin, Adam J; Thrane, Kim; Jiang, Sizun; Reynolds, David L; Meyers, Robin M; Guo, Margaret G; George, Benson M; Mollbrink, Annelie; Bergenstråhle, Joseph; Larsson, Ludvig; Bai, Yunhao; Zhu, Bokai; Bhaduri, Aparna; Meyers, Jordan M; Rovira-Clavé, Xavier; Hollmig, S Tyler; Aasi, Sumaira Z; Nolan, Garry P; Lundeberg, Joakim; Khavari, Paul A | Cell. | 2020 Jul 23; | 32579974 | |
| The Importance of Clinical Tissue Imaging. | Spraggins, Jeffrey M; Schwamborn, Kristina; Heeren, Ron M A; Eberlin, Livia S | Clinical mass spectrometry (Del Mar, Calif.). | 2019 Apr; | 32483555 | |
| Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. | Islam, Mirazul; Chen, Bob; Spraggins, Jeffrey M; Kelly, Ryan T; Lau, Ken S | Gastroenterology. | 2020 Aug; | 32417404 | |
| Discovering New Lipidomic Features Using Cell Type Specific Fluorophore Expression to Provide Spatial and Biological Specificity in a Multimodal Workflow with MALDI Imaging Mass Spectrometry. | Jones, Marissa A; Cho, Sung Hoon; Patterson, Nathan Heath; Van de Plas, Raf; Spraggins, Jeffrey M; Boothby, Mark R; Caprioli, Richard M | Analytical chemistry. | 2020 05 19; | 32298091 | |
| Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu, Yan; Zhang, Kun | Nature reviews. Nephrology. | 2020 07; | 32221477 | |
| Multiplexed single-cell morphometry for hematopathology diagnostics. | Tsai, Albert G; Glass, David R; Juntilla, Marisa; Hartmann, Felix J; Oak, Jean S; Fernandez-Pol, Sebastian; Ohgami, Robert S; Bendall, Sean C | Nature medicine. | 2020 03; | 32161403 | |
| RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. | Wei, Christopher Jen-Yue; Zhang, Kun | Genome research. | 2020 Apr; | 32127417 | |
| Integrated molecular imaging technologies for investigation of metals in biological systems: A brief review. | Perry, William J; Weiss, Andy; Van de Plas, Raf; Spraggins, Jeffrey M; Caprioli, Richard M; Skaar, Eric P | Current opinion in chemical biology. | 2020 Apr; | 32087551 | |
| Inferring TF activation order in time series scRNA-Seq studies. | Lin, Chieh; Ding, Jun; Bar-Joseph, Ziv | PLoS computational biology | 2020 02 | 32069291 | |
| 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 | 2020 04 02 | 32004478 | |
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