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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 (149)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web. | Manz, Trevor; Gold, Ilan; Patterson, Nathan Heath; McCallum, Chuck; Keller, Mark S; Herr 2nd, Bruce W; Börner, Katy; Spraggins, Jeffrey M; Gehlenborg, Nils | Nature methods | 2022 May | 35545714 | |
| 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 | 2022 Mar 28 | 35463156 | |
| 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 | 2022 04 19 | 35443184 | |
| 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 | 2022 Mar 09 | 35434692 | |
| Interactive single-cell data analysis using Cellar. | Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, Ziv | Nature communications | 2022 04 14 | 35422041 | |
| 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 | 2022 05 06 | 35413190 | |
| 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 | 2022 Apr 06 | 35384842 | |
| 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.) | 2022 04 | 35357935 | |
| 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.) | 2022 04 | 35357911 | |
| 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 | 2022 Apr 01 | 35290070 | |
| 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 | 2022 03 | 35277708 | |
| 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 | 2022 Mar 07 | 35255944 | |
| 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 | 2022 Feb 21 | 35247306 | |
| Machine Learning Classifies Ferroptosis and Apoptosis Cell Death Modalities with TfR1 Immunostaining. | Jin, Jenny; Schorpp, Kenji; Samaga, Daniel; Unger, Kristian; Hadian, Kamyar; Stockwell, Brent R | ACS chemical biology | 2022 Mar 18 | 35230809 | |
| Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. | Kruse, Angela R S; Spraggins, Jeffrey M | Frontiers in physiology | 2022 | 35222094 | |
| Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? | Plubell, Deanna L; Käll, Lukas; Webb-Robertson, Bobbie-Jo; Bramer, Lisa M; Ives, Ashley; Kelleher, Neil L; Smith, Lloyd M; Montine, Thomas J; Wu, Christine C; MacCoss, Michael J | Journal of proteome research | 2022 Apr 01 | 35220718 | |
| Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts. | Baskar, Reema; Kimmey, Sam C; Bendall, Sean C | Trends in cell biology | 2022 Feb 16 | 35181197 | |
| Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. | Deng, Yanxiang; Bartosovic, Marek; Kukanja, Petra; Zhang, Di; Liu, Yang; Su, Graham; Enninful, Archibald; Bai, Zhiliang; Castelo-Branco, Gonçalo; Fan, Rong | Science (New York, N.Y.) | 2022 02 11 | 35143307 | |
| The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells. | Melani, Rafael D; Gerbasi, Vincent R; Anderson, Lissa C; Sikora, Jacek W; Toby, Timothy K; Hutton, Josiah E; Butcher, David S; Negrão, Fernanda; Seckler, Henrique S; Srzentić, Kristina; Fornelli, Luca; Camarillo, Jeannie M; LeDuc, Richard D; Cesnik, Anthony J; Lundberg, Emma; Greer, Joseph B; Fellers, Ryan T; Robey, Matthew T; DeHart, Caroline J; Forte, Eleonora; Hendrickson, Christopher L; Abbatiello, Susan E; Thomas, Paul M; Kokaji, Andy I; Levitsky, Josh; Kelleher, Neil L | Science (New York, N.Y.) | 2022 01 28 | 35084980 | |
| Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. | Risom, Tyler; Glass, David R; Averbukh, Inna; Liu, Candace C; Baranski, Alex; Kagel, Adam; McCaffrey, Erin F; Greenwald, Noah F; Rivero-Gutiérrez, Belén; Strand, Siri H; Varma, Sushama; Kong, Alex; Keren, Leeat; Srivastava, Sucheta; Zhu, Chunfang; Khair, Zumana; Veis, Deborah J; Deschryver, Katherine; Vennam, Sujay; Maley, Carlo; Hwang, E Shelley; Marks, Jeffrey R; Bendall, Sean C; Colditz, Graham A; West, Robert B; Angelo, Michael | Cell | 2022 01 20 | 35063072 | |
| Comparison and evaluation of statistical error models for scRNA-seq. | Choudhary, Saket; Satija, Rahul | Genome biology | 2022 01 18 | 35042561 | |
| Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. | Sirén, Jouni; Monlong, Jean; Chang, Xian; Novak, Adam M; Eizenga, Jordan M; Markello, Charles; Sibbesen, Jonas A; Hickey, Glenn; Chang, Pi-Chuan; Carroll, Andrew; Gupta, Namrata; Gabriel, Stacey; Blackwell, Thomas W; Ratan, Aakrosh; Taylor, Kent D; Rich, Stephen S; Rotter, Jerome I; Haussler, David; Garrison, Erik; Paten, Benedict | Science (New York, N.Y.) | 2021 12 17 | 34914532 | |
| Multicellular modules as clinical diagnostic and therapeutic targets. | Baertsch, Marc-A; Nolan, Garry P; Hickey, John W | Trends in cancer | 2022 Mar | 34872889 | |
| geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq. | Missarova, Alsu; Jain, Jaison; Butler, Andrew; Ghazanfar, Shila; Stuart, Tim; Brusko, Maigan; Wasserfall, Clive; Nick, Harry; Brusko, Todd; Atkinson, Mark; Satija, Rahul; Marioni, John C | Genome biology | 2021 12 06 | 34872616 | |
| Cross-Laboratory Standardization of Preclinical Lipidomics Using Differential Mobility Spectrometry and Multiple Reaction Monitoring. | Ghorasaini, Mohan; Mohammed, Yassene; Adamski, Jerzy; Bettcher, Lisa; Bowden, John A; Cabruja, Matias; Contrepois, Kévin; Ellenberger, Mathew; Gajera, Bharat; Haid, Mark; Hornburg, Daniel; Hunter, Christie; Jones, Christina M; Klein, Theo; Mayboroda, Oleg; Mirzaian, Mina; Moaddel, Ruin; Ferrucci, Luigi; Lovett, Jacqueline; Nazir, Kenneth; Pearson, Mackenzie; Ubhi, Baljit K; Raftery, Daniel; Riols, Fabien; Sayers, Rebekah; Sijbrands, Eric J G; Snyder, Michael P; Su, Baolong; Velagapudi, Vidya; Williams, Kevin J; de Rijke, Yolanda B; Giera, Martin | Analytical chemistry | 2021 12 14 | 34859676 | |
| Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. | Hickey, John W; Neumann, Elizabeth K; Radtke, Andrea J; Camarillo, Jeannie M; Beuschel, Rebecca T; Albanese, Alexandre; McDonough, Elizabeth; Hatler, Julia; Wiblin, Anne E; Fisher, Jeremy; Croteau, Josh; Small, Eliza C; Sood, Anup; Caprioli, Richard M; Angelo, R Michael; Nolan, Garry P; Chung, Kwanghun; Hewitt, Stephen M; Germain, Ronald N; Spraggins, Jeffrey M; Lundberg, Emma; Snyder, Michael P; Kelleher, Neil L; Saka, Sinem K | Nature methods | 2022 03 | 34811556 | |
| Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. | Greenwald, Noah F; Miller, Geneva; Moen, Erick; Kong, Alex; Kagel, Adam; Dougherty, Thomas; Fullaway, Christine Camacho; McIntosh, Brianna J; Leow, Ke Xuan; Schwartz, Morgan Sarah; Pavelchek, Cole; Cui, Sunny; Camplisson, Isabella; Bar-Tal, Omer; Singh, Jaiveer; Fong, Mara; Chaudhry, Gautam; Abraham, Zion; Moseley, Jackson; Warshawsky, Shiri; Soon, Erin; Greenbaum, Shirley; Risom, Tyler; Hollmann, Travis; Bendall, Sean C; Keren, Leeat; Graf, William; Angelo, Michael; Van Valen, David | Nature biotechnology | 2021 Nov 18 | 34795433 | |
| 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 | |
| Magnetic resonance linear accelerator technology and adaptive radiation therapy: An overview for clinicians. | Hall, William A; Paulson, Eric; Li, X Allen; Erickson, Beth; Schultz, Christopher; Tree, Alison; Awan, Musaddiq; Low, Daniel A; McDonald, Brigid A; Salzillo, Travis; Glide-Hurst, Carri K; Kishan, Amar U; Fuller, Clifton D | CA: a cancer journal for clinicians | 2022 01 | 34792808 | |
| Anatomical structures, cell types and biomarkers of the Human Reference Atlas. | Börner, Katy; Teichmann, Sarah A; Quardokus, Ellen M; Gee, James C; Browne, Kristen; Osumi-Sutherland, David; Herr 2nd, Bruce W; Bueckle, Andreas; Paul, Hrishikesh; Haniffa, Muzlifah; Jardine, Laura; Bernard, Amy; Ding, Song-Lin; Miller, Jeremy A; Lin, Shin; Halushka, Marc K; Boppana, Avinash; Longacre, Teri A; Hickey, John; Lin, Yiing; Valerius, M Todd; He, Yongqun; Pryhuber, Gloria; Sun, Xin; Jorgensen, Marda; Radtke, Andrea J; Wasserfall, Clive; Ginty, Fiona; Ho, Jonhan; Sunshine, Joel; Beuschel, Rebecca T; Brusko, Maigan; Lee, Sujin; Malhotra, Rajeev; Jain, Sanjay; Weber, Griffin | Nature cell biology | 2021 11 | 34750582 | |
| Cell type ontologies of the Human Cell Atlas. | Osumi-Sutherland, David; Xu, Chuan; Keays, Maria; Levine, Adam P; Kharchenko, Peter V; Regev, Aviv; Lein, Ed; Teichmann, Sarah A | Nature cell biology | 2021 11 | 34750578 | |
| Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations. | Stachtea, Xanthi; Loughrey, Maurice B; Salvucci, Manuela; Lindner, Andreas U; Cho, Sanghee; McDonough, Elizabeth; Sood, Anup; Graf, John; Santamaria-Pang, Alberto; Corwin, Alex; Laurent-Puig, Pierre; Dasgupta, Sonali; Shia, Jinru; Owens, Jonathan R; Abate, Samantha; Van Schaeybroeck, Sandra; Lawler, Mark; Prehn, Jochen H M; Ginty, Fiona; Longley, Daniel B | Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc | 2021 Nov 03 | 34732839 | |
| 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 | |
| Single-cell chromatin state analysis with Signac. | Stuart, Tim; Srivastava, Avi; Madad, Shaista; Lareau, Caleb A; Satija, Rahul | Nature methods | 2021 Nov | 34725479 | |
| 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 | |
| Editorial: Footprints of Immune Cells in the Type 1 Diabetic Pancreas. | Brusko, Todd M; Mallone, Roberto; Rodriguez-Calvo, Teresa | Frontiers in endocrinology | 2021 | 34721308 | |
| Mass spectrometry-based targeted proteomics for analysis of protein mutations. | Lin, Tai-Tu; Zhang, Tong; Kitata, Reta B; Liu, Tao; Smith, Richard D; Qian, Wei-Jun; Shi, Tujin | Mass spectrometry reviews | 2021 Oct 31 | 34719806 | |
| 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 | |
| Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. | Lohoff, T; Ghazanfar, S; Missarova, A; Koulena, N; Pierson, N; Griffiths, J A; Bardot, E S; Eng, C-H L; Tyser, R C V; Argelaguet, R; Guibentif, C; Srinivas, S; Briscoe, J; Simons, B D; Hadjantonakis, A-K; Göttgens, B; Reik, W; Nichols, J; Cai, L; Marioni, J C | Nature biotechnology | 2022 Jan | 34489600 | |
| 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 | |
| Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells. | Martin, Kendall; Zhang, Tong; Lin, Tai-Tu; Habowski, Amber N; Zhao, Rui; Tsai, Chia-Feng; Chrisler, William B; Sontag, Ryan L; Orton, Daniel J; Lu, Yong-Jie; Rodland, Karin D; Yang, Bin; Liu, Tao; Smith, Richard D; Qian, Wei-Jun; Waterman, Marian L; Wiley, H Steven; Shi, Tujin | Journal of proteome research | 2021 09 03 | 34351778 | |
| 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 | |
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