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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 (203)
Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
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Tissue registration and exploration user interfaces in support of a human reference atlas. | Börner, Katy; Bueckle, Andreas; Herr 2nd, Bruce W; Cross, Leonard E; Quardokus, Ellen M; Record, Elizabeth G; Ju, Yingnan; Silverstein, Jonathan C; Browne, Kristen M; Jain, Sanjay; Wasserfall, Clive H; Jorgensen, Marda L; Spraggins, Jeffrey M; Patterson, N Heath; Weber, Griffin M | Communications biology | 2022 Dec 13 | 1369 | 36513738 |
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 | 2022 Nov 18 | 36399478 | |
Single-cell spatial proteomic imaging for human neuropathology. | Vijayaragavan, Kausalia; Cannon, Bryan J; Tebaykin, Dmitry; Bossé, Marc; Baranski, Alex; Oliveria, J P; Bukhari, Syed A; Mrdjen, Dunja; Corces, M Ryan; McCaffrey, Erin F; Greenwald, Noah F; Sigal, Yari; Marquez, Diana; Khair, Zumana; Bruce, Trevor; Goldston, Mako; Bharadwaj, Anusha; Montine, Kathleen S; Angelo, R Michael; Montine, Thomas J; Bendall, Sean C | Acta neuropathologica communications | 2022 Nov 04 | 36333818 | |
Supervised Deep Generation of High-Resolution Arterial Phase Computed Tomography Kidney Substructure Atlas. | Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Yang, Qi; Xu, Xin; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Spraggins, Jeffrey M; Heinrich, Mattias; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 2022 Feb-Mar | 36303577 | |
Annotation of spatially resolved single-cell data with STELLAR. | Brbić, Maria; Cao, Kaidi; Hickey, John W; Tan, Yuqi; Snyder, Michael P; Nolan, Garry P; Leskovec, Jure | Nature methods | 2022 Nov | 36280720 | |
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 | 2022 Nov | 36216958 | |
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 | 2022 Sep 30 | 36206763 | |
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 | 2022 Nov 04 | 36201825 | |
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 | 2022 Oct 04 | 36193887 | |
GBZ file format for pangenome graphs. | Sirén, Jouni; Paten, Benedict | Bioinformatics (Oxford, England) | 2022 Nov 15 | 36179091 | |
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 | 2022 Sep 26 | 36155452 | |
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 | 2022 09 | 36095011 | |
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 | 2022 09 20 | 36067026 | |
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 | 2022 Nov | 36036832 | |
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 | 2022 09 | 35978191 | |
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 | 2022 Aug 11 | 35951581 | |
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 | 2022 Aug 12 | 35947651 | |
Overcoming Selection Bias In Synthetic Lethality Prediction. | Seale, Colm; Tepeli, Yasin; Gonçalves, Joana P | Bioinformatics (Oxford, England) | 2022 Jul 25 | 35876858 | |
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 | 2022 Jul 26 | 35838077 | |
Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications. | Stockwell, Brent R | Cell | 2022 07 07 | 35803244 | |
scSTEM: clustering pseudotime ordered single-cell data. | Song, Qi; Wang, Jingtao; Bar-Joseph, Ziv | Genome biology | 2022 07 07 | 35799304 | |
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 | 2022 07 12 | 35770488 | |
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 | 2022 Jul | 35726067 | |
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 | 2022 Jul | 35654359 | |
Nuclear oligo hashing improves differential analysis of single-cell RNA-seq. | Kim, Hyeon-Jin; Booth, Greg; Saunders, Lauren; Srivatsan, Sanjay; McFaline-Figueroa, José L; Trapnell, Cole | Nature communications | 2022 May 13 | 35562344 | |
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 | |
Epigenetic Regulation of Heart-ECHS. | Gan, Lu; Pei, Liming | JACC. Basic to translational science | 2022 Apr | 35540104 | |
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 | 2022 06 | 35537336 | |
Multi-contrast computed tomography healthy 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 | Computers in biology and medicine | 2022 07 | 35533459 | |
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 | 2022 05 03 | 35508105 | |
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 | 2022 Aug 01 | 35504500 | |
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 | 2022 05 | 35501385 | |
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 | 2021 Oct 25 | 35474899 | |
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 | 2022 05 03 | 35471911 | |
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 | |
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) | 2022 07 18 | 35446460 | |
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 | |
Membrane marker selection for segmenting single cell spatial proteomics data. | Dayao, Monica T; Brusko, Maigan; Wasserfall, Clive; Bar-Joseph, Ziv | Nature communications | 2022 04 14 | 35422106 | |
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 | |
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 | 2022 Jun 06 | 35385679 | |
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 | |
Analyzing Spatial Transcriptomics Data Using Giotto. | Del Rossi, Natalie; Chen, Jiaji G; Yuan, Guo-Cheng; Dries, Ruben | Current protocols | 2022 Apr | 35384407 | |
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 | 2022 Mar 30 | 35378748 | |
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 | 2022 06 | 35361932 | |
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 | 2022 06 | 35361931 | |
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 | |
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 | 2022 07 | 35351966 | |
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 | 2022 Jul | 35347328 | |
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 | 2022 04 12 | 35344335 | |
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 | 2022 Aug | 35332340 | |
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 | |
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 | 2022 Jul-Aug | 35278717 | |
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 | |
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 | 2022 Apr 01 | 35245349 | |
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 | |
Temporal modelling using single-cell transcriptomics. | Ding, Jun; Sharon, Nadav; Bar-Joseph, Ziv | Nature reviews. Genetics | 2022 06 | 35102309 | |
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 | |
Author Correction: Single-cell chromatin state analysis with Signac. | Nature methods | 2022 Feb | 34997233 | ||
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 | |
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. | Zhao, Tongtong; Chiang, Zachary D; Morriss, Julia W; LaFave, Lindsay M; Murray, Evan M; Del Priore, Isabella; Meli, Kevin; Lareau, Caleb A; Nadaf, Naeem M; Li, Jilong; Earl, Andrew S; Macosko, Evan Z; Jacks, Tyler; Buenrostro, Jason D; Chen, Fei | Nature | 2022 01 | 34912115 | |
Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies. | Kotnala, Ankita; Anderson, David M G; Patterson, Nathan Heath; Cantrell, Lee S; Messinger, Jeffrey D; Curcio, Christine A; Schey, Kevin L | Journal of mass spectrometry : JMS | 2021 Dec | 34881479 | |
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 | |
Spatially Resolved Proteomic Analysis of the Lens Extracellular Diffusion Barrier. | Wang, Zhen; Cantrell, Lee S; Schey, Kevin L | Investigative ophthalmology & visual science | 2021 09 02 | 34554179 | |
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 | |
Acceleration of age-induced proteolysis in the guinea pig lens nucleus by in vivo exposure to hyperbaric oxygen: A mass spectrometry analysis. | Giblin, Frank J; Anderson, David M G; Han, Jun; Rose, Kristie L; Wang, Zhen; Schey, Kevin L | Experimental eye research | 2021 09 | 34233175 | |
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 | |
Successive High-Resolution (H2O)n-GCIB and C60-SIMS Imaging Integrates Multi-Omics in Different Cell Types in Breast Cancer Tissue. | Tian, Hua; Sparvero, Louis J; Anthonymuthu, Tamil Selvan; Sun, Wan-Yang; Amoscato, Andrew A; He, Rong-Rong; Bayır, Hülya; Kagan, Valerian E; Winograd, Nicholas | Analytical chemistry | 2021 Jun 15 | 34075742 | |
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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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 | |
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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 | |
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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 | |
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 | 2021 Mar | 33410167 | |
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 | |
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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 | |
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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 | |
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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 | |
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 | 2020 Dec 02 | 32886506 | |
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 | |
Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-?m spatial resolution. | Piehowski, Paul D; Zhu, Ying; Bramer, Lisa M; Stratton, Kelly G; Zhao, Rui; Orton, Daniel J; Moore, Ronald J; Yuan, Jia; Mitchell, Hugh D; Gao, Yuqian; Webb-Robertson, Bobbie-Jo M; Dey, Sudhansu K; Kelly, Ryan T; Burnum-Johnson, Kristin E | Nature communications. | 2020 Jan 07; | 31911630 | |
Immune monitoring using mass cytometry and related high-dimensional imaging approaches. | Hartmann, Felix J; Bendall, Sean C | Nature reviews. Rheumatology. | 2020 02; | 31892734 | |
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. | Hafemeister, Christoph; Satija, Rahul | Genome biology. | 2019 12 23; | 31870423 | |
Uncovering Matrix Effects on Lipid Analyses in MALDI Imaging Mass Spectrometry Experiments. | Perry, William J; Patterson, Nathan Heath; Prentice, Boone M; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of mass spectrometry : JMS. | 2019 Dec 20; | 31860760 | |
Toward a Common Coordinate Framework for the Human Body. | Rood, Jennifer E; Stuart, Tim; Ghazanfar, Shila; Biancalani, Tommaso; Fisher, Eyal; Butler, Andrew; Hupalowska, Anna; Gaffney, Leslie; Mauck, William; Eraslan, Gökçen; Marioni, John C; Regev, Aviv; Satija, Rahul | Cell. | 2019 Dec 12; | 31835027 | |
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 | 2019 Dec 10 | 31822622 | |
High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry. | Yin, Ruichuan; Burnum-Johnson, Kristin E; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Nature protocols. | 2019 12; | 31723300 | |
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. | Chen, Song; Lake, Blue B; Zhang, Kun | Nature biotechnology. | 2019 12; | 31611697 | |
Staphylococcus aureus exhibits heterogeneous siderophore production within the vertebrate host. | Perry, William J; Spraggins, Jeffrey M; Sheldon, Jessica R; Grunenwald, Caroline M; Heinrichs, David E; Cassat, James E; Skaar, Eric P; Caprioli, Richard M | Proceedings of the National Academy of Sciences of the United States of America. | 2019 10 29; | 31611408 | |
Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. | Verbeeck, Nico; Caprioli, Richard M; Van de Plas, Raf | Mass spectrometry reviews. | 2020 May; | 31602691 | |
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. | HuBMAP Consortium | Nature. | 2019 10; | 31597973 | |
High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry. | Spraggins, Jeffrey M; Djambazova, Katerina V; Rivera, Emilio S; Migas, Lukasz G; Neumann, Elizabeth K; Fuetterer, Arne; Suetering, Juergen; Goedecke, Niels; Ly, Alice; Van de Plas, Raf; Caprioli, Richard M | Analytical chemistry. | 2019 11 19; | 31593446 | |
High-Parameter Immune Profiling with CyTOF. | Sahaf, Bita; Rahman, Adeeb; Maecker, Holden T; Bendall, Sean C | Methods in molecular biology (Clifton, N.J.). | 2020; | 31502160 | |
Supervised classification enables rapid annotation of cell atlases. | Pliner, Hannah A; Shendure, Jay; Trapnell, Cole | Nature methods. | 2019 Oct; | 31501545 | |
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. | McFaline-Figueroa, José L; Hill, Andrew J; Qiu, Xiaojie; Jackson, Dana; Shendure, Jay; Trapnell, Cole | Nature genetics. | 2019 Sep; | 31477929 | |
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. | Saka, Sinem K; Wang, Yu; Kishi, Jocelyn Y; Zhu, Allen; Zeng, Yitian; Xie, Wenxin; Kirli, Koray; Yapp, Clarence; Cicconet, Marcelo; Beliveau, Brian J; Lapan, Sylvain W; Yin, Siyuan; Lin, Millicent; Boyden, Edward S; Kaeser, Pascal S; Pihan, German; Church, George M; Yin, Peng | Nature biotechnology. | 2019 Sep; | 31427819 | |
A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. | Judd, Audra M; Gutierrez, Danielle B; Moore, Jessica L; Patterson, Nathan Heath; Yang, Junhai; Romer, Carrie E; Norris, Jeremy L; Caprioli, Richard M | Journal of mass spectrometry : JMS. | 2019 Aug; | 31254303 | |
Two Specific Sulfatide Species Are Dysregulated during Renal Development in a Mouse Model of Alport Syndrome. | Gessel, Megan M; Spraggins, Jeffrey M; Voziyan, Paul A; Abrahamson, Dale R; Caprioli, Richard M; Hudson, Billy G | Lipids. | 2019 06; | 31197846 | |
Comprehensive Integration of Single-Cell Data. | Stuart, Tim; Butler, Andrew; Hoffman, Paul; Hafemeister, Christoph; Papalexi, Efthymia; Mauck 3rd, William M; Hao, Yuhan; Stoeckius, Marlon; Smibert, Peter; Satija, Rahul | Cell. | 2019 Jun 13; | 31178118 | |
MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies. | Ryan, Daniel J; Patterson, Nathan Heath; Putnam, Nicole E; Wilde, Aimee D; Weiss, Andy; Perry, William J; Cassat, James E; Skaar, Eric P; Caprioli, Richard M; Spraggins, Jeffrey M | Analytical chemistry. | 2019 06 18; | 31149808 | |
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. | Kishi, Jocelyn Y; Lapan, Sylvain W; Beliveau, Brian J; West, Emma R; Zhu, Allen; Sasaki, Hiroshi M; Saka, Sinem K; Wang, Yu; Cepko, Constance L; Yin, Peng | Nature methods. | 2019 Jun; | 31110282 | |
Visualizing learner engagement, performance, and trajectories to evaluate and optimize online course design. | Ginda, Michael; Richey, Michael C; Cousino, Mark; Börner, Katy | PloS one. | 2019; | 31059546 | |
Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data. | Lin, Chieh; Bar-Joseph, Ziv | Bioinformatics (Oxford, England). | 2019 Apr 30; | 31038684 | |
The 2019 mathematical oncology roadmap. | Rockne, Russell C; Hawkins-Daarud, Andrea; Swanson, Kristin R; Sluka, James P; Glazier, James A; Macklin, Paul; Hormuth, David A; Jarrett, Angela M; Lima, Ernesto A B F; Tinsley Oden, J; Biros, George; Yankeelov, Thomas E; Curtius, Kit; Al Bakir, Ibrahim; Wodarz, Dominik; Komarova, Natalia; Aparicio, Luis; Bordyuh, Mykola; Rabadan, Raul; Finley, Stacey D; Enderling, Heiko; Caudell, Jimmy; Moros, Eduardo G; Anderson, Alexander R A; Gatenby, Robert A; Kaznatcheev, Artem; Jeavons, Peter; Krishnan, Nikhil; Pelesko, Julia; Wadhwa, Raoul R; Yoon, Nara; Nichol, Daniel; Marusyk, Andriy; Hinczewski, Michael; Scott, Jacob G | Physical biology. | 2019 Jun 19; | 30991381 | |
Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. | Prentice, Boone M; Hart, Nathaniel J; Phillips, Neil; Haliyur, Rachana; Judd, Audra; Armandala, Radhika; Spraggins, Jeffrey M; Lowe, Cindy L; Boyd, Kelli L; Stein, Roland W; Wright, Christopher V; Norris, Jeremy L; Powers, Alvin C; Brissova, Marcela; Caprioli, Richard M | Diabetologia. | 2019 06; | 30955045 | |
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. | Rodriques, Samuel G; Stickels, Robert R; Goeva, Aleksandrina; Martin, Carly A; Murray, Evan; Vanderburg, Charles R; Welch, Joshua; Chen, Linlin M; Chen, Fei; Macosko, Evan Z | Science (New York, N.Y.). | 2019 03 29; | 30923225 | |
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Eng, Chee-Huat Linus; Lawson, Michael; Zhu, Qian; Dries, Ruben; Koulena, Noushin; Takei, Yodai; Yun, Jina; Cronin, Christopher; Karp, Christoph; Yuan, Guo-Cheng; Cai, Long | Nature. | 2019 Apr; | 30911168 | |
Multiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry. | Prentice, Boone M; McMillen, Josiah C; Caprioli, Richard M | International journal of mass spectrometry. | 2019 Mar; | 30906202 | |
Cell lineage inference from SNP and scRNA-Seq data. | Ding, Jun; Lin, Chieh; Bar-Joseph, Ziv | Nucleic acids research. | 2019 Jun 04; | 30820578 | |
The single-cell transcriptional landscape of mammalian organogenesis. | Cao, Junyue; Spielmann, Malte; Qiu, Xiaojie; Huang, Xingfan; Ibrahim, Daniel M; Hill, Andrew J; Zhang, Fan; Mundlos, Stefan; Christiansen, Lena; Steemers, Frank J; Trapnell, Cole; Shendure, Jay | Nature. | 2019 02; | 30787437 | |
Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data. | Rashid, Sabrina; Shah, Sohrab; Bar-Joseph, Ziv; Pandya, Ravi | Bioinformatics (Oxford, England). | 2019 Feb 15; | 30768159 | |
Data visualization literacy: Definitions, conceptual frameworks, exercises, and assessments. | Börner, Katy; Bueckle, Andreas; Ginda, Michael | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Feb 05; | 30718386 | |
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. | Stoeckius, Marlon; Zheng, Shiwei; Houck-Loomis, Brian; Hao, Stephanie; Yeung, Bertrand Z; Mauck 3rd, William M; Smibert, Peter; Satija, Rahul | Genome biology. | 2018 12 19; | 30567574 | |
Forecasting innovations in science, technology, and education. | Börner, Katy; Rouse, William B; Trunfio, Paul; Stanley, H Eugene | Proceedings of the National Academy of Sciences of the United States of America. | 2018 12 11; | 30530683 | |
Protein identification strategies in MALDI imaging mass spectrometry: a brief review. | Ryan, Daniel J; Spraggins, Jeffrey M; Caprioli, Richard M | Current opinion in chemical biology. | 2019 02; | 30476689 | |
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. | Zhu, Qian; Shah, Sheel; Dries, Ruben; Cai, Long; Yuan, Guo-Cheng | Nature biotechnology. | 2018 Oct 29; | 30371680 |