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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.

Title Authors Journal PubMedID Publication Date
Polyphony: an Interactive Transfer Learning Framework for Single-Cell Data Analysis. Cheng, Furui; Keller, Mark S; Qu, Huamin; Gehlenborg, Nils; Wang, Qianwen IEEE transactions on visualization and computer graphics 36155452 2023 Jan
Optimal gap-affine alignment in O(s) space. Marco-Sola, Santiago; Eizenga, Jordan M; Guarracino, Andrea; Paten, Benedict; Garrison, Erik; Moreto, Miquel Bioinformatics (Oxford, England) 36749013 2023 Feb 03
Using single cell atlas data to reconstruct regulatory networks. Song, Qi; Ruffalo, Matthew; Bar-Joseph, Ziv Nucleic acids research 36762475 2023 Apr 24
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. Dayao, Monica T; Trevino, Alexandro; Kim, Honesty; Ruffalo, Matthew; D'Angio, H Blaize; Preska, Ryan; Duvvuri, Umamaheswar; Mayer, Aaron T; Bar-Joseph, Ziv Bioinformatics (Oxford, England) 37387167 2023 Jun 30
OME-Zarr: a cloud-optimized bioimaging file format with international community support. Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E; Gault, David; Ghosh, Satrajit S; Gold, Ilan; Halchenko, Yaroslav O; Hartley, Matthew; Horsfall, Dave; Keller, Mark S; Kittisopikul, Mark; Kovacs, Gabor; Küpcü Yoldaş, Aybüke; Kyoda, Koji; le Tournoulx de la Villegeorges, Albane; Li, Tong; Liberali, Prisca; Lindner, Dominik; Linkert, Melissa; Lüthi, Joel; Maitin-Shepard, Jeremy; Manz, Trevor; Marconato, Luca; McCormick, Matthew; Lange, Merlin; Mohamed, Khaled; Moore, William; Norlin, Nils; Ouyang, Wei; Özdemir, Bugra; Palla, Giovanni; Pape, Constantin; Pelkmans, Lucas; Pietzsch, Tobias; Preibisch, Stephan; Prete, Martin; Rzepka, Norman; Samee, Sameeul; Schaub, Nicholas; Sidky, Hythem; Solak, Ahmet Can; Stirling, David R; Striebel, Jonathan; Tischer, Christian; Toloudis, Daniel; Virshup, Isaac; Walczysko, Petr; Watson, Alan M; Weisbart, Erin; Wong, Frances; Yamauchi, Kevin A; Bayraktar, Omer; Cimini, Beth A; Gehlenborg, Nils; Haniffa, Muzlifah; Hotaling, Nathan; Onami, Shuichi; Royer, Loic A; Saalfeld, Stephan; Stegle, Oliver; Theis, Fabian J; Swedlow, Jason R bioRxiv : the preprint server for biology 36865282 2023 May 07
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. Shao, Xinhao; Gomez, Clarissa D; Kapoor, Nandini; Considine, James M; Grams, Christopher; Gao, Yu Tom; Naba, Alexandra Nucleic acids research 36399478 2023 Jan 06
Senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus. Swahn, Hannah; Li, Kun; Duffy, Tomas; Olmer, Merissa; D'Lima, Darryl D; Mondala, Tony S; Natarajan, Padmaja; Head, Steven R; Lotz, Martin K Annals of the rheumatic diseases 36564153 2023 Mar
Conundrums of choice of 'normal' kidney tissue for single cell studies. Jain, Sanjay Current opinion in nephrology and hypertension 36811638 2023 May 01
Tissue Mass Spectrometry: How Solid Is Our Future? Unsihuay, Daisy; Phipps, William S; Paulovich, Amanda G; Chapman, Jessica R; Ducret, Axel; Eberlin, Livia S; Spraggins, Jeffrey M; Goodwin, Richard J A Clinical chemistry 37293883 2023 Jul 05
Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform. Liao, Yen-Chen; Fulcher, James M; Degnan, David J; Williams, Sarah M; Bramer, Lisa M; Veličković, Dušan; Zemaitis, Kevin J; Veličković, Marija; Sontag, Ryan L; Moore, Ronald J; Paša-Tolić, Ljiljana; Zhu, Ying; Zhou, Mowei Molecular & cellular proteomics : MCP 36603806 2023 Feb
193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI. Zemaitis, Kevin J; Zhou, Mowei; Kew, William; Paša-Tolić, Ljiljana Journal of the American Society for Mass Spectrometry 36622763 2023 Feb 01
Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models. Tang, Xiaofang; Luo, Yingjun; Yuan, Dongqiang; Calandrelli, Riccardo; Malhi, Naseeb Kaur; Sriram, Kiran; Miao, Yifei; Lou, Chih-Hong; Tsark, Walter; Tapia, Alonso; Chen, Aleysha T; Zhang, Guangyu; Roeth, Daniel; Kalkum, Markus; Wang, Zhao V; Chien, Shu; Natarajan, Rama; Cooke, John P; Zhong, Sheng; Chen, Zhen Bouman The Journal of clinical investigation 36512424 2023 Feb 01
Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer. Dashzeveg, Nurmaa K; Jia, Yuzhi; Zhang, Youbin; Gerratana, Lorenzo; Patel, Priyam; Shajahan, Asif; Dandar, Tsogbadrakh; Ramos, Erika K; Almubarak, Hannah F; Adorno-Cruz, Valery; Taftaf, Rokana; Schuster, Emma J; Scholten, David; Sokolowski, Michael T; Reduzzi, Carolina; El-Shennawy, Lamiaa; Hoffmann, Andrew D; Manai, Maroua; Zhang, Qiang; D'Amico, Paolo; Azadi, Parastoo; Colley, Karen J; Platanias, Leonidas C; Shah, Ami N; Gradishar, William J; Cristofanilli, Massimo; Muller, William A; Cobb, Brian A; Liu, Huiping Cancer discovery 37272843 2023 Jun 05
Anatomic nomenclature and 3-dimensional regional model of the human ovary: call for a new paradigm. O'Neill, Kathleen E; Maher, Jacqueline Y; Laronda, Monica M; Duncan, Francesca E; LeDuc, Richard D; Lujan, Marla E; Oktay, Kutluk H; Pouch, Alison M; Segars, James H; Tsui, Elizabeth L; Zelinski, Mary B; Halvorson, Lisa M; Gomez-Lobo, Veronica American journal of obstetrics and gynecology 36191605 2023 Mar
Creating a common language for the subanatomy of the ovary. Tsui, Elizabeth L; O'Neill, Kathleen E; LeDuc, Richard D; Shikanov, Ariella; Gomez-Lobo, Veronica; Laronda, Monica M Biology of reproduction 36308436 2023 Jan 14
The expanding vistas of spatial transcriptomics. Tian, Luyi; Chen, Fei; Macosko, Evan Z Nature biotechnology 36192637 2023 Jun
Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids. Bagheri, Pegah; Hoang, Khang; Kuo, Chan-Yu; Trivedi, Hetvi; Jang, Hongje; Shi, Lingyan Journal of visualized experiments : JoVE 37246865 2023 May 12
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 34719806 2023 Mar
Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. Yang, Manxi; Unsihuay, Daisy; Hu, Hang; Nguele Meke, Frederick; Qu, Zihan; Zhang, Zhong-Yin; Laskin, Julia Analytical chemistry 36917636 2023 Mar 28
Multiomic Analysis and CRISPR Perturbation Screens Identify Endothelial Cell Programs and Novel Therapeutic Targets for Coronary Artery Disease. Gupta, Rajat M; Schnitzler, Gavin R; Fang, Shi; Lee-Kim, Vivian S; Barry, Aurelie Arteriosclerosis, thrombosis, and vascular biology 36994731 2023 May
Systems biology approaches to unravel lymphocyte subsets and function. Kim, YeEun; Greenleaf, William J; Bendall, Sean C Current opinion in immunology 37028221 2023 Jun
Prospective validation of diffusion-weighted MRI as a biomarker of tumor response and oncologic outcomes in head and neck cancer: Results from an observational biomarker pre-qualification study. Joint Head and Neck Radiotherapy-MRI Development Cooperative; Mohamed, Abdallah S R; Abusaif, Abdelrahman; He, Renjie; Wahid, Kareem A; Salama, Vivian; Youssef, Sara; McDonald, Brigid A; Naser, Mohamed; Ding, Yao; Salzillo, Travis C; AboBakr, Moamen A; Wang, Jihong; Lai, Stephen Y; Fuller, Clifton D Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology 36990394 2023 Jun
Integration of spatial and single-cell data across modalities with weak linkage. Chen, Shuxiao; Zhu, Bokai; Huang, Sijia; Hickey, John W; Lin, Kevin Z; Snyder, Michael; Greenleaf, William J; Nolan, Garry P; Zhang, Nancy R; Ma, Zongming bioRxiv : the preprint server for biology 36711792 2023 Jan 16
Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. Sharman, Kavya; Patterson, Nathan Heath; Weiss, Andy; Neumann, Elizabeth K; Guiberson, Emma R; Ryan, Daniel J; Gutierrez, Danielle B; Spraggins, Jeffrey M; Van de Plas, Raf; Skaar, Eric P; Caprioli, Richard M Journal of proteome research 35849531 2023 May 05
A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics. Tsai, Chia-Feng; Wang, Yi-Ting; Hsu, Chuan-Chih; Kitata, Reta Birhanu; Chu, Rosalie K; Velickovic, Marija; Zhao, Rui; Williams, Sarah M; Chrisler, William B; Jorgensen, Marda L; Moore, Ronald J; Zhu, Ying; Rodland, Karin D; Smith, Richard D; Wasserfall, Clive H; Shi, Tujin; Liu, Tao Communications biology 36653408 2023 Jan 18
Stabilized mosaic single-cell data integration using unshared features. Ghazanfar, Shila; Guibentif, Carolina; Marioni, John C Nature biotechnology 37231260 2023 May 25
Dictionary learning for integrative, multimodal and scalable single-cell analysis. Hao, Yuhan; Stuart, Tim; Kowalski, Madeline H; Choudhary, Saket; Hoffman, Paul; Hartman, Austin; Srivastava, Avi; Molla, Gesmira; Madad, Shaista; Fernandez-Granda, Carlos; Satija, Rahul Nature biotechnology 37231261 2023 May 25
Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. Ginley, Brandon; Lucarelli, Nicholas; Zee, Jarcy; Jain, Sanjay; Han, Seung Sook; Rodrigues, Luis; Ozrazgat-Baslanti, Tezcan; Wong, Michelle L; Nadkarni, Girish; Jen, Kuang-Yu; Sarder, Pinaki bioRxiv : the preprint server for biology 37292965 2023 May 18
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces. Deshpande, Atul; Loth, Melanie; Sidiropoulos, Dimitrios N; Zhang, Shuming; Yuan, Long; Bell, Alexander T F; Zhu, Qingfeng; Ho, Won Jin; Santa-Maria, Cesar; Gilkes, Daniele M; Williams, Stephen R; Uytingco, Cedric R; Chew, Jennifer; Hartnett, Andrej; Bent, Zachary W; Favorov, Alexander V; Popel, Aleksander S; Yarchoan, Mark; Kiemen, Ashley; Wu, Pei-Hsun; Fujikura, Kohei; Wirtz, Denis; Wood, Laura D; Zheng, Lei; Jaffee, Elizabeth M; Anders, Robert A; Danilova, Ludmila; Stein-O'Brien, Genevieve; Kagohara, Luciane T; Fertig, Elana J Cell systems 37080163 2023 Apr 19
Integrated Physiology of the Exocrine and Endocrine Compartments in Pancreatic Diseases: Workshop Proceedings. Mastracci, Teresa L; Apte, Minoti; Amundadottir, Laufey T; Alvarsson, Alexandra; Artandi, Steven; Bellin, Melena D; Bernal-Mizrachi, Ernesto; Caicedo, Alejandro; Campbell-Thompson, Martha; Cruz-Monserrate, Zobeida; El Ouaamari, Abdelfattah; Gaulton, Kyle J; Geisz, Andrea; Goodarzi, Mark O; Hara, Manami; Hull-Meichle, Rebecca L; Kleger, Alexander; Klein, Alison P; Kopp, Janel L; Kulkarni, Rohit N; Muzumdar, Mandar D; Naren, Anjaparavanda P; Oakes, Scott A; Olesen, Søren S; Phelps, Edward A; Powers, Alvin C; Stabler, Cherie L; Tirkes, Temel; Whitcomb, David C; Yadav, Dhiraj; Yong, Jing; Zaghloul, Norann A; Pandol, Stephen J; Sander, Maike Diabetes 36940317 2023 Apr 01
Super-resolution SRS microscopy with A-PoD. Jang, Hongje; Li, Yajuan; Fung, Anthony A; Bagheri, Pegah; Hoang, Khang; Skowronska-Krawczyk, Dorota; Chen, Xiaoping; Wu, Jane Y; Bintu, Bogdan; Shi, Lingyan Nature methods 36797410 2023 Mar
A Multicompartmental Diffusion Model for Improved Assessment of Whole-Body Diffusion-weighted Imaging Data and Evaluation of Prostate Cancer Bone Metastases. Conlin, Christopher C; Feng, Christine H; Digma, Leonardino A; Rodríguez-Soto, Ana E; Kuperman, Joshua M; Rakow-Penner, Rebecca; Karow, David S; White, Nathan S; Seibert, Tyler M; Hahn, Michael E; Dale, Anders M Radiology. Imaging cancer 36705559 2023 Jan
An integrated cell atlas of the lung in health and disease. Sikkema, Lisa; Ramírez-Suástegui, Ciro; Strobl, Daniel C; Gillett, Tessa E; Zappia, Luke; Madissoon, Elo; Markov, Nikolay S; Zaragosi, Laure-Emmanuelle; Ji, Yuge; Ansari, Meshal; Arguel, Marie-Jeanne; Apperloo, Leonie; Banchero, Martin; Bécavin, Christophe; Berg, Marijn; Chichelnitskiy, Evgeny; Chung, Mei-I; Collin, Antoine; Gay, Aurore C A; Gote-Schniering, Janine; Hooshiar Kashani, Baharak; Inecik, Kemal; Jain, Manu; Kapellos, Theodore S; Kole, Tessa M; Leroy, Sylvie; Mayr, Christoph H; Oliver, Amanda J; von Papen, Michael; Peter, Lance; Taylor, Chase J; Walzthoeni, Thomas; Xu, Chuan; Bui, Linh T; De Donno, Carlo; Dony, Leander; Faiz, Alen; Guo, Minzhe; Gutierrez, Austin J; Heumos, Lukas; Huang, Ni; Ibarra, Ignacio L; Jackson, Nathan D; Kadur Lakshminarasimha Murthy, Preetish; Lotfollahi, Mohammad; Tabib, Tracy; Talavera-López, Carlos; Travaglini, Kyle J; Wilbrey-Clark, Anna; Worlock, Kaylee B; Yoshida, Masahiro; Lung Biological Network Consortium; van den Berge, Maarten; Bossé, Yohan; Desai, Tushar J; Eickelberg, Oliver; Kaminski, Naftali; Krasnow, Mark A; Lafyatis, Robert; Nikolic, Marko Z; Powell, Joseph E; Rajagopal, Jayaraj; Rojas, Mauricio; Rozenblatt-Rosen, Orit; Seibold, Max A; Sheppard, Dean; Shepherd, Douglas P; Sin, Don D; Timens, Wim; Tsankov, Alexander M; Whitsett, Jeffrey; Xu, Yan; Banovich, Nicholas E; Barbry, Pascal; Duong, Thu Elizabeth; Falk, Christine S; Meyer, Kerstin B; Kropski, Jonathan A; Pe'er, Dana; Schiller, Herbert B; Tata, Purushothama Rao; Schultze, Joachim L; Teichmann, Sara A; Misharin, Alexander V; Nawijn, Martijn C; Luecken, Malte D; Theis, Fabian J Nature medicine 37291214 2023 Jun
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Sibbesen, Jonas A; Eizenga, Jordan M; Novak, Adam M; Sirén, Jouni; Chang, Xian; Garrison, Erik; Paten, Benedict Nature methods 36646895 2023 Feb
SCS: cell segmentation for high-resolution spatial transcriptomics. Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv bioRxiv : the preprint server for biology 37398213 2023 Jun 16
Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives. Naba, Alexandra Molecular & cellular proteomics : MCP 36918099 2023 Apr
Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. Petrov, Petar B; Considine, James M; Izzi, Valerio; Naba, Alexandra bioRxiv : the preprint server for biology 37131773 2023 Apr 20
Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Diray-Arce, Joann; Fourati, Slim; Doni Jayavelu, Naresh; Patel, Ravi; Maguire, Cole; Chang, Ana C; Dandekar, Ravi; Qi, Jingjing; Lee, Brian H; van Zalm, Patrick; Schroeder, Andrew; Chen, Ernie; Konstorum, Anna; Brito, Anderson; Gygi, Jeremy P; Kho, Alvin; Chen, Jing; Pawar, Shrikant; Gonzalez-Reiche, Ana Silvia; Hoch, Annmarie; Milliren, Carly E; Overton, James A; Westendorf, Kerstin; IMPACC Network; Cairns, Charles B; Rouphael, Nadine; Bosinger, Steven E; Kim-Schulze, Seunghee; Krammer, Florian; Rosen, Lindsey; Grubaugh, Nathan D; van Bakel, Harm; Wilson, Michael; Rajan, Jayant; Steen, Hanno; Eckalbar, Walter; Cotsapas, Chris; Langelier, Charles R; Levy, Ofer; Altman, Matthew C; Maecker, Holden; Montgomery, Ruth R; Haddad, Elias K; Sekaly, Rafick P; Esserman, Denise; Ozonoff, Al; Becker, Patrice M; Augustine, Alison D; Guan, Leying; Peters, Bjoern; Kleinstein, Steven H Cell reports. Medicine 37327781 2023 Jun 20
High-Throughput Mass Spectrometry Imaging of Biological Systems: Current Approaches and Future Directions. Jiang, Li-Xue; Yang, Manxi; Wali, Syeda Nazifa; Laskin, Julia Trends in analytical chemistry : TRAC 37206615 2023 Jun
Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. Zhang, Bingjie; Srivastava, Avi; Mimitou, Eleni; Stuart, Tim; Raimondi, Ivan; Hao, Yuhan; Smibert, Peter; Satija, Rahul Nature biotechnology 35332340 2022 Aug
Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. Kruse, Angela R S; Spraggins, Jeffrey M Frontiers in physiology 35222094 2022
Clinical Implementation and Initial Experience With a 1.5 Tesla MR-Linac for MR-Guided Radiation Therapy for Gynecologic Cancer: An R-IDEAL Stage 1 and 2a First in Humans Feasibility Study of New Technology Implementation. Lakomy, David S; Yang, Jinzhong; Vedam, Sastry; Wang, Jihong; Lee, Belinda; Sobremonte, Angela; Castillo, Pamela; Hughes, Neil; Mohammedsaid, Mustefa; Jhingran, Anuja; Klopp, Ann H; Choi, Seungtaek; Fuller, C David; Lin, Lilie L Practical radiation oncology 35278717 2022
MITI minimum information guidelines for highly multiplexed tissue images. Schapiro, Denis; Yapp, Clarence; Sokolov, Artem; Reynolds, Sheila M; Chen, Yu-An; Sudar, Damir; Xie, Yubin; Muhlich, Jeremy; Arias-Camison, Raquel; Arena, Sarah; Taylor, Adam J; Nikolov, Milen; Tyler, Madison; Lin, Jia-Ren; Burlingame, Erik A; Human Tumor Atlas Network; Chang, Young H; Farhi, Samouil L; Thorsson, Vésteinn; Venkatamohan, Nithya; Drewes, Julia L; Pe'er, Dana; Gutman, David A; Herrmann, Markus D; Gehlenborg, Nils; Bankhead, Peter; Roland, Joseph T; Herndon, John M; Snyder, Michael P; Angelo, Michael; Nolan, Garry; Swedlow, Jason R; Schultz, Nikolaus; Merrick, Daniel T; Mazzili, Sarah A; Cerami, Ethan; Rodig, Scott J; Santagata, Sandro; Sorger, Peter K Nature methods 35277708 2022 Mar
A complete reference genome improves analysis of human genetic variation. Aganezov, Sergey; Yan, Stephanie M; Soto, Daniela C; Kirsche, Melanie; Zarate, Samantha; Avdeyev, Pavel; Taylor, Dylan J; Shafin, Kishwar; Shumate, Alaina; Xiao, Chunlin; Wagner, Justin; McDaniel, Jennifer; Olson, Nathan D; Sauria, Michael E G; Vollger, Mitchell R; Rhie, Arang; Meredith, Melissa; Martin, Skylar; Lee, Joyce; Koren, Sergey; Rosenfeld, Jeffrey A; Paten, Benedict; Layer, Ryan; Chin, Chen-Shan; Sedlazeck, Fritz J; Hansen, Nancy F; Miller, Danny E; Phillippy, Adam M; Miga, Karen H; McCoy, Rajiv C; Dennis, Megan Y; Zook, Justin M; Schatz, Michael C Science (New York, N.Y.) 35357935 2022 Apr
Interactive single-cell data analysis using Cellar. Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, Ziv Nature communications 35422041 2022 Apr 14
Unsupervised cell functional annotation for single-cell RNA-seq. Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv Genome research 35764397 2022 Jun 28
Deep learning identification of stiffness markers in breast cancer. Sneider, Alexandra; Kiemen, Ashley; Kim, Joo Ho; Wu, Pei-Hsun; Habibi, Mehran; White, Marissa; Phillip, Jude M; Gu, Luo; Wirtz, Denis Biomaterials 35537336 2022 Jun
New Views of Old Proteins: Clarifying the Enigmatic Proteome. Burnum-Johnson, Kristin E; Conrads, Thomas P; Drake, Richard R; Herr, Amy E; Iyengar, Ravi; Kelly, Ryan T; Lundberg, Emma; MacCoss, Michael J; Naba, Alexandra; Nolan, Garry P; Pevzner, Pavel A; Rodland, Karin D; Sechi, Salvatore; Slavov, Nikolai; Spraggins, Jeffrey M; Van Eyk, Jennifer E; Vidal, Marc; Vogel, Christine; Walt, David R; Kelleher, Neil L Molecular & cellular proteomics : MCP 35654359 2022 Jul
Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. Su, Pei; McGee, John P; Durbin, Kenneth R; Hollas, Michael A R; Yang, Manxi; Neumann, Elizabeth K; Allen, Jamie L; Drown, Bryon S; Butun, Fatma Ayaloglu; Greer, Joseph B; Early, Bryan P; Fellers, Ryan T; Spraggins, Jeffrey M; Laskin, Julia; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L Science advances 35947651 2022 Aug 12
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 36303577 2022
A census of the lung: CellCards from LungMAP. Sun, Xin; Perl, Anne-Karina; Li, Rongbo; Bell, Sheila M; Sajti, Eniko; Kalinichenko, Vladimir V; Kalin, Tanya V; Misra, Ravi S; Deshmukh, Hitesh; Clair, Geremy; Kyle, Jennifer; Crotty Alexander, Laura E; Masso-Silva, Jorge A; Kitzmiller, Joseph A; Wikenheiser-Brokamp, Kathryn A; Deutsch, Gail; Guo, Minzhe; Du, Yina; Morley, Michael P; Valdez, Michael J; Yu, Haoze V; Jin, Kang; Bardes, Eric E; Zepp, Jarod A; Neithamer, Terren; Basil, Maria C; Zacharias, William J; Verheyden, Jamie; Young, Randee; Bandyopadhyay, Gautam; Lin, Sara; Ansong, Charles; Adkins, Joshua; Salomonis, Nathan; Aronow, Bruce J; Xu, Yan; Pryhuber, Gloria; Whitsett, Jeff; Morrisey, Edward E; NHLBI LungMAP Consortium Developmental cell 34936882 2022 Jan 10
Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection. Zemaitis, Kevin J; Veličković, Dušan; Kew, William; Fort, Kyle L; Reinhardt-Szyba, Maria; Pamreddy, Annapurna; Ding, Yanli; Kaushik, Dharam; Sharma, Kumar; Makarov, Alexander A; Zhou, Mowei; Paša-Tolić, Ljiljana Analytical chemistry 36067026 2022 Sep 20
PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. Chen, Xu; Calandrelli, Riccardo; Girardini, John; Yan, Zhangming; Tan, Zhiqun; Xu, Xiangmin; Hiniker, Annie; Zhong, Sheng Cell metabolism 35508105 2022 May 03
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 35230809 2022 Mar 18
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 36280720 2022 Nov
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 34811556 2022 Mar
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 34732839 2022 Apr
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 34795433 2022 Apr
Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. Baskar, Reema; Chen, Amy F; Favaro, Patricia; Reynolds, Warren; Mueller, Fabian; Borges, Luciene; Jiang, Sizun; Park, Hyun Shin; Kool, Eric T; Greenleaf, William J; Bendall, Sean C Cell reports methods 35463156 2022 Mar 28
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 35220718 2022 Apr 01
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. LeDuc, Richard D; Deutsch, Eric W; Binz, Pierre-Alain; Fellers, Ryan T; Cesnik, Anthony J; Klein, Joshua A; Van Den Bossche, Tim; Gabriels, Ralf; Yalavarthi, Arshika; Perez-Riverol, Yasset; Carver, Jeremy; Bittremieux, Wout; Kawano, Shin; Pullman, Benjamin; Bandeira, Nuno; Kelleher, Neil L; Thomas, Paul M; Vizcaíno, Juan Antonio Journal of proteome research 35290070 2022 Apr 01
Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. Yang, Manxi; Hu, Hang; Su, Pei; Thomas, Paul M; Camarillo, Jeannie M; Greer, Joseph B; Early, Bryan P; Fellers, Ryan T; Kelleher, Neil L; Laskin, Julia Angewandte Chemie (International ed. in English) 35446460 2022 Jul 18
Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications. Stockwell, Brent R Cell 35803244 2022 Jul 07
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Analyzing Spatial Transcriptomics Data Using Giotto. Del Rossi, Natalie; Chen, Jiaji G; Yuan, Guo-Cheng; Dries, Ruben Current protocols 35384407 2022 Apr
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Two Specific Sulfatide Species Are Dysregulated during Renal Development in a Mouse Model of Alport Syndrome. Gessel, Megan M; Spraggins, Jeffrey M; Voziyan, Paul A; Abrahamson, Dale R; Caprioli, Richard M; Hudson, Billy G Lipids 31197846 2019 06
The Importance of Clinical Tissue Imaging. Spraggins, Jeffrey M; Schwamborn, Kristina; Heeren, Ron M A; Eberlin, Livia S Clinical mass spectrometry (Del Mar, Calif.) 32483555 2019 Apr
The 2019 mathematical oncology roadmap. Rockne, Russell C; Hawkins-Daarud, Andrea; Swanson, Kristin R; Sluka, James P; Glazier, James A; Macklin, Paul; Hormuth, David A; Jarrett, Angela M; Lima, Ernesto A B F; Tinsley Oden, J; Biros, George; Yankeelov, Thomas E; Curtius, Kit; Al Bakir, Ibrahim; Wodarz, Dominik; Komarova, Natalia; Aparicio, Luis; Bordyuh, Mykola; Rabadan, Raul; Finley, Stacey D; Enderling, Heiko; Caudell, Jimmy; Moros, Eduardo G; Anderson, Alexander R A; Gatenby, Robert A; Kaznatcheev, Artem; Jeavons, Peter; Krishnan, Nikhil; Pelesko, Julia; Wadhwa, Raoul R; Yoon, Nara; Nichol, Daniel; Marusyk, Andriy; Hinczewski, Michael; Scott, Jacob G Physical biology 30991381 2019 Jun 19
Visualizing learner engagement, performance, and trajectories to evaluate and optimize online course design. Ginda, Michael; Richey, Michael C; Cousino, Mark; Börner, Katy PloS one 31059546 2019
Comprehensive Integration of Single-Cell Data. Stuart, Tim; Butler, Andrew; Hoffman, Paul; Hafemeister, Christoph; Papalexi, Efthymia; Mauck 3rd, William M; Hao, Yuhan; Stoeckius, Marlon; Smibert, Peter; Satija, Rahul Cell 31178118 2019 06 13
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Hafemeister, Christoph; Satija, Rahul Genome biology 31870423 2019 12 23
Cell lineage inference from SNP and scRNA-Seq data. Ding, Jun; Lin, Chieh; Bar-Joseph, Ziv Nucleic acids research 30820578 2019 06 04
Deep learning for inferring gene relationships from single-cell expression data. Yuan, Ye; Bar-Joseph, Ziv Proceedings of the National Academy of Sciences of the United States of America 31822622 2019 Dec 26
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. McFaline-Figueroa, José L; Hill, Andrew J; Qiu, Xiaojie; Jackson, Dana; Shendure, Jay; Trapnell, Cole Nature genetics 31477929 2019 09
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Kishi, Jocelyn Y; Lapan, Sylvain W; Beliveau, Brian J; West, Emma R; Zhu, Allen; Sasaki, Hiroshi M; Saka, Sinem K; Wang, Yu; Cepko, Constance L; Yin, Peng Nature methods 31110282 2019 06
Toward a Common Coordinate Framework for the Human Body. Rood, Jennifer E; Stuart, Tim; Ghazanfar, Shila; Biancalani, Tommaso; Fisher, Eyal; Butler, Andrew; Hupalowska, Anna; Gaffney, Leslie; Mauck, William; Eraslan, Gökçen; Marioni, John C; Regev, Aviv; Satija, Rahul Cell 31835027 2019 12 12
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. Saka, Sinem K; Wang, Yu; Kishi, Jocelyn Y; Zhu, Allen; Zeng, Yitian; Xie, Wenxin; Kirli, Koray; Yapp, Clarence; Cicconet, Marcelo; Beliveau, Brian J; Lapan, Sylvain W; Yin, Siyuan; Lin, Millicent; Boyden, Edward S; Kaeser, Pascal S; Pihan, German; Church, George M; Yin, Peng Nature biotechnology 31427819 2019 09
Protein identification strategies in MALDI imaging mass spectrometry: a brief review. Ryan, Daniel J; Spraggins, Jeffrey M; Caprioli, Richard M Current opinion in chemical biology 30476689 2019 02
MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies. Ryan, Daniel J; Patterson, Nathan Heath; Putnam, Nicole E; Wilde, Aimee D; Weiss, Andy; Perry, William J; Cassat, James E; Skaar, Eric P; Caprioli, Richard M; Spraggins, Jeffrey M Analytical chemistry 31149808 2019 06 18
A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. Judd, Audra M; Gutierrez, Danielle B; Moore, Jessica L; Patterson, Nathan Heath; Yang, Junhai; Romer, Carrie E; Norris, Jeremy L; Caprioli, Richard M Journal of mass spectrometry : JMS 31254303 2019 Aug
High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry. Spraggins, Jeffrey M; Djambazova, Katerina V; Rivera, Emilio S; Migas, Lukasz G; Neumann, Elizabeth K; Fuetterer, Arne; Suetering, Juergen; Goedecke, Niels; Ly, Alice; Van de Plas, Raf; Caprioli, Richard M Analytical chemistry 31593446 2019 11 19
Staphylococcus aureus exhibits heterogeneous siderophore production within the vertebrate host. Perry, William J; Spraggins, Jeffrey M; Sheldon, Jessica R; Grunenwald, Caroline M; Heinrichs, David E; Cassat, James E; Skaar, Eric P; Caprioli, Richard M Proceedings of the National Academy of Sciences of the United States of America 31611408 2019 10 29
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Chen, Song; Lake, Blue B; Zhang, Kun Nature biotechnology 31611697 2019 12
Forecasting innovations in science, technology, and education. Börner, Katy; Rouse, William B; Trunfio, Paul; Stanley, H Eugene Proceedings of the National Academy of Sciences of the United States of America 30530683 2018 12 11
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Stoeckius, Marlon; Zheng, Shiwei; Houck-Loomis, Brian; Hao, Stephanie; Yeung, Bertrand Z; Mauck 3rd, William M; Smibert, Peter; Satija, Rahul Genome biology 30567574 2018 12 19
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. Zhu, Qian; Shah, Sheel; Dries, Ruben; Cai, Long; Yuan, Guo-Cheng Nature biotechnology 30371680 2018 Oct 29

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