Program Publications
Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| 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 |
| 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.) | 35143307 | 2022 Feb 11 |
| Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping. | 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 E; Hafler, David; Fan, Rong | Research square | 35378748 | 2022 Mar 30 |
| 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 | 35545714 | 2022 May |
| 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 | 36513738 | 2022 Dec 13 |
| 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 | 34489600 | 2022 Jan |
| Comparison and evaluation of statistical error models for scRNA-seq. | Choudhary, Saket; Satija, Rahul | Genome biology | 35042561 | 2022 Jan 18 |
| 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 | 34792808 | 2022 01 |
| Machine-learning based investigation of prognostic indicators for oncological outcome of pancreatic ductal adenocarcinoma. | Chang, Jeremy; Liu, Yanan; Saey, Stephanie A; Chang, Kevin C; Shrader, Hannah R; Steckly, Kelsey L; Rajput, Maheen; Sonka, Milan; Chan, Carlos H F | Frontiers in oncology | 36568148 | 2022 |
| Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. | Bailey, Andrew D; Talkish, Jason; Ding, Hongxu; Igel, Haller; Duran, Alejandra; Mantripragada, Shreya; Paten, Benedict; Ares, Manuel | eLife | 35384842 | 2022 Apr 06 |
| 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 | 34619231 | 2022 Jan |
| Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments. | Richardson, Luke T; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M; Solouki, Touradj | Analytical chemistry | 35344335 | 2022 Apr 12 |
| Hanging drop sample preparation improves sensitivity of spatial proteomics. | Kwon, Yumi; Piehowski, Paul D; Zhao, Rui; Sontag, Ryan L; Moore, Ronald J; Burnum-Johnson, Kristin E; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T; Zhu, Ying | Lab on a chip | 35838077 | 2022 Jul 26 |
| Reproducible, high-dimensional imaging in archival human tissue by multiplexed ion beam imaging by time-of-flight (MIBI-TOF). | Liu, Candace C; Bosse, Marc; Kong, Alex; Kagel, Adam; Kinders, Robert; Hewitt, Stephen M; Varma, Sushama; van de Rijn, Matt; Nowak, Stanisław H; Bendall, Sean C; Angelo, Michael | Laboratory investigation; a journal of technical methods and pathology | 35351966 | 2022 Jul |
| Gestationally dependent immune organization at the maternal-fetal interface. | Moore, Amber R; Vivanco Gonzalez, Nora; Plummer, Katherine A; Mitchel, Olivia R; Kaur, Harleen; Rivera, Moises; Collica, Brian; Goldston, Mako; Filiz, Ferda; Angelo, Michael; Palmer, Theo D; Bendall, Sean C | Cell reports | 36384130 | 2022 Nov 15 |
| Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. | Kishi, Jocelyn Y; Liu, Ninning; West, Emma R; Sheng, Kuanwei; Jordanides, Jack J; Serrata, Matthew; Cepko, Constance L; Saka, Sinem K; Yin, Peng | Nature methods | 36216958 | 2022 Nov |
| Ductal Carcinoma In Situ of Breast: From Molecular Etiology to Therapeutic Management. | Hophan, Shelby Lynn; Odnokoz, Olena; Liu, Huiping; Luo, Yuan; Khan, Seema; Gradishar, William; Zhou, Zhuan; Badve, Sunil; Torres, Mylin A; Wan, Yong | Endocrinology | 35245349 | 2022 Apr 01 |
| An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue. | Lukowski, Jessica K; Olson, Heather; Velickovic, Marija; Wang, Juan; Kyle, Jennifer E; Kim, Young-Mo; Williams, Sarah M; Zhu, Ying; Huyck, Heidi L; McGraw, Matthew D; Poole, Cory; Rogers, Lisa; Misra, Ravi; Alexandrov, Theodore; Ansong, Charles; Pryhuber, Gloria S; Clair, Geremy; Adkins, Joshua N; Carson, James P; Anderton, Christopher R | Frontiers in molecular biosciences | 36465564 | 2022 |
| Unilateral Radiation Therapy for Tonsillar Cancer: Treatment Outcomes in the Era of Human Papillomavirus, Positron-Emission Tomography, and Intensity Modulated Radiation Therapy. | Taku, Nicolette; Chronowski, Gregory; Brandon Gunn, G; Morrison, William H; Gross, Neil D; Moreno, Amy C; Ferrarotto, Renata; Frank, Steven J; Fuller, C David; Goepfert, Ryan P; Phan, Jack; Lai, Stephen Y; Reddy, Jay P; Rosenthal, David I; Garden, Adam S | International journal of radiation oncology, biology, physics | 35504500 | 2022 Aug 01 |
| Temporal modelling using single-cell transcriptomics. | Ding, Jun; Sharon, Nadav; Bar-Joseph, Ziv | Nature reviews. Genetics | 35102309 | 2022 Jun |
| Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. | Goenka, Sneha D; Gorzynski, John E; Shafin, Kishwar; Fisk, Dianna G; Pesout, Trevor; Jensen, Tanner D; Monlong, Jean; Chang, Pi-Chuan; Baid, Gunjan; Bernstein, Jonathan A; Christle, Jeffrey W; Dalton, Karen P; Garalde, Daniel R; Grove, Megan E; Guillory, Joseph; Kolesnikov, Alexey; Nattestad, Maria; Ruzhnikov, Maura R Z; Samadi, Mehrzad; Sethia, Ankit; Spiteri, Elizabeth; Wright, Christopher J; Xiong, Katherine; Zhu, Tong; Jain, Miten; Sedlazeck, Fritz J; Carroll, Andrew; Paten, Benedict; Ashley, Euan A | Nature biotechnology | 35347328 | 2022 Jul |
| Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. | Mc Cartney, Ann M; Shafin, Kishwar; Alonge, Michael; Bzikadze, Andrey V; Formenti, Giulio; Fungtammasan, Arkarachai; Howe, Kerstin; Jain, Chirag; Koren, Sergey; Logsdon, Glennis A; Miga, Karen H; Mikheenko, Alla; Paten, Benedict; Shumate, Alaina; Soto, Daniela C; Sović, Ivan; Wood, Jonathan M D; Zook, Justin M; Phillippy, Adam M; Rhie, Arang | Nature methods | 35361931 | 2022 Jun |
| UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Journal of computational biology : a journal of computational molecular cell biology | 36036832 | 2022 Nov |
| Multicellular modules as clinical diagnostic and therapeutic targets. | Baertsch, Marc-A; Nolan, Garry P; Hickey, John W | Trends in cancer | 34872889 | 2022 Mar |
| Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. | Andreasson, Johan O L; Gotrik, Michael R; Wu, Michelle J; Wayment-Steele, Hannah K; Kladwang, Wipapat; Portela, Fernando; Wellington-Oguri, Roger; Eterna Participants; Das, Rhiju; Greenleaf, William J | Proceedings of the National Academy of Sciences of the United States of America | 35471911 | 2022 May 03 |
| A single-cell regulatory map of postnatal lung alveologenesis in humans and mice. | Duong, Thu Elizabeth; Wu, Yan; Sos, Brandon Chin; Dong, Weixiu; Limaye, Siddharth; Rivier, Lauraine H; Myers, Greg; Hagood, James S; Zhang, Kun | Cell genomics | 35434692 | 2022 Mar 09 |
| A reference tissue atlas for the human kidney. | Hansen, Jens; Sealfon, Rachel; Menon, Rajasree; Eadon, Michael T; Lake, Blue B; Steck, Becky; Anjani, Kavya; Parikh, Samir; Sigdel, Tara K; Zhang, Guanshi; Velickovic, Dusan; Barwinska, Daria; Alexandrov, Theodore; Dobi, Dejan; Rashmi, Priyanka; Otto, Edgar A; Rivera, Miguel; Rose, Michael P; Anderton, Christopher R; Shapiro, John P; Pamreddy, Annapurna; Winfree, Seth; Xiong, Yuguang; He, Yongqun; de Boer, Ian H; Hodgin, Jeffrey B; Barisoni, Laura; Naik, Abhijit S; Sharma, Kumar; Sarwal, Minnie M; Zhang, Kun; Himmelfarb, Jonathan; Rovin, Brad; El-Achkar, Tarek M; Laszik, Zoltan; He, John Cijiang; Dagher, Pierre C; Valerius, M Todd; Jain, Sanjay; Satlin, Lisa M; Troyanskaya, Olga G; Kretzler, Matthias; Iyengar, Ravi; Azeloglu, Evren U; Kidney Precision Medicine Project | Science advances | 35675394 | 2022 Jun 10 |
| 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 | 35533459 | 2022 Jul |
| Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation. | Schachner, Luis F; Soye, Benjamin Des; Ro, Soo; Kenney, Grace E; Ives, Ashley N; Su, Taojunfeng; Goo, Young Ah; Jewett, Michael C; Rosenzweig, Amy C; Kelleher, Neil L | ACS chemical biology | 35951581 | 2022 Oct 21 |
| Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program. | Shapira, Suzanne N; Naji, Ali; Atkinson, Mark A; Powers, Alvin C; Kaestner, Klaus H | Cell metabolism | 36206763 | 2022 Dec 06 |
| Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. | Ramos, Erika K; Tsai, Chia-Feng; Jia, Yuzhi; Cao, Yue; Manu, Megan; Taftaf, Rokana; Hoffmann, Andrew D; El-Shennawy, Lamiaa; Gritsenko, Marina A; Adorno-Cruz, Valery; Schuster, Emma J; Scholten, David; Patel, Dhwani; Liu, Xia; Patel, Priyam; Wray, Brian; Zhang, Youbin; Zhang, Shanshan; Moore, Ronald J; Mathews, Jeremy V; Schipma, Matthew J; Liu, Tao; Tokars, Valerie L; Cristofanilli, Massimo; Shi, Tujin; Shen, Yang; Dashzeveg, Nurmaa K; Liu, Huiping | eLife | 36193887 | 2022 Oct 04 |
| High-Throughput Nano-DESI Mass Spectrometry Imaging of Biological Tissues Using an Integrated Microfluidic Probe. | Li, Xiangtang; Hu, Hang; Yin, Ruichuan; Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Analytical chemistry | 35770488 | 2022 Jul 12 |
| 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 | 34912115 | 2022 Jan |
| 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 | 35063072 | 2022 Jan 20 |
| 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.) | 35084980 | 2022 Jan 28 |
| Analyzing Spatial Transcriptomics Data Using Giotto. | Del Rossi, Natalie; Chen, Jiaji G; Yuan, Guo-Cheng; Dries, Ruben | Current protocols | 35384407 | 2022 Apr |
| TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data. | Li, Dongshunyi; Velazquez, Jeremy J; Ding, Jun; Hislop, Joshua; Ebrahimkhani, Mo R; Bar-Joseph, Ziv | Genome biology | 35255944 | 2022 Mar 07 |
| Complete genomic and epigenetic maps of human centromeres. | Altemose, Nicolas; Logsdon, Glennis A; Bzikadze, Andrey V; Sidhwani, Pragya; Langley, Sasha A; Caldas, Gina V; Hoyt, Savannah J; Uralsky, Lev; Ryabov, Fedor D; Shew, Colin J; Sauria, Michael E G; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A; Dvorkina, Tatiana; Kunyavskaya, Olga; Vollger, Mitchell R; Rhie, Arang; McCartney, Ann M; Asri, Mobin; Lorig-Roach, Ryan; Shafin, Kishwar; Lucas, Julian K; Aganezov, Sergey; Olson, Daniel; de Lima, Leonardo Gomes; Potapova, Tamara; Hartley, Gabrielle A; Haukness, Marina; Kerpedjiev, Peter; Gusev, Fedor; Tigyi, Kristof; Brooks, Shelise; Young, Alice; Nurk, Sergey; Koren, Sergey; Salama, Sofie R; Paten, Benedict; Rogaev, Evgeny I; Streets, Aaron; Karpen, Gary H; Dernburg, Abby F; Sullivan, Beth A; Straight, Aaron F; Wheeler, Travis J; Gerton, Jennifer L; Eichler, Evan E; Phillippy, Adam M; Timp, Winston; Dennis, Megan Y; O'Neill, Rachel J; Zook, Justin M; Schatz, Michael C; Pevzner, Pavel A; Diekhans, Mark; Langley, Charles H; Alexandrov, Ivan A; Miga, Karen H | Science (New York, N.Y.) | 35357911 | 2022 Apr |
| Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. | Formenti, Giulio; Rhie, Arang; Walenz, Brian P; Thibaud-Nissen, Françoise; Shafin, Kishwar; Koren, Sergey; Myers, Eugene W; Jarvis, Erich D; Phillippy, Adam M | Nature methods | 35361932 | 2022 Jun |
| Membrane marker selection for segmenting single cell spatial proteomics data. | Dayao, Monica T; Brusko, Maigan; Wasserfall, Clive; Bar-Joseph, Ziv | Nature communications | 35422106 | 2022 Apr 14 |
| GBZ file format for pangenome graphs. | Sirén, Jouni; Paten, Benedict | Bioinformatics (Oxford, England) | 36179091 | 2022 Nov 15 |
| A Parallelization Strategy for the Time Efficient Analysis of Thousands of LC/MS Runs in High-Performance Computing Environment. | van Zalm, Patrick; Viodé, Arthur; Smolen, Kinga; Fatou, Benoit; Hayati, Arash Nemati; Schlaffner, Christoph N; Levy, Ofer; Steen, Judith; Steen, Hanno | Journal of proteome research | 36201825 | 2022 Nov 04 |
| 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.) | 34628030 | 2022 Feb |
| Overcoming selection bias in synthetic lethality prediction. | Seale, Colm; Tepeli, Yasin; Gonçalves, Joana P | Bioinformatics (Oxford, England) | 35876858 | 2022 Sep 15 |
| Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation. | Menon, Rajasree; Bomback, Andrew S; Lake, Blue B; Stutzke, Christy; Grewenow, Stephanie M; Menez, Steven; D'Agati, Vivette D; Jain, Sanjay; Kidney Precision Medicine Project | Kidney international | 35339536 | 2022 Jun |
| Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts. | Baskar, Reema; Kimmey, Sam C; Bendall, Sean C | Trends in cell biology | 35181197 | 2022 Jun |
| 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 | 36333818 | 2022 Nov 04 |
| scSTEM: clustering pseudotime ordered single-cell data. | Song, Qi; Wang, Jingtao; Bar-Joseph, Ziv | Genome biology | 35799304 | 2022 Jul 07 |
| CINS: Cell Interaction Network inference from Single cell expression data. | Yuan, Ye; Cosme Jr, Carlos; Adams, Taylor Sterling; Schupp, Jonas; Sakamoto, Koji; Xylourgidis, Nikos; Ruffalo, Matthew; Li, Jiachen; Kaminski, Naftali; Bar-Joseph, Ziv | PLoS computational biology | 36095011 | 2022 Sep |
| Multiset multicover methods for discriminative marker selection. | Hasanaj, Euxhen; Alavi, Amir; Gupta, Anupam; Póczos, Barnabás; Bar-Joseph, Ziv | Cell reports methods | 36452867 | 2022 Nov 21 |
| Limited extent and consequences of pancreatic SARS-CoV-2 infection. | van der Heide, Verena; Jangra, Sonia; Cohen, Phillip; Rathnasinghe, Raveen; Aslam, Sadaf; Aydillo, Teresa; Geanon, Daniel; Handler, Diana; Kelley, Geoffrey; Lee, Brian; Rahman, Adeeb; Dawson, Travis; Qi, Jingjing; D'Souza, Darwin; Kim-Schulze, Seunghee; Panzer, Julia K; Caicedo, Alejandro; Kusmartseva, Irina; Posgai, Amanda L; Atkinson, Mark A; Albrecht, Randy A; García-Sastre, Adolfo; Rosenberg, Brad R; Schotsaert, Michael; Homann, Dirk | Cell reports | 35247306 | 2022 Mar 15 |
| Cell Trafficking at the Intersection of the Tumor-Immune Compartments. | Du, Wenxuan; Nair, Praful; Johnston, Adrian; Wu, Pei-Hsun; Wirtz, Denis | Annual review of biomedical engineering | 35385679 | 2022 Jun 06 |
| NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. | Chen, Amy F; Parks, Benjamin; Kathiria, Arwa S; Ober-Reynolds, Benjamin; Goronzy, Jorg J; Greenleaf, William J | Nature methods | 35501385 | 2022 May |
| 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 | 35562344 | 2022 May 13 |
| Mapping the Proteoform Landscape of Five Human Tissues. | Drown, Bryon S; Jooß, Kevin; Melani, Rafael D; Lloyd-Jones, Cameron; Camarillo, Jeannie M; Kelleher, Neil L | Journal of proteome research | 35413190 | 2022 May 06 |
| A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling. | Lekschas, Fritz; Zhou, Xinyi; Chen, Wei; Gehlenborg, Nils; Bach, Benjamin; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics | 33026994 | 2021 Feb |
| Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data. | Rashid, Sabrina; Shah, Sohrab; Bar-Joseph, Ziv; Pandya, Ravi | Bioinformatics (Oxford, England) | 30768159 | 2021 Jul 12 |
| Characteristics of p.Gln368Ter Myocilin Variant and Influence of Polygenic Risk on Glaucoma Penetrance in the UK Biobank. | Zebardast, Nazlee; Sekimitsu, Sayuri; Wang, Jiali; Elze, Tobias; Gharahkhani, Puya; Cole, Brian S; Lin, Michael M; Segrè, Ayellet V; Wiggs, Janey L; International Glaucoma Genetics Consortium | Ophthalmology | 33713785 | 2021 Sep |
| Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study. | IMPACC Manuscript Writing Team; IMPACC Network Steering Committee | Science immunology | 34376480 | 2021 Aug 10 |
| Phase identification for dynamic CT enhancements with generative adversarial network. | Tang, Yucheng; Gao, Riqiang; Lee, Ho Hin; Chen, Yunqiang; Gao, Dashan; Bermudez, Camilo; Bao, Shunxing; Huo, Yuankai; Savoie, Brent V; Landman, Bennett A | Medical physics | 33410167 | 2021 Mar |
| 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 | 34531632 | 2021 |
| 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 | 34449196 | 2021 09 14 |
| 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 | 34667487 | 2021 Apr |
| 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 | 34075742 | 2021 Jun 15 |
| Spatial Segmentation of Mass Spectrometry Imaging Data by Combining Multivariate Clustering and Univariate Thresholding. | Hu, Hang; Yin, Ruichuan; Brown, Hilary M; Laskin, Julia | Analytical chemistry | 33570915 | 2021 02 23 |
| Advances in spatial transcriptomic data analysis. | Dries, Ruben; Chen, Jiaji; Del Rossi, Natalie; Khan, Mohammed Muzamil; Sistig, Adriana; Yuan, Guo-Cheng | Genome research | 34599004 | 2021 Oct |
| Single-cell metabolic profiling of human cytotoxic T cells. | Hartmann, Felix J; Mrdjen, Dunja; McCaffrey, Erin; Glass, David R; Greenwald, Noah F; Bharadwaj, Anusha; Khair, Zumana; Verberk, Sanne G S; Baranski, Alex; Baskar, Reema; Graf, William; Van Valen, David; Van den Bossche, Jan; Angelo, Michael; Bendall, Sean C | Nature biotechnology | 32868913 | 2021 02 |
| 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 | 34351778 | 2021 Sep 03 |
| 3D virtual reality vs. 2D desktop registration user interface comparison. | Bueckle, Andreas; Buehling, Kilian; Shih, Patrick C; Börner, Katy | PloS one | 34705835 | 2021 |
| Single-cell chromatin state analysis with Signac. | Stuart, Tim; Srivastava, Avi; Madad, Shaista; Lareau, Caleb A; Satija, Rahul | Nature methods | 34725479 | 2021 Nov |
| Automated biomarker candidate discovery in imaging mass spectrometry data through spatially localized Shapley additive explanations. | Tideman, Leonoor E M; Migas, Lukasz G; Djambazova, Katerina V; Patterson, Nathan Heath; Caprioli, Richard M; Spraggins, Jeffrey M; Van de Plas, Raf | Analytica chimica acta | 34482894 | 2021 Sep 08 |
| 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 | 33753784 | 2021 03 22 |
| Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. | Kennedy-Darling, Julia; Bhate, Salil S; Hickey, John W; Black, Sarah; Barlow, Graham L; Vazquez, Gustavo; Venkataraaman, Vishal G; Samusik, Nikolay; Goltsev, Yury; Schürch, Christian M; Nolan, Garry P | European journal of immunology | 33548142 | 2021 05 |
| 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 | 34859676 | 2021 Dec 14 |
| Spatial multi-omics sequencing for fixed tissue via DBiT-seq. | Su, Graham; Qin, Xiaoyu; Enninful, Archibald; Bai, Zhiliang; Deng, Yanxiang; Liu, Yang; Fan, Rong | STAR protocols | 34027489 | 2021 Jun 18 |
| Giotto: a toolbox for integrative analysis and visualization of spatial expression data. | Dries, Ruben; Zhu, Qian; Dong, Rui; Eng, Chee-Huat Linus; Li, Huipeng; Liu, Kan; Fu, Yuntian; Zhao, Tianxiao; Sarkar, Arpan; Bao, Feng; George, Rani E; Pierson, Nico; Cai, Long; Yuan, Guo-Cheng | Genome biology | 33685491 | 2021 Mar 08 |
| 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 | 34043341 | 2021 Jul 07 |
| Quantitative Mass Spectrometry Imaging of Biological Systems. | Unsihuay, Daisy; Mesa Sanchez, Daniela; Laskin, Julia | Annual review of physical chemistry | 33441032 | 2021 04 20 |
| 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 | 34722959 | 2021 |
| 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 | 34353350 | 2021 08 05 |
| Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics. | Tsai, Chia-Feng; Zhang, Pengfei; Scholten, David; Martin, Kendall; Wang, Yi-Ting; Zhao, Rui; Chrisler, William B; Patel, Dhwani B; Dou, Maowei; Jia, Yuzhi; Reduzzi, Carolina; Liu, Xia; Moore, Ronald J; Burnum-Johnson, Kristin E; Lin, Miao-Hsia; Hsu, Chuan-Chih; Jacobs, Jon M; Kagan, Jacob; Srivastava, Sudhir; Rodland, Karin D; Steven Wiley, H; Qian, Wei-Jun; Smith, Richard D; Zhu, Ying; Cristofanilli, Massimo; Liu, Tao; Liu, Huiping; Shi, Tujin | Communications biology | 33649493 | 2021 Mar 01 |
| 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 | 34093591 | 2021 |
| 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 | 34650278 | 2021 Nov |
| 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.) | 34210887 | 2021 07 02 |
| 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 | 34711971 | 2021 Nov |
| Deep learning of gene relationships from single cell time-course expression data. | Yuan, Ye; Bar-Joseph, Ziv | Briefings in bioinformatics | 33876191 | 2021 09 02 |
| 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.) | 34914532 | 2021 Dec 17 |
| 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 | 34354322 | 2021 |
| Body Part Regression With Self-Supervision. | Tang, Yucheng; Gao, Riqiang; Han, Shizhong; Chen, Yunqiang; Gao, Dashan; Nath, Vishwesh; Bermudez, Camilo; Savona, Michael R; Bao, Shunxing; Lyu, Ilwoo; Huo, Yuankai; Landman, Bennett A | IEEE transactions on medical imaging | 33560981 | 2021 May |
| Spatially Resolved Proteomic Analysis of the Lens Extracellular Diffusion Barrier. | Wang, Zhen; Cantrell, Lee S; Schey, Kevin L | Investigative ophthalmology & visual science | 34554179 | 2021 09 02 |
| 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 | 34642644 | 2021 Dec |
| 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 | 34038090 | 2021 06 08 |
| Supervised Adversarial Alignment of Single-Cell RNA-seq Data. | Ge, Songwei; Wang, Haohan; Alavi, Amir; Xing, Eric; Bar-Joseph, Ziv | Journal of computational biology : a journal of computational molecular cell biology | 33470876 | 2021 05 |
| 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 | 34750578 | 2021 Nov |
| 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 | 34215862 | 2021 Aug |
| 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 | 34239102 | 2021 Jul |
| Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. | Uzun, Yasin; Wu, Hao; Tan, Kai | Genome research | 33219054 | 2021 01 |
| CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data. | Hu, Yuxuan; Peng, Tao; Gao, Lin; Tan, Kai | Science advances | 33853780 | 2021 04 |
| 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 | 34750582 | 2021 Nov |
| 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 | 34872616 | 2021 Dec 06 |
| Identifying signaling genes in spatial single-cell expression data. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 32886099 | 2021 May 17 |
| 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 | 34725481 | 2021 Nov |
| Computational tools for analyzing single-cell data in pluripotent cell differentiation studies. | Ding, Jun; Alavi, Amir; Ebrahimkhani, Mo R; Bar-Joseph, Ziv | Cell reports methods | 35474899 | 2021 Oct 25 |
| Editorial: Footprints of Immune Cells in the Type 1 Diabetic Pancreas. | Brusko, Todd M; Mallone, Roberto; Rodriguez-Calvo, Teresa | Frontiers in endocrinology | 34721308 | 2021 |
| Pancreas Optical Clearing and 3-D Microscopy in Health and Diabetes. | Campbell-Thompson, Martha; Tang, Shiue-Cheng | Frontiers in endocrinology | 33981285 | 2021 |
| Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data. | Hickey, John W; Tan, Yuqi; Nolan, Garry P; Goltsev, Yury | Frontiers in immunology | 34484237 | 2021 |
| 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 | 34625255 | 2021 Nov 01 |
| 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 | 34795254 | 2021 Nov 18 |
| 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 | 34233175 | 2021 09 |
| 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 | 34881479 | 2021 Dec |
| Integrated spatial genomics reveals global architecture of single nuclei. | Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, Shengbao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, Long | Nature | 33505024 | 2021 02 |
| SpatialDWLS: accurate deconvolution of spatial transcriptomic data. | Dong, Rui; Yuan, Guo-Cheng | Genome biology | 33971932 | 2021 05 10 |
| 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 | 33844503 | 2021 04 27 |
| 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 | 34099939 | 2021 Jun |
| Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. | Hurley, Killian; Ding, Jun; Villacorta-Martin, Carlos; Herriges, Michael J; Jacob, Anjali; Vedaie, Marall; Alysandratos, Konstantinos D; Sun, Yuliang L; Lin, Chieh; Werder, Rhiannon B; Huang, Jessie; Wilson, Andrew A; Mithal, Aditya; Mostoslavsky, Gustavo; Oglesby, Irene; Caballero, Ignacio S; Guttentag, Susan H; Ahangari, Farida; Kaminski, Naftali; Rodriguez-Fraticelli, Alejo; Camargo, Fernando; Bar-Joseph, Ziv; Kotton, Darrell N | Cell stem cell | 32004478 | 2020 Apr 02 |
| Inferring TF activation order in time series scRNA-Seq studies. | Lin, Chieh; Ding, Jun; Bar-Joseph, Ziv | PLoS computational biology | 32069291 | 2020 02 |
| Uncovering matrix effects on lipid analyses in MALDI imaging mass spectrometry experiments. | Perry, William J; Patterson, Nathan Heath; Prentice, Boone M; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of mass spectrometry : JMS | 31860760 | 2020 Apr |
| Integrated molecular imaging technologies for investigation of metals in biological systems: A brief review. | Perry, William J; Weiss, Andy; Van de Plas, Raf; Spraggins, Jeffrey M; Caprioli, Richard M; Skaar, Eric P | Current opinion in chemical biology | 32087551 | 2020 04 |
| Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. | Islam, Mirazul; Chen, Bob; Spraggins, Jeffrey M; Kelly, Ryan T; Lau, Ken S | Gastroenterology | 32417404 | 2020 08 |
| Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. | McMillen, Josiah C; Fincher, Jarod A; Klein, Dustin R; Spraggins, Jeffrey M; Caprioli, Richard M | Journal of mass spectrometry : JMS | 33241625 | 2020 Dec |
| Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High-Resolution Imaging Mass Spectrometry. | Anderson, David M G; Messinger, Jeffrey D; Patterson, Nathan H; Rivera, Emilio S; Kotnala, Ankita; Spraggins, Jeffrey M; Caprioli, Richard M; Curcio, Christine A; Schey, Kevin L | Journal of the American Society for Mass Spectrometry | 32628476 | 2020 Dec 02 |
| Localization of the lens intermediate filament switch by imaging mass spectrometry. | Wang, Zhen; Ryan, Daniel J; Schey, Kevin L | Experimental eye research | 32682822 | 2020 09 |
| Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. | Ji, Andrew L; Rubin, Adam J; Thrane, Kim; Jiang, Sizun; Reynolds, David L; Meyers, Robin M; Guo, Margaret G; George, Benson M; Mollbrink, Annelie; Bergenstråhle, Joseph; Larsson, Ludvig; Bai, Yunhao; Zhu, Bokai; Bhaduri, Aparna; Meyers, Jordan M; Rovira-Clavé, Xavier; Hollmig, S Tyler; Aasi, Sumaira Z; Nolan, Garry P; Lundeberg, Joakim; Khavari, Paul A | Cell | 32579974 | 2020 07 23 |
| Immune monitoring using mass cytometry and related high-dimensional imaging approaches. | Hartmann, Felix J; Bendall, Sean C | Nature reviews. Rheumatology | 31892734 | 2020 02 |
| An Integrated Microfluidic Probe for Mass Spectrometry Imaging of Biological Samples*. | Li, Xiangtang; Yin, Ruichuan; Hu, Hang; Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Angewandte Chemie (International ed. in English) | 32743957 | 2020 12 07 |
| Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells. | Martin, Kendall; Zhang, Tong; Zhang, Pengfei; Chrisler, William B; Thomas, Fillmore L; Liu, Fen; Liu, Tao; Qian, Wei-Jun; Smith, Richard D; Shi, Tujin | Journal of visualized experiments : JoVE | 33226031 | 2020 Nov 06 |
| Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. | Verbeeck, Nico; Caprioli, Richard M; Van de Plas, Raf | Mass spectrometry reviews | 31602691 | 2020 05 |
| Discovering New Lipidomic Features Using Cell Type Specific Fluorophore Expression to Provide Spatial and Biological Specificity in a Multimodal Workflow with MALDI Imaging Mass Spectrometry. | Jones, Marissa A; Cho, Sung Hoon; Patterson, Nathan Heath; Van de Plas, Raf; Spraggins, Jeffrey M; Boothby, Mark R; Caprioli, Richard M | Analytical chemistry | 32298091 | 2020 05 19 |
| Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. | Rivera, Emilio S; Djambazova, Katerina V; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of mass spectrometry : JMS | 32955134 | 2020 Dec |
| CDKL5: a promising new therapeutic target for acute kidney injury? | de Caestecker, Mark | American journal of physiology. Renal physiology | 33073588 | 2020 11 01 |
| Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. | Schürch, Christian M; Bhate, Salil S; Barlow, Graham L; Phillips, Darci J; Noti, Luca; Zlobec, Inti; Chu, Pauline; Black, Sarah; Demeter, Janos; McIlwain, David R; Kinoshita, Shigemi; Samusik, Nikolay; Goltsev, Yury; Nolan, Garry P | Cell | 32763154 | 2020 09 03 |
| High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. | Liu, Yang; Yang, Mingyu; Deng, Yanxiang; Su, Graham; Enninful, Archibald; Guo, Cindy C; Tebaldi, Toma; Zhang, Di; Kim, Dongjoo; Bai, Zhiliang; Norris, Eileen; Pan, Alisia; Li, Jiatong; Xiao, Yang; Halene, Stephanie; Fan, Rong | Cell | 33188776 | 2020 12 10 |
| Iterative point set registration for aligning scRNA-seq data. | Alavi, Amir; Bar-Joseph, Ziv | PLoS computational biology | 33108369 | 2020 10 |
| A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. | Keyes, Timothy J; Domizi, Pablo; Lo, Yu-Chen; Nolan, Garry P; Davis, Kara L | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 32602650 | 2020 08 |
| Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu, Yan; Zhang, Kun | Nature reviews. Nephrology | 32221477 | 2020 07 |
| Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. | Neumann, Elizabeth K; Djambazova, Katerina V; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of the American Society for Mass Spectrometry | 32886506 | 2020 Dec 02 |
| RIPK3-mediated inflammation is a conserved β cell response to ER stress. | Yang, Bingyuan; Maddison, Lisette A; Zaborska, Karolina E; Dai, Chunhua; Yin, Linlin; Tang, Zihan; Zang, Liqing; Jacobson, David A; Powers, Alvin C; Chen, Wenbiao | Science advances | 33355143 | 2020 12 |
| Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution. | Piehowski, Paul D; Zhu, Ying; Bramer, Lisa M; Stratton, Kelly G; Zhao, Rui; Orton, Daniel J; Moore, Ronald J; Yuan, Jia; Mitchell, Hugh D; Gao, Yuqian; Webb-Robertson, Bobbie-Jo M; Dey, Sudhansu K; Kelly, Ryan T; Burnum-Johnson, Kristin E | Nature communications | 31911630 | 2020 01 07 |
| Advances in Proximity Ligation in situ Hybridization (PLISH). | Nagendran, Monica; Andruska, Adam M; Harbury, Pehr B; Desai, Tushar J | Bio-protocol | 33659462 | 2020 Nov 05 |
| Guidelines for reporting single-cell RNA-seq experiments. | Füllgrabe, Anja; George, Nancy; Green, Matthew; Nejad, Parisa; Aronow, Bruce; Fexova, Silvie Korena; Fischer, Clay; Freeberg, Mallory Ann; Huerta, Laura; Morrison, Norman; Scheuermann, Richard H; Taylor, Deanne; Vasilevsky, Nicole; Clarke, Laura; Gehlenborg, Nils; Kent, Jim; Marioni, John; Teichmann, Sarah; Brazma, Alvis; Papatheodorou, Irene | Nature biotechnology | 33188371 | 2020 Dec |
| Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. | Shafin, Kishwar; Pesout, Trevor; Lorig-Roach, Ryan; Haukness, Marina; Olsen, Hugh E; Bosworth, Colleen; Armstrong, Joel; Tigyi, Kristof; Maurer, Nicholas; Koren, Sergey; Sedlazeck, Fritz J; Marschall, Tobias; Mayes, Simon; Costa, Vania; Zook, Justin M; Liu, Kelvin J; Kilburn, Duncan; Sorensen, Melanie; Munson, Katy M; Vollger, Mitchell R; Monlong, Jean; Garrison, Erik; Eichler, Evan E; Salama, Sofie; Haussler, David; Green, Richard E; Akeson, Mark; Phillippy, Adam; Miga, Karen H; Carnevali, Paolo; Jain, Miten; Paten, Benedict | Nature biotechnology | 32686750 | 2020 09 |
| Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures. | Salahudeen, Ameen A; Choi, Shannon S; Rustagi, Arjun; Zhu, Junjie; de la O, Sean M; Flynn, Ryan A; Margalef-Català, Mar; Santos, António J M; Ju, Jihang; Batish, Arpit; van Unen, Vincent; Usui, Tatsuya; Zheng, Grace X Y; Edwards, Caitlin E; Wagar, Lisa E; Luca, Vincent; Anchang, Benedict; Nagendran, Monica; Nguyen, Khanh; Hart, Daniel J; Terry, Jessica M; Belgrader, Phillip; Ziraldo, Solongo B; Mikkelsen, Tarjei S; Harbury, Pehr B; Glenn, Jeffrey S; Garcia, K Christopher; Davis, Mark M; Baric, Ralph S; Sabatti, Chiara; Amieva, Manuel R; Blish, Catherine A; Desai, Tushar J; Kuo, Calvin J | bioRxiv : the preprint server for biology | 32743583 | 2020 Jul 27 |
| High-Parameter Immune Profiling with CyTOF. | Sahaf, Bita; Rahman, Adeeb; Maecker, Holden T; Bendall, Sean C | Methods in molecular biology (Clifton, N.J.) | 31502160 | 2020 |
| Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. | Zhou, Xin X; Bracken, Colton J; Zhang, Kaihua; Zhou, Jie; Mou, Yun; Wang, Lei; Cheng, Yifan; Leung, Kevin K; Wells, James A | Journal of the American Chemical Society | 32924468 | 2020 10 14 |
| Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. | Salahudeen, Ameen A; Choi, Shannon S; Rustagi, Arjun; Zhu, Junjie; van Unen, Vincent; de la O, Sean M; Flynn, Ryan A; Margalef-Català, Mar; Santos, António J M; Ju, Jihang; Batish, Arpit; Usui, Tatsuya; Zheng, Grace X Y; Edwards, Caitlin E; Wagar, Lisa E; Luca, Vincent; Anchang, Benedict; Nagendran, Monica; Nguyen, Khanh; Hart, Daniel J; Terry, Jessica M; Belgrader, Phillip; Ziraldo, Solongo B; Mikkelsen, Tarjei S; Harbury, Pehr B; Glenn, Jeffrey S; Garcia, K Christopher; Davis, Mark M; Baric, Ralph S; Sabatti, Chiara; Amieva, Manuel R; Blish, Catherine A; Desai, Tushar J; Kuo, Calvin J | Nature | 33238290 | 2020 Dec |
| The impact of air transport availability on research collaboration: A case study of four universities. | Ploszaj, Adam; Yan, Xiaoran; Börner, Katy | PloS one | 32886681 | 2020 |
| Landscape of coordinated immune responses to H1N1 challenge in humans. | Rahil, Zainab; Leylek, Rebecca; Schürch, Christian M; Chen, Han; Bjornson-Hooper, Zach; Christensen, Shannon R; Gherardini, Pier Federico; Bhate, Salil S; Spitzer, Matthew H; Fragiadakis, Gabriela K; Mukherjee, Nilanjan; Kim, Nelson; Jiang, Sizun; Yo, Jennifer; Gaudilliere, Brice; Affrime, Melton; Bock, Bonnie; Hensley, Scott E; Idoyaga, Juliana; Aghaeepour, Nima; Kim, Kenneth; Nolan, Garry P; McIlwain, David R | The Journal of clinical investigation | 33044226 | 2020 11 02 |
| Tetraspanin-7 regulation of L-type voltage-dependent calcium channels controls pancreatic β-cell insulin secretion. | Dickerson, Matthew T; Dadi, Prasanna K; Butterworth, Regan B; Nakhe, Arya Y; Graff, Sarah M; Zaborska, Karolina E; Schaub, Charles M; Jacobson, David A | The Journal of physiology | 32790176 | 2020 Nov |
| Changes to Zonular Tension Alters the Subcellular Distribution of AQP5 in Regions of Influx and Efflux of Water in the Rat Lens. | Petrova, Rosica S; Bavana, Nandini; Zhao, Rusin; Schey, Kevin L; Donaldson, Paul J | Investigative ophthalmology & visual science | 32945844 | 2020 09 01 |
| Multiplexed single-cell morphometry for hematopathology diagnostics. | Tsai, Albert G; Glass, David R; Juntilla, Marisa; Hartmann, Felix J; Oak, Jean S; Fernandez-Pol, Sebastian; Ohgami, Robert S; Bendall, Sean C | Nature medicine | 32161403 | 2020 03 |
| An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. | Glass, David R; Tsai, Albert G; Oliveria, John Paul; Hartmann, Felix J; Kimmey, Samuel C; Calderon, Ariel A; Borges, Luciene; Glass, Marla C; Wagar, Lisa E; Davis, Mark M; Bendall, Sean C | Immunity | 32668225 | 2020 07 14 |
| Data visualization literacy: Definitions, conceptual frameworks, exercises, and assessments. | Börner, Katy; Bueckle, Andreas; Ginda, Michael | Proceedings of the National Academy of Sciences of the United States of America | 30718386 | 2019 02 05 |
| Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. | Prentice, Boone M; Hart, Nathaniel J; Phillips, Neil; Haliyur, Rachana; Judd, Audra; Armandala, Radhika; Spraggins, Jeffrey M; Lowe, Cindy L; Boyd, Kelli L; Stein, Roland W; Wright, Christopher V; Norris, Jeremy L; Powers, Alvin C; Brissova, Marcela; Caprioli, Richard M | Diabetologia | 30955045 | 2019 Jun |
| The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. | HuBMAP Consortium | Nature | 31597973 | 2019 Oct |
| The single-cell transcriptional landscape of mammalian organogenesis. | Cao, Junyue; Spielmann, Malte; Qiu, Xiaojie; Huang, Xingfan; Ibrahim, Daniel M; Hill, Andrew J; Zhang, Fan; Mundlos, Stefan; Christiansen, Lena; Steemers, Frank J; Trapnell, Cole; Shendure, Jay | Nature | 30787437 | 2019 02 |
| Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Eng, Chee-Huat Linus; Lawson, Michael; Zhu, Qian; Dries, Ruben; Koulena, Noushin; Takei, Yodai; Yun, Jina; Cronin, Christopher; Karp, Christoph; Yuan, Guo-Cheng; Cai, Long | Nature | 30911168 | 2019 04 |
| Supervised classification enables rapid annotation of cell atlases. | Pliner, Hannah A; Shendure, Jay; Trapnell, Cole | Nature methods | 31501545 | 2019 10 |
| Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. | Rodriques, Samuel G; Stickels, Robert R; Goeva, Aleksandrina; Martin, Carly A; Murray, Evan; Vanderburg, Charles R; Welch, Joshua; Chen, Linlin M; Chen, Fei; Macosko, Evan Z | Science (New York, N.Y.) | 30923225 | 2019 03 29 |
| High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry. | Yin, Ruichuan; Burnum-Johnson, Kristin E; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Nature protocols | 31723300 | 2019 12 |
| Continuous-state HMMs for modeling time-series single-cell RNA-Seq data. | Lin, Chieh; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 31038684 | 2019 11 01 |
| Multiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry. | Prentice, Boone M; McMillen, Josiah C; Caprioli, Richard M | International journal of mass spectrometry | 30906202 | 2019 Mar |
| 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 |
