Publications Tracker

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We are tracking 41 publications.

Author(s)ContactTitleNotesCurrent Stage
MC-IU TeamKaty BörnerCommon Coordinate System User Interfaces: Design, Validation, and UsageTo be submitted to Plos One/ arxivBegan writing: 11/07/2019
Griffin M Weber, Yingnan Ju, Katy BörnerKaty BörnerConsiderations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human BodyFrontiers in Cardiovascular Medicine 7 (29): doi: 10.3389/fcvm.2020.00029. arxivPublished: 03/13/2020
Ruben Dries, Qian Zhu, Chee-Huat Linus Eng, Arpan Sarkar, Feng Bao, Rani E George, Nico Pierson, Long Cai, Guo-Cheng YuanGuo-Cheng YuanGiotto, a pipeline for integrative analysis and visualization of single-cell spatial transcriptomic data Submitted to Nature BiotechSubmitted: 11/07/2019
IEC, TCs, MCs, some TMCsNick NystromHuBMAP Architecture Paper marker paper. Venue not yet decidedBegan writing: 11/07/2019
Andreas Bueckle, Kilian Buehling, Leonard Cross, Katy BörnerKaty BörnerThe Common Coordinate Framework Registration User Interface (CCF RUI): A Comparison of Three ModalitiesTo be submitted to Plos One/arxivBegan writing: 11/07/2019
Paul D. Piehowski*, Ying Zhu*, Lisa M. Bramer, Kelly G. Stratton, Rui Zhao, Daniel J. Orton, Ronald J. Moore, Jia Yuan, Hugh D. Mitchell, Yuqian Gao, Bobbie-Jo M. Webb-Robertson, Sudhansu K. Dey, Ryan T. Kelly & Kristin E. Burnum-Johnson Kristin Burnum-JohnsonAutomated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution Published: 01/07/2020
R. Yin, K. E. Burnum-Johnson, X. Sun, S. K. Dey, J. LaskinJulia LaskinHigh Spatial Resolution Imaging of Biological Tissues Using Nanospray Desorption Electrospray Ionization Mass Spectrometryfeatured on the cover of Nature ProtocolsPublished: 11/13/2019
X. Li, R. Yin, H. Hu, Y. Li, X. Sun, S.K. Dey, and J. LaskinJulia LaskinAn Integrated Microfluidic Probe for Mass Spectrometry Imaging of Biological Samples submitted to Angew Chem and ChemRxiv: 12/01/2020
X. Li, R. Yin, H. Hu, Y. Li, X. Sun, S.K. Dey, and J. LaskinJulia LaskinHigh-throughput imaging using iMPFBegan writing: 04/15/2020
Dong R, Yuan GC.Guo-Cheng YuanGiniClust3: a fast and memory-efficient tool for rare cell type identification.Published in BMC BioinformaticsPublished: 04/25/2020
Hurley K, Ding J, Villacorta-Martin C, Herriges MJ, Jacob A, Vedaie M, Alysandratos KD, Sun YL, Lin C, Werder RB, Huang J, Wilson AA, Mithal A, Mostoslavsky G, Oglesby I, Caballero IS, Guttentag SH, Ahangari F, Kaminski N, Rodriguez-Fraticelli A, Camargo F, Bar-Joseph Z, Kotton DN.Ziv Bar-JosephReconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors.Published in Cell Stem CellPublished: 04/02/2020
ComponentZiv Bar-JosephInferring TF activation order in time series scRNA-Seq studies.Published in PLoS Xomput. BiolPublished: 02/18/2020
Chen S, Lake BB, Zhang K.Song ChenHigh-throughput sequencing of the transcriptome and chromatin accessibility in the same cellPublished in Nature BiotechnologyPublished: 10/14/2019
HuBMAP ConsortiumMichael P SnyderThe human body at cellular resolutionPublished in NaturePublished: 10/09/2019
Ding J, Lin C, Bar-Joseph Z.Ziv Bar-JosephCell lineage inference from SNP and scRNA-Seq data.Published in Nucleic Acid Res.Published: 06/04/2019
Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P.Jocelyn KishiSABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues.Published in Nat. MethodsPublished: 06/01/2019
Lin C, Bar-Joseph Z.Ziv Bar-JosephContinuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data.Published in BioinformaticsPublished: 11/01/2019
Prentice BM, Hart NJ, Phillips N, Haliyur R, Judd A, Armandala R, Spraggins JM, Lowe CL, Boyd KL, Stein RW, Wright CV, Norris JL, Powers AC, Brissova M, Caprioli RM.Jeff SpragginsImaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue.published in DiabetologiaPublished: 06/19/2020
Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L.Long CaiTranscriptome-scale super-resolved imaging in tissues by RNA seqFISH.Published in NaturePublished: 04/01/2019
Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang, Daniel M. Ibrahim, Andrew J. Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J. Steemers, Cole Trapnell & Jay ShendureJay ShendureThe single-cell transcriptional landscape of mammalian organogenesisPublished in NaturePublished: 02/20/2019
Rashid S, Shah S, Bar-Joseph Z, Pandya R.Ziv Bar-JosephDhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data.Published in BioinformaticsPublished: 02/15/2019
Katy Börner, Andreas Bueckle, and Michael GindaKaty BörnerData visualization literacy: Definitions, conceptual frameworks, exercises, and assessmentsPublished in PNASPublished: 02/05/2019
Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z. Yeung, William M. Mauck III, Peter Smibert, and Rahul SatijaRahul SatijaCell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomicsPublished in Genome BiologyPublished: 12/19/2018
Katy Börner, William B. Rouse, Paul Trunfio, and H. Eugene StanleyKaty BörnerForecasting innovations in science, technology, and educationPublished in PNASPublished: 12/11/2018
Ryan DJ, Spraggins JM, Caprioli RM.Richard CaprioliProtein identification strategies in MALDI imaging mass spectrometry: a brief review.Published in Curr Opin Chem BiolPublished: 02/01/2019
Zhu Q, Shah S, Dries R, Cai L, Yuan GC.Guo-Cheng YuanIdentification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data.Published in Nat Biotechnol Published: 10/29/2018
Prentice BM, McMillen JC, Caprioli RMRichard CaprioliMultiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry.Published in Int J Mass SpectromPublished: 03/01/2019
C Hafemeister†, R Satija†Rahul SatijaNormalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regressionPublished in Genome BiologyPublished: 12/18/2019
T Stuart*, A Butler*, P Hoffman, C Hafemeister, E Papalexi, WM Mauck, M Stoeckius, P Smibert, R Satija†Rahul SatijaComprehensive Integration of Single-Cell DataPublished In CellPublished: 04/05/2019
Rood J, Stuart T*, Ghazanfar S*, Biancalini T*, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck WM, Eraslan G, Marioni JC*, Regev A*, Satija R*Rahul SatijaTowards a Common Coordinate Framework for the Human BodyPublished In CellPublished: 12/21/2019
Saka SK, Wang Yu, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES Boyden, Kaeser PS, Pihan G, Church GM, Yin P.Sinem SakaImmuno-SABER enables highly multiplexed and amplified protein imaging in tissuesPublished in Nature BiotechnologyPublished: 08/19/2019
Elizabeth K. Neumann, Lukasz G. Migas, Jamie L. Allen, Richard M. Caprioli, Raf Van de Plas, and Jeffrey M. SpragginsJeff Spraggins/Elizabeth NeumannSpatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging Mass SpectrometrySubmitted: 07/07/2020
Emilio S. Rivera, Kate V. Djambazova, Elizabeth K. Neumann, Richard M. Caprioli, Jeff M. SpragginsJeff Spraggins/Elizabeth Neumann Integrating Ion Mobility and Imaging Mass Spectrometry for Comprehensive Analysis of Biological Tissues: A brief review and perspectivePublished: 07/07/2020
Elizabeth K. Neumann, Kate V. Djambazova, Richard M. Caprioli, Jeff M. Spraggins Jeff Spraggins/Elizabeth NeumannMultimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and MedicineSubmitted: 07/07/2020
Elizabeth K. Neumann, Tina Tsui, N. Heath Patterson, Raf Van de Plas, Richard M. Caprioli, and Jeffrey M. Spraggins Jeff Spraggins/Elizabeth NeumannMultimodal Imaging Quality Assurance/Control Methods for Reproducible Chemical Imaging Began writing: 07/07/2020
N. Heath Patterson, Elizabeth K. Neumann, Dave Anderson, Jamie Allen, Maya Brewer, Mark deCastecer, Raf van de Plas, Richard Caprioli, and Jeff M. Spraggins Jeff Spraggins/Elizabeth Neumann3-D Multimodal IMS on Human KidneyBegan writing: 07/07/2020
Elizabeth K. Neumann, Lukasz Migas, N. Heath Patterson, Jamie Allen, Maya Brewer, Dave Anderson, Mark deCastacer, Raf van de Plas, Rcihard M. Caprioli, Jeff SpragginsJeff Spraggins/Elizabeth NeumannMetabolic Profiles of Human Kidney Functional RegionsBegan writing: 07/07/2020
TC-Harvard, TMC Vanderbilt, MC-IUNils GehlenborgViv: Multiscale Visualization of High-Resolution Multiplexed Tissue Data on the WebPreprint (8/12): writing: 07/01/2020
TC-HarvardNils GehlenborgA Generic Framework and Library for Exploration of Small Multiples through Interactive PilingPreprint (8/15): 10/01/2020
TC-HarvardNils GehlenborgVitessce: Integrative single-cell and spatial tissue data visualizationBegan writing: 11/01/2020
Angelo, Michael; Beuschel, Rebecca; Bock, Yoni; Camarillo, Jeannie; Chung, Kwanghun; Croteau, Josh; Engle, Liz; Fisher, Jeremy; Hatler, Julia; Hewitt, Stephen; Hickey, John; Hiltke, Tara; Kelleher, Neil; Lundberg, Emma; McDonough, Liz; Neumann, Elizabeth; Orstad, Steve; Radtke, Andrea; Saka, Sinem; Small, Eliza; Snyder, Mike; Sood, Anup; Spraggins, Jeffrey; Taube, Janis; Wiblin, AnneJeanie CamarilloThe potential, promise, and pitfalls of multiplexed antibody based imagingBegan writing: 05/29/2020
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