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1 | Target Submission Date | Last updated | Status | preprint url | paper url | Referenced Data DOI | Status of Data Processing | Group | Author name(s) | PoC name | PoC email | Title | Brief description | Notes | |||||||||||||
2 | 05/08/2020 | Published | | TTD-CalTech | Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L. | Long Cai | lcai@caltech.edu | Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Published in Nature | ||||||||||||||||||
3 | 05/08/2020 | Published | | TTD-CalTech | Zhu Q, Shah S, Dries R, Cai L, Yuan GC. | Guo-Cheng Yuan | gcyuan@jimmy.harvard.edu | Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. | Published in Nat Biotechnol | ||||||||||||||||||
4 | 05/08/2020 | Published | | TTD-CalTech | Dong R, Yuan GC. | Guo-Cheng Yuan | gcyuan@jimmy.harvard.edu | GiniClust3: a fast and memory-efficient tool for rare cell type identification. | Published in BMC Bioinformatics | ||||||||||||||||||
5 | 01/19/2021 | Draft in Progress | | TMC-UF | Mark Atkinson | atkinson@ufl.edu | Circulation in the human spleen | Littoral cell and arteriole mapping of red and white pulp in the human spleen | |||||||||||||||||||
6 | 01/19/2021 | Draft in Progress | | TMC-UF | Mark Atkinson | atkinson@ufl.edu | Thymic lobule mapping across age | 3D map of the lobules | |||||||||||||||||||
7 | 01/19/2021 | Draft in Progress | | TMC-UF | Mark Atkinson | atkinson@ufl.edu | Spleen and LN mapping across age | 3D map of primary and secondary follicles with markers of T and B cell memory | |||||||||||||||||||
8 | 04/20/2021 | Published | | TTD-CalTech | Ruben Dries, Qian Zhu, Chee-Huat Linus Eng, Arpan Sarkar, Feng Bao, Rani E George, Nico Pierson, Long Cai, Guo-Cheng Yuan | Guo-Cheng Yuan | guo-cheng.yuan@mssm.edu | Giotto, a toolbox for integrative analysis and visualization of spatial expression data | Genome Biology | ||||||||||||||||||
9 | 10/20/2021 | Draft in Progress | | TTD-Purdue | Helminiak, Ye | DongHye Ye | donghye.ye@marquette.edu | DLADS 2.0 | Advanced development of DLADS | ||||||||||||||||||
10 | 10/20/2021 | Draft in Progress | | TTD-Purdue | Li, Laskin | Julia Laskin | jlaskin@purdue.edu | Development of a plastic microfluidic probe for nano-DESI MSI | |||||||||||||||||||
11 | 11/03/2021 | doi: https://doi.org/10.1021/acs.jproteome.1c00403) | | HIVE MC-NYGC | Bingjie Zhang, Avi Srivastava, Eleni Mimitou, Tim Stuart, Ivan Raimondi, Yuhan Hao, Peter Smibert, Rahul Satija | Rahul Satija | rsatija@nygenome.org | Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro | Introducing scCUT&Tag-pro (single-cell profiling of histone modifications and cell surface proteins), scChromHMM (inferring chromatin states in single cells), and an integrated reference of 9 molecular modalities in human PBMC | Published on bioRxiv, Under Review | |||||||||||||||||
12 | 11/16/2021 | Published | https://arxiv.org/abs/1911.02995 | | All | HuBMAP Consortium | Michael P Snyder | mpsnyder@stanford.edu | The human body at cellular resolution | Published in Nature | |||||||||||||||||
13 | 11/16/2021 | Draft in Progress | | TMC-VU-kidney | Elizabeth K. Neumann, Tina Tsui, N. Heath Patterson, Raf Van de Plas, Richard M. Caprioli, and Jeffrey M. Spraggins | Jeff Spraggins/Elizabeth Neumann | jeff.spraggins@vanderbilt.edu | Multimodal Imaging Quality Assurance/Control Methods for Reproducible Chemical Imaging | QA/QC Method for MALDI IMS | Target Journal: Analytical Chemistry or JASMS - Still in prep | |||||||||||||||||
14 | 11/16/2021 | Published | doi: https://doi.org/10.1038/s42003-021-01797-9) | | HIVE MC-NYGC | Hao Y*, Hao S*, Andersen-Nissen E, Mauck WM, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zagar M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LB, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P*, Satija R* | Rahul Satija | rsatija@nygenome.org | Integrated Analysis of Multimodal Single-Cell Data. Cell, 2021 | Introduces Azimuth and Seurat v4 | Published in Cell | ||||||||||||||||
15 | 11/16/2021 | Published | doi: https://doi.org/10.1101/2020.12.23.424201 | | HIVE MC-NYGC | Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z. Yeung, William M. Mauck III, Peter Smibert, and Rahul Satija | Rahul Satija | rsatija@nygenome.org | Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics | Published in Genome Biology | |||||||||||||||||
16 | 11/16/2021 | Published | https://biorxiv.org/cgi/content/short/2021.10.20.465151v1 | | HIVE TC-CMU | 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-Joseph | zivbj@cs.cmu.edu | Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. | Published in Cell Stem Cell | |||||||||||||||||
17 | 11/16/2021 | Published | https://biorxiv.org/cgi/content/short/2022.02.15.480384v1 | | HIVE TC-CMU | Component | Ziv Bar-Joseph | zivbj@cs.cmu.edu | Inferring TF activation order in time series scRNA-Seq studies. | Published in PLoS Xomput. Biol | |||||||||||||||||
18 | 11/16/2021 | Published | https://chemrxiv.org/engage/chemrxiv/article-details/60c74b12f96a001f0e287564 | | HIVE TC-CMU | Ding J, Lin C, Bar-Joseph Z. | Ziv Bar-Joseph | zivbj@cs.cmu.edu | Cell lineage inference from SNP and scRNA-Seq data. | Published in Nucleic Acid Res. | |||||||||||||||||
19 | 11/16/2021 | Published | https://chemrxiv.org/engage/chemrxiv/article-details/60c753234c89192bdfad427b | | HIVE TC-CMU | Lin C, Bar-Joseph Z. | Ziv Bar-Joseph | zivbj@cs.cmu.edu | Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data. | Published in Bioinformatics | |||||||||||||||||
20 | 11/16/2021 | Published | https://chemrxiv.org/engage/chemrxiv/article-details/610dc1ac45805dfc5a825394 | | HIVE TC-CMU | Rashid S, Shah S, Bar-Joseph Z, Pandya R. | Ziv Bar-Joseph | zivbj@cs.cmu.edu | Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data. | Published in Bioinformatics | |||||||||||||||||
21 | 11/16/2021 | Published | | TMC-VU-kidney | Marissa Jones, Sung Hoon Cho, Nathan Heath Patterson, Raf Van de Plas, Jeff Spraggins, Mark Boothby, and Richard Caprioli | Jeff Spraggins | jeff.spraggins@vanderbilt.edu | 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 | multimodal analysis of spleen | Published in Analytical Chemistry | |||||||||||||||||
22 | 11/16/2021 | Draft in Progress | | TMC-VU-kidney | Elizabeth K. Neumann, Leonoor Tidman, Lukasz Migas, N. Heath Patterson, Jamie Allen, Maya Brewer, Dave Anderson, Danielle Gutierrez, Raymond Harris, Mark deCastacker, Agnes Fogo, Joana Goncalves, Richard Caprioli, Raf van de Plas, Jeff Spraggins | Jeff Spraggins | jeff.spraggins@vanderbilt.edu | A Multimodal Molecular Functional Tissue Unit Atlas of the Human Kidney | Our V1 kidney atlas including MALDI IMS, AF microscopy, stained microscopy, CODEX, and RNAseq. Sptially driven data mining and analysis is based on larger functional tissue units including cortex, medulla, and glomeruli and span a wide range of molecular classes including lipidomics, proteomics and transcriptomics. | Would like to include in the Consortium Package | |||||||||||||||||
23 | 11/16/2021 | Draft in Progress | | TMC-VU-kidney | 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/Heath Patterson | jeff.spraggins@vanderbilt.edu | 3-D Multimodal IMS on Human Kidney | experimental and computational tools for generating high resolution 3-D multimodal molecular imaging data including IMS and microscopy | Would include as part of a consortium package if there are methods papers included for publication in secondary journals (e.g. Nature Methods). - Still in prep | |||||||||||||||||
24 | 11/16/2021 | Published | | TMC-CalTech | 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 Shendure | Jay Shendure | shendure@uw.edu | The single-cell transcriptional landscape of mammalian organogenesis | Published in Nature | ||||||||||||||||||
25 | 11/16/2021 | Submitted | bioRxiv 2021.09.13.460120; doi: https://doi.org/10.1101/2021.09.13.460120 | | HIVE MC-NYGC | Saket Choudhary, Rahul Satija | Rahul Satija | rsatija@nygenome.org | Comparison and evaluation of statistical error models for scRNA-seq | We provide recommendations for the usage of statistical error models in scRNA-seq analyses based on a meta-analyses of 58 datasets across technologies and systems | Submitted to Genome Biology | ||||||||||||||||
26 | 11/16/2021 | Submitted | | TMC-VU-kidney | Elizabeth Neumann, Emilio Rivera, Nathan Heath Patterson, Jamie Allen, Maya Brewer, Mark deCaestecker, Agnes Fogo, Richard Caprioli, Jeff Spraggins | Elizaabeth Neumann/Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Highly Multiplexed Immunofluorescence of the Human Kidney using Co-Detection by Indexing. | CODEX of human kidney | In review at Kidney International. Preprint on bioRxiv https://doi.org/10.1101/2020.12.04.412429 | |||||||||||||||||
27 | 11/16/2021 | Draft in Progress | | TMC-VU-kidney | Jarod Fincher, Katerian Djambazova, Dustin Klein, Martin Dufresne, Kukasz Migas, Raf Van de Plas, Richard Caprioli, Jeff Spraggins | Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Molecular Imaging of Neutral Lipids using Silicon Nanopost Arrays and Trapped Ion-Mobility Time-of-Flight Mass Spectrometry | Using Nanopost arrays and TIMS to visualize and differentiate lipid isobars and isomers in tissue | Target Journal: Analytical Chemistry | |||||||||||||||||
28 | 11/16/2021 | Draft in Progress | | TTD-Purdue | Yang,Li, Laskin | Julia Laskin | jlaskin@purdue.edu | Correlative imaging of lipids and proteins | |||||||||||||||||||
29 | 11/16/2021 | Published | | HIVE TC-CMU | J Ding, Z Bar-Joseph. | Ziv Bar-Joseph | zivbj@andrew.cmu.edu | Analysis of time series regulatory networks . Current Opinion in Systems Biology. , 21, Pages 16-24, 2020 | |||||||||||||||||||
30 | 11/16/2021 | Published | | HIVE TC-CMU | H. Zafar, C. Lin, Z. Bar-Joseph. | Ziv Bar-Joseph | zivbj@andrew.cmu.edu | Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data Nature Communications , 11:3055, 2020 | |||||||||||||||||||
31 | 11/16/2021 | Published | | HIVE TC-CMU | C. Lin, J. Ding, Z. Bar-Joseph. | Ziv Bar-Joseph | zivbj@andrew.cmu.edu | Inferring TF activation order in time series scRNA-Seq studies PLoS Comput Biol. , 16(2):e1007644, 2020 | |||||||||||||||||||
32 | 11/16/2021 | Published | | HIVE TC-CMU | G. Songwei, H. Wang, A. Alavi, E. Xing and Z. Bar-Joseph | Ziv Bar-Joseph | zivbj@andrew.cmu.edu | Supervised Adversarial Alignment of Single-Cell RNA-seq Data Journal of Computational Biology , Online ahead of print, 2021 | Original version appeared in Proceedings of the 24th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp 72-87, 2020 | ||||||||||||||||||
33 | 11/16/2021 | | HIVE TC-CMU | Y. Yuan and Z. Bar-Joseph. | Ziv Bar-Joseph | zivbj@andrew.cmu.edu | Deep learning of gene relationships from single cell time-course expression data. Briefings in Bioinformatics. In press, 2021 | ||||||||||||||||||||
34 | 11/16/2021 | Concept | | TTD-Purdue | Li, Laskin | Julia Laskin | jlaskin@purdue.edu | Nano-DESI Imaging with High THroughput and High Spatial Resolution | High throughput/high resolution nano-DESI imaging | ||||||||||||||||||
35 | 11/16/2021 | Published | https://www.biorxiv.org/content/10.1101/2021.08.10.455720v1 | | TTD-PNNL-Shi | Chia-Feng Tsai, Pengfei Zhang, David Scholten, Kendall Martin, Yi-Ting Wang, Rui Zhao, William B. Chrisler, Dhwani B. Patel, Maowei Dou, Yuzhi Jia, Carolina Reduzzi, Xia Liu, Ronald J. Moore, Kristin E. Burnum-Johnson, Miao-Hsia Lin, Chuan-Chih Hsu, Jon M. Jacobs, Jacob Kagan, Sudhir Srivastava, Karin D. Rodland, H. Steven Wiley, Wei-Jun Qian, Richard D. Smith, Ying Zhu, Massimo Cristofanilli, Tao Liu, Huiping Liu & Tujin Shi | Tujin Shi | Tujin.Shi@pnnl.gov | Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics | The developed surfactant-assisted one-pot sample preparation coupled with mass spectrometry (SOP-MS) method enables routine and precise quantitative single-cell proteomics without transfer of samples minimizing sample loss. | Published: Commun Biol. 2021, 4, 265. doi: 10.1038/s42003-021-01797-9 | ||||||||||||||||
36 | 11/16/2021 | Published | https://www.biorxiv.org/content/10.1101/2021.09.08.459490v1 | | TTD-PNNL-Shi | Kendall Martin, Tong Zhang, Tai-Tu Lin, Amber N. Habowski, Rui Zhao, Chia-Feng Tsai, William B. Chrisler, Ryan L. Sontag, Daniel J. Orton, Yong-Jie Lu, Karin D. Rodland, Bin Yang, Tao Liu, Richard D. Smith, Wei-Jun Qian, Marian L. Waterman, H. Steven Wiley, Tujin Shi | Tujin Shi | Tujin.Shi@pnnl.gov | Facile one-pot nanoproteomics for label-free proteome profiling of 50-1000 mammalian cells | The developed one-pot nanoproteomics enables a facile and robust sample preparation method towards deep proteome profiling of small numbers of cells and low-input samples. | Published: J. Proteome Res. 2021, 20, 9, 4452–4461 doi.: 10.1021/acs.jproteome.1c00403 | ||||||||||||||||
37 | 11/16/2021 | Submitted | https://www.biorxiv.org/content/10.1101/507566v1.full | | TMC-Stanford | Maria Brbic, Kaidi Cao, John Hickey, Yuqi Tan, Mike Snyder, Garry Nolan, Jure Leskovec | John Hickey | jwhickey@stanford.edu | Location-Aware Annotation of Spatially ResolvedSingle-cell Datasets with Geometric Deep Learning | Geometric deep learning for transferring cell type labels and discovering new ones in other spatial datasets | Would like to be a part of the package | ||||||||||||||||
38 | 11/16/2021 | Published | https://www.biorxiv.org/content/10.1101/576827v2 | | TMC-Stanford | John Hickey, Yuqi Tan, Yury Goltsev, Garry Nolan | John Hickey | jwhickey@stanford.edu | Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data | Comparison of normalization and unsupervised clustering techniques for CODEX Multiplexed imaging data | Published in Frontiers Immunology | ||||||||||||||||
39 | 11/16/2021 | Published | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941488/ | | TMC-VU-kidney | Elizabeth K. Neumann, Lukasz G. Migas, Jamie L. Allen, Richard M. Caprioli, Raf Van de Plas, and Jeffrey M. Spraggins | Jeff Spraggins/Elizabeth Neumann | jeff.spraggins@vanderbilt.edu | Spatial Metabolomics of the Human Kidney using MALDI Trapped Ion Mobility Imaging Mass Spectrometry | MALDI IMS of small metabolites in human kdiney | Published in Analytical Chemistry | ||||||||||||||||
40 | 11/16/2021 | Published | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6946663/ | | TMC-VU-kidney | Josiah McMillen, Jarod Fincher, Dustin Klein, Jeff Spraggins, Richard Caprioli | Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Effect of MALDI matrices on lipid analysis of biological tissues using MALDI-2 postionization mass spectrometry | Published in the Journal of Mass Spectrometry | |||||||||||||||||
41 | 11/16/2021 | Submitted | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8553253/ | | TMC-VU-kidney | Josiah Mc Millen, Danielle Gutierrez, Audra Judd, Jeff Spraggins, Richard Caprioli | Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Enhancement of tryptic peptide signals from tissue sections using MALDI IMS post-ionization (MALDI-2) | utalization of MALDI-2 for improving sensitivity of typtic peptide IMS experiments | In review at Analytical Chemistry | ||||||||||||||||
42 | 11/16/2021 | Draft in Progress | | TMC-VU-kidney | Nathan Heath Patterson, Elizabeth Neumann, Kavya Sharman, David Anderson, Jamie Allen, Maya Brewer, Mark deCastecker, Richard Caprioli, Raf Van de Plas, Jeff Spraggins | Heath Patterson/Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Autofluorescnec microscopy as a label free tool for renal histology and glomerular segmentation | Developing methods for AF microscopy segmentation of fuctional tissue units in the human kidney. | Submitting to Kidney International as a technical note in Feb 2021. | |||||||||||||||||
43 | 11/16/2021 | Published | | TMC-VU-eye,pancreas | 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 Spraggins | jeff.spraggins@vanderbilt.edu | Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. | published in Diabetologia | ||||||||||||||||||
44 | 11/16/2021 | Published | | TMC-VU-kidney | Ryan DJ, Spraggins JM, Caprioli RM. | Richard Caprioli | richard.m.caprioli@Vanderbilt.Edu | Protein identification strategies in MALDI imaging mass spectrometry: a brief review. | Published in Curr Opin Chem Biol | ||||||||||||||||||
45 | 11/16/2021 | Published | | TMC-VU-kidney | Prentice BM, McMillen JC, Caprioli RM | Richard Caprioli | richard.m.caprioli@Vanderbilt.Edu | Multiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry. | Published in Int J Mass Spectrom | ||||||||||||||||||
46 | 11/16/2021 | Published | | TMC-VU-kidney | Emilio S. Rivera, Kate V. Djambazova, Elizabeth K. Neumann, Richard M. Caprioli, Jeff M. Spraggins | Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Integrating Ion Mobility and Imaging Mass Spectrometry for Comprehensive Analysis of Biological Tissues: A brief review and perspective | Review on ion mobility IMS | Published in the Journal of Mass Spectrometry | |||||||||||||||||
47 | 11/16/2021 | Published | | TMC-VU-kidney | Elizabeth K. Neumann, Kate V. Djambazova, Richard M. Caprioli, Jeff M. Spraggins | Jeff Spraggins/Elizabeth Neumann | jeff.spraggins@vanderbilt.edu | Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine | Review on multimodal IMS | Published in the Journal of the American Society of Mass Spectrometry | |||||||||||||||||
48 | 11/16/2021 | Published | | TMC-VU-eye,pancreas | Mirazul Islam, Bob Chen, Jeff Spraggins, Ryan Kelly, Ken Lau | Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Use of single cell-omic technologies to study the gastrointestical tract and diseases, from single cell identities to patient features | review | Published in Gastroenterology | |||||||||||||||||
49 | 11/16/2021 | Submitted | | TMC-VU-kidney | Lee HH, Tang Y, Xu K, Bao S, Fogo AB, Harris R, deCaestecker MP, Heinrich M, Spraggins JM, Huo Y, and Landman BA | Bennett Landman/Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Multi-Contrast Computed Tomography Healthy Kidney Atlas | average anatomical atlas of human kidney | In review at IEEE Transactions on Biomedical Engineering | |||||||||||||||||
50 | 11/16/2021 | Submitted | | TMC-VU-kidney | Tang Y, Bao S, Gao R, Mathurin C, Lee HH, Yu X, Nath V, Savoie BV, Huo Y, Xu Z, Harris R, de Caestecker MP, Spraggins JM, Fogo AB, and Landman BA | Bennett Landman/Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Automatic Segmentation of the Renal Cortex, Medulla and Pelvicalyceal System with Deep Neural Networks: Assessment of Quantitative Measurements and Reproducibility | Methods for segmenting histological regions of the kidney from CT scans | In review at Radiology: Artificial Intelligence | |||||||||||||||||
51 | 11/16/2021 | Draft in Progress | | TMC-VU-kidney | Elizabeth Neumann, Kavya Sharman, Nathan Heath Patterson, Andy Weiss, Jamie Allen, Jessica Sheldon, Raf Van de Plas, Richard Caprioli, Eric Skaar, and Jeff Spraggins | Jeff Spraggins | jeff.spraggins@vanderbilt.edu | Deciphering Host Immune Responses with MALDI IMS and CODEX Immunofluorescence | Multimdoal imaging (IMS, CODEX, AF, Stained Microscopy) of staph infected tissues. Using this analysis pipeline to uncover molecular profiles associated with specific cell types and FTUs in the tissue microenvironment | Target Journal: Nature Methods | |||||||||||||||||
52 | 11/16/2021 | Draft in Progress | | TMC-UF | Mark Atkinson | atkinson@ufl.edu | T follicular helper cells in human spleen and lymph nodes | Mapping of these cells in context of maturity of immune system has not been done in humans | |||||||||||||||||||
53 | 11/16/2021 | Published | | HIVE TC-CMU | Y. Yuan, Z. Bar-Joseph | Ziv Bar-Joseph | zivbj@andrew.cmu.edu | GCNG: Graph convolutional networks for inferring cell-cell interactions Genome Biology , 21(1):300, 2020 | |||||||||||||||||||
54 | 11/16/2021 | Published | | HIVE TC-CMU | D. Li, J. Ding, Z. Bar-Joseph | Ziv Bar-Joseph | zivbj@andrew.cmu.edu | Identifying signaling genes in spatial single cell expression data. Bioinformatics , in press, 2020 | |||||||||||||||||||
55 | 11/16/2021 | Published | | HIVE TC-CMU | A. Alavi, Z. Bar-Joseph. | Ziv Bar-Joseph | zivbj@andrew.cmu.edu | Iterative point set registration for aligning scRNA-seq data. PLoS Comput Biol. , 16(10):e1007939, 2020 | |||||||||||||||||||
56 | 11/30/2021 | Draft in Progress | https://osf.io/z9gm3/ | | HIVE TC-HMS | HIVE team | Nils Gehlenborg | nils@hms.harvard.edu | HuBMAP Data Portal: A Resource for Multi-Modal Spatial and Single-Cell Data of Human Tissues | Manuscript introducing the HuBMAP Portal | |||||||||||||||||
57 | 12/03/2021 | Published | https://www.nature.com/articles/s41592-019-0404-0 | | TTD-Harvard | Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P. | Jocelyn Kishi | Jocelyn.Kishi@wyss.harvard.edu | SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. | Published in Nat. Methods | |||||||||||||||||
58 | 12/06/2021 | Published | https://www.sciencedirect.com/science/article/pii/S0092867420313908?via%3Dihub | | TTD-Yale | Liu Y#, Yang M#, Deng Y#, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. | Rong Fan | rong.fan@yale.edu | High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue | Deterministic barcoding in tissue enables NGS-based spatial multi-omics mapping. DBiT-seq identified spatial patterning of major tissue types in mouse embryos. Revealed retinal pigmented epithelium and microvascular endothelium at cellular level. Direct integration with scRNA-seq data allows for rapid cell type identification | |||||||||||||||||
59 | 12/06/2021 | Draft in Progress | https://www.biorxiv.org/content/10.1101/2020.10.13.338475v2 | | TTD-Yale | Liu Y, Enninful A, Deng Y, Fan R. Spatial transcriptome sequencing of FFPE tissues at the cellular level. | Rong Fan | rong.fan@yale.edu | Spatial transcriptome sequencing of FFPE tissues at cellular level | we demonstrated spatial transcriptome sequencing of embryonic and adult mouse FFPE tissue sections at cellular level (25μm pixel size) with high coverage (>1,000 genes per pixel). Spatial transcriptome of an E10.5 mouse embryo identified all major anatomical features in the brain and abdominal region. Integration with singlecell RNA-seq data for cell type identification indicated that most tissue pixels were dominated by single-cell transcriptional phenotype. | Currently under review in Nature Biotechnology 2021 | ||||||||||||||||
60 | 12/06/2021 | Draft in Progress | | TTD-Yale | Liu Y, Fan R. | Rong Fan | rong.fan@yale.edu | Liu Y, Fan R. High-plex antibody based spatial protein sequencing of human tonsil | To be sumitted to Nature Methods. 2021 | ||||||||||||||||||
61 | 12/06/2021 | Submitted | https://doi.org/10.1101/2021.03.11.434985 | | TTD-Yale | Deng Y, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Fan R. | Rong Fan | rong.fan@yale.edu | Spatial Epigenome Sequencing at Tissue Scale and Cellular Level | Currently under review | |||||||||||||||||
62 | 12/06/2021 | Submitted | https://doi.org/10.1101/2021.06.06.447244 | | TTD-Yale | Deng Y, Bartosovic M, Ma S, Zhang D, Liu Y, Qin X, Su G, Xu M, Halene S, Craft J, Castelo-Branco G, Fan R. | Rong Fan | rong.fan@yale.edu | Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level | Currently under review | |||||||||||||||||
63 | 12/28/2021 | Published | doi: https://doi.org/10.1101/2021.07.16.452703 | | HIVE MC-NYGC | C Hafemeister†, R Satija† | Rahul Satija | rsatija@nygenome.org | Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression | Published in Genome Biology | |||||||||||||||||
64 | 12/28/2021 | Published | doi: https://doi.org/10.1101/2021.07.28.454201 | | HIVE MC-NYGC | T Stuart*, A Butler*, P Hoffman, C Hafemeister, E Papalexi, WM Mauck, M Stoeckius, P Smibert, R Satija† | Rahul Satija | rsatija@nygenome.org | Comprehensive Integration of Single-Cell Data | Published In Cell | |||||||||||||||||
65 | 12/28/2021 | Published | https://arxiv.org/abs/2005.00595 | | HIVE MC-NYGC | 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 Satija | rsatija@nygenome.org | Towards a Common Coordinate Framework for the Human Body | Published In Cell | |||||||||||||||||
66 | 12/28/2021 | Submitted | https://arxiv.org/abs/2102.12030 | | HIVE MC-NYGC | Alsu Missarova, Jaison Jain, Andrew Butler, Shila Ghazanfar, Tim Stuart, Maigan Brusko, Clive Wasserfall, Henry Nick, Todd Brusko, Mark Atkinson, Rahul Satija, John Marioni | John Marioni | john.marioni@ebi.ac.uk | geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq | wW have developed a novel cluster-free, batch-aware and flexible approach, geneBasis, which takes scRNA-seq data and the number of genes to be selected and returns a ranked gene panel of the designated size. Importantly, we provide a comprehensive set of metrics – at multiple levels of granularity - that can be used to assess the completeness of the suggested panel. | Submitted to Genome Biology | ||||||||||||||||
67 | 12/28/2021 | Published | https://arxiv.org/abs/2112.02159 | | HIVE MC-NYGC, TTD-Caltech | T. Lohoff, S. Ghazanfar, A. Missarova, N. Koulena, N. Pierson, J. A. Griffiths, E. S. Bardot, C.-H. L. Eng, R. C. V. Tyser, R. Argelaguet, C. Guibentif, S. Srinivas, J. Briscoe, B. D. Simons, A.-K. Hadjantonakis, B. Göttgens, W. Reik, J. Nichols, L. Cai & J. C. Marioni | John Marioni | john.marioni@ebi.ac.uk | Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis | We apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8–12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo , and characterize fundamental steps in the patterning of the midbrain–hindbrain boundary (MHB) and the developing gut tube. | Published; Nature Biotechnology (2021) | ||||||||||||||||
68 | 02/14/2022 | Published | 10.26434/chemrxiv.12494705.v1 | | Cross-consortia | John W. Hickey, Elizabeth K. Neumann, Andrea J. Radtke, Jeannie M. Camarillo, Rebecca T. Beuschel,Alexandre Albanese, Elizabeth McDonough, Julia Hatler, Anne E. Wiblin, Jeremy Fisher, Josh Croteau, Anup Sood, Richard M. Caprioli, R. Michael Angelo, Garry P. Nolan, Kwanghun Chung, Stephen M. Hewitt, Ronald N. Germain, Jeffrey M. Spraggins, Emma Lundberg, Mike P. Snyder, Neil L. Kelleher, Sinem K. Saka | Sinem Saka | sinem.saka@embl.de | Spatial mapping of protein composition and tissue organization: A primer for multiplexed antibody-based imaging | A primer and guide for multiplexed antibody-based imaging | arXiv: https://arxiv.org/abs/2107.07953 (posted on 16 July 2021) Accepted to Nature Methods on 03.08.2021 | ||||||||||||||||
69 | 2/15/22 | Concept | | TMC-UCSD-Zhang | Gloria Pryhuber | gloria_pryhuber@urmc.rochester.edu | Description of process and outcome of Policy WG for HuBMAP Consortium | Looking for co-authors | |||||||||||||||||||
70 | 02/17/2022 | Submitted | | TTD-UCSD | Xu Chen, Riccardo Calandrelli, John Girardini, Zhangming Yan, Zhiqun Tan, Xiangmin Xu, Annie Hiniker, Sheng Zhong | Sheng Zhong | szhong@ucsd.edu | PHGDH expression increases with progression of Alzheimer’s disease pathology and symptoms | Combining single-cell nucleus RNA-seq, spatial protein staining to reveal a consistent increase of phosphoglycerate dehydrogenase (PHGDH) mRNA and protein levels in two mouse models and four human cohorts in Alzheimer’s disease brains compared to age- and sex-matched control brains. Remarkably, the increase of PHGDH expression in human brain correlates with symptomatic development and disease pathology. | Accepted | |||||||||||||||||
71 | 02/23/2022 | Published | https://www.nature.com/articles/s41587-019-0207-y | | TTD-Harvard | 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 Saka | sinem.saka@wyss.harvard.edu | Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues | Published in Nature Biotechnology | |||||||||||||||||
72 | 03/07/2022 | Published | | TTD-Purdue | David Helminiak, Hang Hu, Julia Laskin, DongHye Ye | DongHye Ye | donghye.ye@marquette.edu | Deep Learning Approach for Dynamic Sparse Sampling for High-Throughput Mass Spectrometry Imaging | First paper on DLADS | Published In: Proceedings of the 2021 IS&T International Symposium on Electronic Imaging (EI 2021), January 18–22, 2021 | |||||||||||||||||
73 | 03/07/2022 | Published | | TTD-Purdue | R. Yin, K. E. Burnum-Johnson, X. Sun, S. K. Dey, J. Laskin | Julia Laskin | jlaskin@purdue.edu | High Spatial Resolution Imaging of Biological Tissues Using Nanospray Desorption Electrospray Ionization Mass Spectrometry | Nat. Protoc. 14, 3445–3470 (2019). DOI: 10.1038/s41596-019-0237-4 | featured on the cover of Nature Protocols | |||||||||||||||||
74 | 03/07/2022 | Published | | TTD-Purdue | 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-Johnson | kristin.burnum-johnson@pnnl.gov | Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution | Nat Commun 11, 8 (2020). https://doi.org/10.1038/s41467-019-13858-z | ||||||||||||||||||
75 | 03/08/2022 | Published | https://doi.org/10.1038/s41587-019-0290-0 | | TMC-UCSD | Chen S, Lake BB, Zhang K. | Song Chen | sochen@ucsd.edu | High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell | Published in Nature Biotechnology | |||||||||||||||||
76 | 03/14/2022 | Published | https://arxiv.org/abs/2112.02159 | https://doi.org/10.3389/frvir.2021.727344 | Kidney, male, left: https://doi.org/10.48539/hbm792.npxx.335 RUI experiment + Luddy: https://doi.org/10.5281/zenodo.5658725 RUI control: https://doi.org/10.5281/zenodo.5189516 | | HIVE MC-IU | Bueckle, Andreas, Kilian Buehling, Patrick C. Shih, Katy Börner | Andreas Bueckle | abueckle@iu.edu | Optimizing Performance and Satisfaction in Matching and Movement Tasks in Virtual Reality with Interventions Using the Data Visualization Literacy Framework | Published in Frontiers in Virtual Reality: https://doi.org/10.3389/frvir.2021.727344 | |||||||||||||||
77 | 03/15/2022 | Submitted | https://osf.io/y8thv/ | | HIVE TC-HMS | Nils Gehlenborg | nils@hms.harvard.edu | User-Centric Process of Designing a Molecular & Cellular Query Interface for Biomedical Research | Description of the design process and results for the molecular and cellular query interface in the HuBMAP portal | ||||||||||||||||||
78 | 03/15/2022 | Submitted | https://www.biorxiv.org/content/10.1101/2021.08.16.456524v2 | TMC-UCSD-Zhang | Brendon R Lutnick, David Manthey, Jan U Becker, Brandon Ginley, Katharina Moos, Jonathan E Zuckerman, Luis Rodrigues, Alexander J Gallan, Laura Barisoni, Charles E Alpers, Xiaoxin Wang, Komuraiah Myakala, Bryce A Jones, Moshe Levi, Jeffrey B Kopp, Teruhiko Yoshida, Seung Seok Han, Sanjay Jain, Avi Z Rosenberg, Kuang Yu Jen, Pinaki Sarder, for the Kidney Precision Medicine Project | Pinaki Sarder | pinakisa@buffalo.edu | A user-friendly tool for cloud-based whole slide image segmentation, with examples from renal histopathology | An automated online tool for end-users for segmentation of tissue micro-compartments from brightfield microscopy tissue biopsy images, with opportunity to improve segmentation via human AI interaction via using an interactive training method. Tool has been tested extensively in kidney tissues and in paraffin sections. It can be easily extended for frozen sections and other organ systems. The source code is available on GitHub at https://github.com/SarderLab/Histo-cloud, and packaged as a pre-built Docker image https://hub.docker.com/r/sarderlab/histo-cloud. This data sharing allows for easy deployment on a remote server for use as well as further development by the community over the web. Additionally, a publicly available instance of Histo-Cloud is available for the community at: athena.ccr.buffalo.edu. All the models described are available in the <Collections> section in the <Segmentation models> folder on athena.ccr.buffalo.edu or at https://bit.ly/3ejZhab. Documentation for using this tool is available at https://bit.ly/3nNMpfH. A video overview of Histo-Cloud is available at https://bit.ly/3r5GrZr. | In revision | |||||||||||||||||
79 | 03/17/2022 | Draft in Progress | | TMC-CHOP | TBD, representing the CHOP TMC heart team | Liming Pei | peil@chop.edu | A multimodal atlas of human heart at single-cell resolution | |||||||||||||||||||
80 | 03/17/2022 | Submitted | https://www.biorxiv.org/content/10.1101/2021.01.25.427845v1 | | TMC-CHOP | Pang M, Peng T, Chen GM, Tan K | Kai Tan | tank1@chop.edu | GLUER: integrative analysis of single-cell omics and imaging data by deep neural network | ||||||||||||||||||
81 | 03/17/2022 | Published | https://www.science.org/doi/10.1126/sciadv.abf1356?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed | | TMC-CHOP | Hu Y, Peng T, Gao L, Tan K | Kai Tan | tank1@chop.edu | CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data | ||||||||||||||||||
82 | 03/17/2022 | Published | https://genome.cshlp.org/content/31/1/101.long | | TMC-CHOP | Uzun Y, Wu H, Tan K | Kai Tan | tank1@chop.edu | Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data | ||||||||||||||||||
83 | 03/17/2022 | Published | https://opg.optica.org/oe/fulltext.cfm?uri=oe-30-2-2453&id=468365 | | TMC-CHOP | Xie H, Pan Z, Zhou L, Zaman FA, Chen DZ, Jonas JB, Xu W, Wang Y, Wu X | Xiaodong Wu | xiaodong-wu@uiowa.edu | Globally optimal OCT surface segmentation using a constrained IPM optimization | ||||||||||||||||||
84 | 03/21/2022 | Submitted | https://www.biorxiv.org/content/10.1101/2021.10.20.465151v1 | | TMC-UF | Seth Currlin, Harry S. Nick, Marda Jorgensen, Jerelyn A. Nick, Maigan A. Brusko, Hunter Hakimian, Jesus Penaloza-Aponte, Natalie Rodriguez, Miguel Medina-Serpas, Mingder Yang, Irina Kusmartseva, Todd M. Brusko, Kevin Otto, Amanda L. Posgai, Clive H. Wasserfall, View ORCID ProfileMark A. Atkinson | Mark Atkinson | atkinson@ufl.edu | Innervation of human spleen, thymus and LN | light sheet mapping of nerves and blood vessels | https://biorxiv.org/cgi/content/short/2021.10.20.465151v1 | ||||||||||||||||
85 | 04/04/2022 | Submitted | https://osf.io/gzu27/ | | HIVE TC-HMS | Nils Gehlenborg | nils@hms.harvard.edu | Drava: Disentangled Representation Learning as A Visual Analysis Approach for Concept-Driven Exploration of Small Multiples | |||||||||||||||||||
86 | 04/04/2022 | Submitted | https://osf.io/b76nt/ | | HIVE TC-HMS | Nils Gehlenborg | nils@hms.harvard.edu | Polyphony: an Interactive Transfer Learning Framework for Single Cell Data Integration and Analysis | |||||||||||||||||||
87 | 04/04/2022 | Published | https://arxiv.org/abs/2005.00595 | https://doi.org/10.1109/TVCG.2020.3028948 | | HIVE TC-HMS | Nils Gehlenborg | nils@hms.harvard.edu | A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling | Generalized visualization framework for small multiple visualization. | |||||||||||||||||
88 | 04/14/2022 | Submitted | High-throughput Nano-DESI Mass Spectrometry Imaging of Biological Tissues Using an Integrated Microfluidic Probe | Analytical Chemistry | ChemRxiv | Cambridge Open Engage | | TTD-Purdue | X. Li, H. Hu, R. Yin, Y. Li, X. Sun, S. K. Dey, and J. Laskin | Julia Laskin | jlaskin@purdue.edu | High-throughput Nano-DESI Mass Spectrometry Imaging of Biological Tissues Using an Integrated Microfluidic Probe | ||||||||||||||||||
89 | 04/14/2022 | Published | https://chemrxiv.org/articles/An_Integrated_Microfluidic_Probe_for_Mass_Spectrometry_Imaging_of_Biological_Samples/12275507 | | TTD-Purdue | X. Li, R. Yin, H. Hu, Y. Li, X. Sun, S.K. Dey, and J. Laskin | Julia Laskin | jlaskin@purdue.edu | An Integrated Microfluidic Probe for Mass Spectrometry Imaging of Biological Samples | Angew. Chem., 59, 22388-22391 (2020). DOI: 10.1002/anie.202006531 | submitted to Angew Chem and ChemRxiv: https://chemrxiv.org/articles/An_Integrated_Microfluidic_Probe_for_Mass_Spectrometry_Imaging_of_Biological_Samples/12275507 | ||||||||||||||||
90 | 04/14/2022 | Published | https://chemrxiv.org/engage/chemrxiv/article-details/60c753234c89192bdfad427b | | TTD-Purdue | Hang Hu, Ruichuan Yin, Hilary M. Brown, Julia Laskin | Julia Laskin | jlaskin@purdue.edu | Spatial Segmentation of Mass Spectrometry Imaging Data by Combining Multivariate Clustering and Univariate Thresholding | New method for the automated segmentation of MSI data | Published: Anal Chem, 2021 DOI:10.1021/acs.analchem.0c04798; Chemrxiv: https://chemrxiv.org/engage/chemrxiv/article-details/60c753234c89192bdfad427b | ||||||||||||||||
91 | 04/14/2022 | Published | https://chemrxiv.org/engage/chemrxiv/article-details/610dc1ac45805dfc5a825394 | | TTD-Purdue | Hang Hu, Ruichuan Yin, Hilary M. Brown, Julia Laskin | Julia Laskin | jlaskin@purdue.edu | Self-supervised Clustering of Mass Spectrometry Imaging Data Using Contrastive Learning | New approach for self-supervised classification of mass spec imaging data using contrastive learning | Advance article in Chemical Science: https://pubs.rsc.org/en/Content/ArticleLanding/2021/SC/D1SC04077D, Chemrxiv: https://chemrxiv.org/engage/chemrxiv/article-details/610dc1ac45805dfc5a825394 | ||||||||||||||||
92 | 04/19/2022 | Published | PhD thesis; no preprint | https://www.doi.org/10.13140/RG.2.2.33214.00328 | Kidney, male, left: https://doi.org/10.48539/hbm792.npxx.335 RUI experiment + Luddy: https://doi.org/10.5281/zenodo.5658725 RUI control: https://doi.org/10.5281/zenodo.5189516 | | HIVE MC-IU | Andreas Bueckle | Katy Börner | katy@indiana.edu | Optimizing performance and satisfaction in virtual reality environments with interventions using the data visualization literacy framework (PhD thesis) | Defended and published | |||||||||||||||
93 | 04/19/2022 | Draft in Progress | | HIVE MC-IU | Quardokus|Caron|Balhoff|Hardi|Roncaglia|Musen|Herr|Osumi-Sutherland | David Osumi-Sutherland | davidos@ebi.ac.uk | A general strategy for generating expert-guided, simplified views of ontologies | Abstract The use of common biomedical ontology standards within and across different communities improves data integration. Expanding to fit the needs of these multiple communities and to conform to good engineering practices required for scalable development, means that widely used biomedical ontologies inevitably become larger, and more complex than the immediate requirements of individual communities and users. This can often make ontologies daunting for non-experts to use, even with tooling that lowers the barriers to searching and browsing. We, therefore, need mechanisms to provide simple, tailored views of these ontologies - limiting the displayed classes and relationship types. The ASCT+B tables are an expert-curated resource detailing human anatomical structures, cell types, biomarkers, and their relationships to each other. These tables support the development of a 3D atlas of human anatomy, integrating diverse omics analysis datasets, many at the single-cell level, using a combination of semantic and image/coordinate based approaches. Entries in these tables are mapped to the multi-species anatomy ontology Uberon, and the Cell Ontology (CL). Here we describe a method for validating these tables against the CL and Uberon, using the results to harmonise and improve both tables and source ontologies and to drive the generation of a simplified, combined view of Uberon and CL in which all relationships are true according to the semantics of the source ontologies. | Partial text | |||||||||||||||||
94 | 04/19/2022 | Submitted | https://osf.io/wd2gu/ | | HIVE TC-HMS | Nils Gehlenborg | nils@hms.harvard.edu | Viv: Multiscale Visualization of High-Resolution Multiplexed Tissue Data on the Web | Advanced imaging data visualization with modern web technologies. | Submitted | |||||||||||||||||
95 | 04/19/2022 | Published | https://arxiv.org/abs/2102.12030 | https://doi.org/10.1371/journal.pone.0258103 | https://doi.org/10.5281/zenodo.5189516 Kidney, male, left: https://doi.org/10.48539/hbm792.npxx.335 | | HIVE MC-IU | Andreas Bueckle, Kilian Buehling, Patrick C. Shih Katy Börner | Katy Börner | katy@indiana.edu | 3D Virtual Reality vs. 2D Desktop Registration User Interface Comparison | Published in PLOS ONE | |||||||||||||||
96 | 04/19/2022 | Published | https://www.biorxiv.org/content/10.1101/2021.05.31.446440v1 | https://www.nature.com/articles/s41556-021-00788-6 | Requested new DOI for 1st and 2nd ASCT+B and 3D ref organ release from IEC DOIs for 11 ASCT+B tables and 26 organs see https://static-content.springer.com/esm/art%3A10.1038%2Fs41556-021-00788-6/MediaObjects/41556_2021_788_MOESM1_ESM.pdf | | HIVE MC-IU | Katy Börner, Sarah A. Teichmann, Ellen M. Quardokus, James Gee, Kristen Browne, David Osumi-Sutherland, Bruce W. Herr II, Andreas Bueckle, Hrishikesh Paul, Muzlifah A. Haniffa, Laura Jardine, Amy Bernard, Song-Lin Ding, Jeremy A. Miller, Shin Lin, Marc K. Halushka, Avinash Boppana, Teri A. Longacre, John Hickey, Yiing Lin, M. Todd Valerius, Yongqun He, Gloria Pryhuber, Xin Sun, Marda Jorgensen, Andrea J. Radtke, Clive Wasserfall, Fiona Ginty, Jonhan Ho, Joel Sunshine, Rebecca T. Beuschel, Maigan Brusko, Sujin Lee, Rajeev Malhotra, Sanjay Jain, Griffin Weber | Katy Börner | katy@indiana.edu | Anatomical Structures, Cell Types, and Biomarkers of the Human Reference Atlas | Published in Nature Cell Biology | |||||||||||||||
97 | 04/28/2022 | Draft in Progress | | TMC-PNNL | Swensen AC, Chen J, Campbell-Thompson M, Mathews CE, Qian W | Weijun Qian | Weijun.Qian@pnnl.gov | Endoplasmic Reticulum Dysfunction and Translational Deficiency in Islets of Subjects with Pre-symptomatic Stage 1 Type 1 Diabetes Revealed by Nanoproteomics Profiling | Prior to the onset of type-1 diabetes (T1D) we know little of the molecular changes that occur in human islets . Herein, we applied a nanoproteomics approach to identify proteomic changes in human islets of subjects with pre-symptomatic T1D. Islet sections were collected through laser microdissection (LMD) of frozen pancreatic tissues of organ donors positive for islet autoantibodies compared to age/sex-matched controls. The overall analyses revealed alterations associated with several major functions, including reduced translation and protein synthesis, ER dysfunction and stress, increased immune response, cell death, and increased compensatory upregulation in metabolism and exocytosis. | ||||||||||||||||||
98 | 05/19/2022 | Draft in Progress | TMC-UCSD-Laurent | TMC-UCSD-Laurent | Scott Lindsay-Hewett, Cayla Mason, Bill Flynn, Valentina Stanley, Marni Jacobs, Ana Rodriguez-Soto, Chanond Nasamran, Elise Courtois, Santhosh Sivajothi, Rebecca Rakow-Penner, Paul Robson, Mana Parast, Louise Laurent, Kathleen Fisch | Kathleen Fisch | kfisch@health.ucsd.edu | A spatially-resolved multimodal atlas of the human term placenta | Version 1 of the human placenta atlas includes bulk RNAseq, bulk ATACseq, 10x multiome, single cell RNAseq, IMC, GeoMX spatial transcriptomics, MRI, ultrasound, ECM proteomics from 4 regions from each placenta including maternal and fetal surface from two regions, balanced with fetal sexes and mode of delivery (cesarian vs vaginal) | ||||||||||||||||||
99 | 06/22/2022 | Published | https://doi.org/10.1016/j.aca.2021.338522 | | TMC-VU-kidney | Leonoor Tideman, Lukasz Migas, Katerina Djambazova, Nathan Heath Patterson, Richard Caprioli, Jeff Spraggins, Raf Van de Plas | Raf Van de Plas/Jeff Spraggins | raf.vandeplas@tudelft.nl | Automated Biomarker Candidate Discovery in Imaging Mass Spectrometry Data Through Spatially Localized Shapley Additive Explanations | Interpretive machinel learning for IMS data mining | In review at Analytica Chimica Acta. Preprint available on bioRxiv at https://doi.org/10.1101/2020.12.23.424201 | ||||||||||||||||
100 | 06/23/2022 | Submitted | https://chemrxiv.org/engage/chemrxiv/article-details/62aa4ea5f70c21fa962fdb7c | | TTD-Purdue | Hu, Helminiak, Ye, Laskin | Julia Laskin | jlaskin@purdue.edu | High-Throughput Mass Spectrometry Imaging with Dynamic Sparse Sampling | Experimental implementation of DLADS | Submitted to ACS Measurement Science Au |