HuBMAP Nature Paper Collection

HuBMAP Nature Paper Collection

 



Nat. Cell Biol.
07/19/2023
Advances and Prospects for the Human BioMolecular Atlas Program (HuBMAP)


Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M; HuBMAP Consortium; Börner K, Snyder MP.





Nature
07/19/2023
A spatially resolved timeline of the human maternal-fetal interface


Greenbaum S, Averbukh I, Soon E, Rizzuto G, Baranski A, Greenwald NF, Kagel A, Bosse M, Jaswa EG, Khair Z, Kwok S, Warshawsky S, Piyadasa H, Goldston M, Spence A, Miller G, Schwartz M, Graf W, Van Valen D, Winn VD, Hollmann T, Keren L, van de Rijn M, Angelo M.

A multiomics approach is used to produce a spatiotemporal atlas of the human maternal–fetal interface in the first half of pregnancy, revealing relationships among gestational age, extravillous trophoblasts and spiral artery remodelling.

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Nature
07/19/2023
An atlas of healthy and injured cell states and niches in the human kidney


Lake BB, Menon R, Winfree S, Hu Q, Ferreira RM, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, Eddy S, Zhang B, Wu Y, Salamon D, Williams JC, Wang X, Balderrama KS, Hoover PJ, Murray E, Marshall JL, Noel T, Vijayan A, Hartman A, Chen F, Waikar SS, Rosas SE, Wilson FP, Palevsky PM, Kiryluk K, Sedor JR, Toto RD, Parikh CR, Kim EH, Satija R, Greka A, Macosko EZ, Kharchenko PV, Gaut JP, Hodgin JB; KPMP Consortium; Eadon MT, Dagher PC, El-Achkar TM, Zhang K, Kretzler M, Jain S.

We present a foundational multimodal single cell and spatial reference atlas of major, minor and rare cell types and states of the human kidney with identification of distinct immune and stromal neighborhoods and genes associated with worsening kidney function in patients.

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Nature
07/19/2023
Organization of the Human Intestine at Single Cell Resolution


Hickey JW, Becker WR, Nevins SA, Horning A, Perez AE, Zhu C, Zhu B, Wei B, Chiu R, Chen DC, Cotter DL, Esplin ED, Weimer AK, Caraccio C, Venkataraaman V, Schürch CM, Black S, Brbić M, Cao K, Chen S, Zhang W, Monte E, Zhang NR, Ma Z, Leskovec J, Zhang Z, Lin S, Longacre T, Plevritis SK, Lin Y, Nolan GP, Greenleaf WJ, Snyder M.

We present a detailed single cell map of the healthy human with single cell RNAseq/ATACseq merged with the first multiplexed imaging reference describing distinct abundance, differentiation, regulation, and organization of cells found across eight unique sites of the intestine that also can serve as an important reference for intestinal diseases.

Additional resources




Commun Biol.
07/19/2023
3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging


Ghose S, Ju Y, McDonough E, Ho J, Karunamurthy A, Chadwick C, Cho S, Rose R, Corwin A, Surrette C, Martinez J, Williams E, Sood A, Al-Kofahi Y, Falo LD Jr, Börner K, Ginty F.

We present a 3D map of skin cells and spatial maps of immune cell density, vascular distance and UV damage markers.

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Nat. Commun.
07/19/2023
A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease


Canela VH, Bowen WS, Ferreira RM, Syed F, Lingeman JE, Sabo AR, Barwinska D, Winfree S, Lake BB, Cheng YH, Gaut JP, Ferkowicz M, LaFavers KA, Zhang K, Coe FL, Worcester E; Kidney Precision Medicine Project; Jain S, Eadon MT, Williams JC Jr, El-Achkar TM.

We define the spatial molecular landscape and specific pathways contributing to stone-mediated injury in the human renal papilla and identify associated urinary biomarkers.

Additional resources




Sci. Data.
07/19/2023
Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature


Boppana A, Lee S, Malhotra R, Halushka M, Gustilo KS, Quardokus EM, Herr BW 2nd, Börner K, Weber GM.

We describe the first open, computer-readable, and comprehensive database of the adult human blood vasculature.

Additional resources




Nat. Methods.
07/19/2023
Organ Mapping Antibody Panels (OMAPs): A community resource for standardized multiplexed tissue imaging


Quardokus EM, Saunders DC, McDonough E, Hickey JW, Werlein C, Surrette C, Rajbhandari P, Casals AM, Tian H, Lowery L, Neumann EK, Björklund F, Neelakantan TV, Croteau J, Wiblin AE, Fisher J, Livengood AJ, Dowell KG, Silverstein JC, Spraggins JM, Pryhuber GS, Deutsch G, Ginty F, Nolan GP, Melov S, Jonigk D, Caldwell MA, Vlachos IS, Muller W, Gehlenborg N, Stockwell BR, Lundberg E, Snyder MP, Germain RN, Camarillo JM, Kelleher NL, Börner K, Radtke AJ.

Organ Mapping Antibody Panels (OMAPs) are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.

Additional resources




Commun. Biol.
07/19/2023
Segmentation of human functional tissue units in support of a Human Reference Atlas


Jain Y, Godwin LL, Ju Y, Sood N, Quardokus EM, Bueckle A, Longacre T, Horning A, Lin Y, Esplin ED, Hickey JW, Snyder MP, Patterson NH, Spraggins JM, Börner K.

We present the design and analysis of the machine learning algorithm development Kaggle competition, "Hacking the Kidney", aimed at developing algorithms to segment glomeruli in PAS-stained kidney tissue images.

Additional resources




Sci Data
03/27/2023
Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas


Herr BW 2nd, Hardi J, Quardokus EM, Bueckle A, Chen L, Wang F, Caron AR, Osumi-Sutherland D, Musen MA, Börner K.

This paper introduces the Common Coordinate Framework (CCF) Ontology v2.0.1 that interlinks specimen, biological structure, and spatial data, together with the CCF API that makes the HRA programmatically accessible and interoperable with Linked Open Data (LOD).

Additional resources




Commun Biol.
12/13/2022
Tissue registration and exploration user interfaces in support of a human reference atlas


Börner K, Bueckle A, Herr BW 2nd, Cross LE, Quardokus EM, Record EG, Ju Y, Silverstein JC, Browne KM, Jain S, Wasserfall CH, Jorgensen ML, Spraggins JM, Patterson NH, Weber GM.

We present software tools and user interfaces developed to spatially and semantically annotate (“register”) and explore the tissue data and the evolving Human Reference Atlas.

Additional resources




Nat. Methods
11/30/2022
Annotation of Spatially Resolved Single-cell Data with STELLAR


Brbić M, Cao K, Hickey JW, Tan Y, Snyder MP, Nolan GP, Leskovec J.

Here we present STELLAR, a geometric deep learning method for cell-type discovery and identification in spatially resolved single-cell datasets that automatically assigns cells to cell types present in the annotated reference dataset and discovers novel cell types and cell states.

Additional resources




Commun Med (Lond)
08/19/2022
A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology


Lutnick B, Manthey D, Becker JU, Ginley B, Moos K, Zuckerman JE, Rodrigues L, Gallan AJ, Barisoni L, Alpers CE, Wang XX, Myakala K, Jones BA, Levi M, Kopp JB, Yoshida T, Zee J, Han SS, Jain S, Rosenberg AZ, Jen KY, Sarder P; Kidney Precision Medicine Project.

A cloud based tool for end-users for training and inference in segmenting renal tissue compartments from whole slide images.

Additional resources




Nat Commun.
02/21/2024
Multi-molecular hyperspectral PRM-SRS microscopy


Zhang W, Li Y, Fung AA, Li Z, Jang H, Zha H, Chen X, Gao F, Wu JY, Sheng H, Yao J, Skowronska-Krawczyk D, Jain S, Shi L..

We developed an algorithm for reference matching with penalty to detect various small and large molecules in situ in cells and tissues, for mapping metabolic heterogeneity in situ from relative large scale organ tissue to small cellular organelle levels.





Nat Commun.
01/10/2024
The chromatin landscape of healthy and injured cell types in the human kidney


Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Stout L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, De Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Winfree S, Jefferson N, Türkmen A, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S; Kidney Precision Medicine Project (KPMP); Jain S, Rauchman M, Eadon MT.





Nat Biotechnol.
10/09/2023
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq


Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Nam J, Gao F, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R.

We present spatial-CITE-seq for high-plex protein and whole transcriptome co-mapping, for both mouse and human tissues.

Additional resources




Nat. Rev. Mol. Cell Biol.
10/02/2023
The technological landscape and applications of single-cell multi-omics


Baysoy A, Bai Z, Satija R, Fan R.

We review current and emerging single-cell and spatial multi-omics technologies, computational pipelines, and the applications in molecular and cellular biology including human tissue atlas building.





Nature
07/31/2023
KRAS(G12D) drives lepidic adenocarcinoma through stem-cell reprogramming


Juul NH, Yoon JK, Martinez MC, Rishi N, Kazadaeva YI, Morri M, Neff NF, Trope WL, Shrager JB, Sinha R, Desai TJ.





Kidney Int Rep.
06/03/2023
PodoCount: A Robust, Fully Automated, Whole-Slide Podocyte Quantification Tool


Santo BA, Govind D, Daneshpajouhnejad P, Yang X, Wang XX, Myakala K, Jones BA, Levi M, Kopp JB, Yoshida T, Niedernhofer LJ, Manthey D, Moon KC, Han SS, Zee J, Rosenberg AZ, Sarder P.

A machine learning tool for estimating podocytes at single cell level from brightfield immunohistochemistry whole slide images

Additional resources




Mol Biol Cell.
05/15/2023
Evaluation of cell segmentation methods without reference segmentations


Chen H, Murphy RF.

Additional resources


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