HuBMAP Nature Paper Collection

HuBMAP Nature Paper Collection


Nat. Cell Biol.
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.

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.

Additional resources

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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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.

Nat. Commun.
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.

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Sci. Data.
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.
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.
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
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).

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Commun Biol.
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
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)
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 Biotechnol.
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.
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.

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.
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.

Curr Opin Nephrol Hypertens.
Conundrums of Choice of 'Normal' Kidney Tissue for Single Cell Studies

Jain S.

The review discusses choices and challenges to be considered in each of the steps in planning omics experiments with a detailed discussion about strengths and weaknesses of various "healthy" tissue sources for omics and atlas studies.

Spatial epigenome-transcriptome co-profiling of mammalian tissues

Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R.

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