Literature DB >> 31835027

Toward a Common Coordinate Framework for the Human Body.

Jennifer E Rood1, Tim Stuart2, Shila Ghazanfar3, Tommaso Biancalani1, Eyal Fisher3, Andrew Butler4, Anna Hupalowska1, Leslie Gaffney1, William Mauck4, Gökçen Eraslan1, John C Marioni5, Aviv Regev6, Rahul Satija7.   

Abstract

Understanding the genetic and molecular drivers of phenotypic heterogeneity across individuals is central to biology. As new technologies enable fine-grained and spatially resolved molecular profiling, we need new computational approaches to integrate data from the same organ across different individuals into a consistent reference and to construct maps of molecular and cellular organization at histological and anatomical scales. Here, we review previous efforts and discuss challenges involved in establishing such a common coordinate framework, the underlying map of tissues and organs. We focus on strategies to handle anatomical variation across individuals and highlight the need for new technologies and analytical methods spanning multiple hierarchical scales of spatial resolution.
Copyright © 2019 Elsevier Inc. All rights reserved.

Entities:  

Mesh:

Year:  2019        PMID: 31835027      PMCID: PMC6934046          DOI: 10.1016/j.cell.2019.11.019

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  49 in total

1.  Volumetric transformation of brain anatomy.

Authors:  G E Christensen; S C Joshi; M I Miller
Journal:  IEEE Trans Med Imaging       Date:  1997-12       Impact factor: 10.048

2.  Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.

Authors:  Joshua D Welch; Velina Kozareva; Ashley Ferreira; Charles Vanderburg; Carly Martin; Evan Z Macosko
Journal:  Cell       Date:  2019-06-06       Impact factor: 41.582

3.  Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.

Authors:  Samuel G Rodriques; Robert R Stickels; Aleksandrina Goeva; Carly A Martin; Evan Murray; Charles R Vanderburg; Joshua Welch; Linlin M Chen; Fei Chen; Evan Z Macosko
Journal:  Science       Date:  2019-03-28       Impact factor: 47.728

Review 4.  Boundaries, junctions and transitions in the gastrointestinal tract.

Authors:  Adrianna K San Roman; Ramesh A Shivdasani
Journal:  Exp Cell Res       Date:  2011-07-23       Impact factor: 3.905

5.  SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

Authors:  Yinlong Xie; Gengxiong Wu; Jingbo Tang; Ruibang Luo; Jordan Patterson; Shanlin Liu; Weihua Huang; Guangzhu He; Shengchang Gu; Shengkang Li; Xin Zhou; Tak-Wah Lam; Yingrui Li; Xun Xu; Gane Ka-Shu Wong; Jun Wang
Journal:  Bioinformatics       Date:  2014-02-13       Impact factor: 6.937

6.  A four-dimensional probabilistic atlas of the human brain.

Authors:  J Mazziotta; A Toga; A Evans; P Fox; J Lancaster; K Zilles; R Woods; T Paus; G Simpson; B Pike; C Holmes; L Collins; P Thompson; D MacDonald; M Iacoboni; T Schormann; K Amunts; N Palomero-Gallagher; S Geyer; L Parsons; K Narr; N Kabani; G Le Goualher; J Feidler; K Smith; D Boomsma; H Hulshoff Pol; T Cannon; R Kawashima; B Mazoyer
Journal:  J Am Med Inform Assoc       Date:  2001 Sep-Oct       Impact factor: 4.497

7.  Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

Authors:  Laleh Haghverdi; Aaron T L Lun; Michael D Morgan; John C Marioni
Journal:  Nat Biotechnol       Date:  2018-04-02       Impact factor: 54.908

8.  The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

Authors: 
Journal:  Nature       Date:  2019-10-09       Impact factor: 69.504

9.  TopHat: discovering splice junctions with RNA-Seq.

Authors:  Cole Trapnell; Lior Pachter; Steven L Salzberg
Journal:  Bioinformatics       Date:  2009-03-16       Impact factor: 6.937

10.  EMAGE mouse embryo spatial gene expression database: 2014 update.

Authors:  Lorna Richardson; Shanmugasundaram Venkataraman; Peter Stevenson; Yiya Yang; Julie Moss; Liz Graham; Nicholas Burton; Bill Hill; Jianguo Rao; Richard A Baldock; Chris Armit
Journal:  Nucleic Acids Res       Date:  2013-11-21       Impact factor: 16.971

View more
  20 in total

Review 1.  IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues.

Authors:  Andrea J Radtke; Colin J Chu; Ziv Yaniv; Li Yao; James Marr; Rebecca T Beuschel; Hiroshi Ichise; Anita Gola; Juraj Kabat; Bradley Lowekamp; Emily Speranza; Joshua Croteau; Nishant Thakur; Danny Jonigk; Jeremy L Davis; Jonathan M Hernandez; Ronald N Germain
Journal:  Nat Protoc       Date:  2022-01-12       Impact factor: 13.491

Review 2.  Scalable tissue labeling and clearing of intact human organs.

Authors:  Hongcheng Mai; Zhouyi Rong; Shan Zhao; Ruiyao Cai; Hanno Steinke; Ingo Bechmann; Ali Ertürk
Journal:  Nat Protoc       Date:  2022-07-20       Impact factor: 17.021

3.  A roadmap for the Human Developmental Cell Atlas.

Authors:  Muzlifah Haniffa; Deanne Taylor; Sten Linnarsson; Bruce J Aronow; Gary D Bader; Roger A Barker; Pablo G Camara; J Gray Camp; Alain Chédotal; Andrew Copp; Heather C Etchevers; Paolo Giacobini; Berthold Göttgens; Guoji Guo; Ania Hupalowska; Kylie R James; Emily Kirby; Arnold Kriegstein; Joakim Lundeberg; John C Marioni; Kerstin B Meyer; Kathy K Niakan; Mats Nilsson; Bayanne Olabi; Dana Pe'er; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Rahul Satija; Sarah A Teichmann; Barbara Treutlein; Roser Vento-Tormo; Simone Webb
Journal:  Nature       Date:  2021-09-08       Impact factor: 69.504

4.  Toward a unified information framework for cell atlas assembly.

Authors:  Sijie Chen; Yanting Luo; Haoxiang Gao; Fanhong Li; Jiaqi Li; Yixin Chen; Renke You; Hairong Lv; Kui Hua; Rui Jiang; Xuegong Zhang
Journal:  Natl Sci Rev       Date:  2021-09-27       Impact factor: 23.178

Review 5.  Spatial components of molecular tissue biology.

Authors:  Giovanni Palla; David S Fischer; Aviv Regev; Fabian J Theis
Journal:  Nat Biotechnol       Date:  2022-02-07       Impact factor: 68.164

Review 6.  Strategic vision for improving human health at The Forefront of Genomics.

Authors:  Eric D Green; Chris Gunter; Leslie G Biesecker; Valentina Di Francesco; Carla L Easter; Elise A Feingold; Adam L Felsenfeld; David J Kaufman; Elaine A Ostrander; William J Pavan; Adam M Phillippy; Anastasia L Wise; Jyoti Gupta Dayal; Britny J Kish; Allison Mandich; Christopher R Wellington; Kris A Wetterstrand; Sarah A Bates; Darryl Leja; Susan Vasquez; William A Gahl; Bettie J Graham; Daniel L Kastner; Paul Liu; Laura Lyman Rodriguez; Benjamin D Solomon; Vence L Bonham; Lawrence C Brody; Carolyn M Hutter; Teri A Manolio
Journal:  Nature       Date:  2020-10-28       Impact factor: 49.962

Review 7.  Computational principles and challenges in single-cell data integration.

Authors:  Ricard Argelaguet; Anna S E Cuomo; Oliver Stegle; John C Marioni
Journal:  Nat Biotechnol       Date:  2021-05-03       Impact factor: 54.908

8.  Model-based prediction of spatial gene expression via generative linear mapping.

Authors:  Yasushi Okochi; Shunta Sakaguchi; Ken Nakae; Takefumi Kondo; Honda Naoki
Journal:  Nat Commun       Date:  2021-06-17       Impact factor: 14.919

9.  Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland.

Authors:  Samantha Henry; Marygrace C Trousdell; Samantha L Cyrill; Yixin Zhao; Mary J Feigman; Julia M Bouhuis; Dominik A Aylard; Adam Siepel; Camila O Dos Santos
Journal:  J Mammary Gland Biol Neoplasia       Date:  2021-05-14       Impact factor: 2.673

Review 10.  Immunometabolism: new insights and lessons from antigen-directed cellular immune responses.

Authors:  Renata Ramalho; Martin Rao; Chao Zhang; Chiara Agrati; Giuseppe Ippolito; Fu-Sheng Wang; Alimuddin Zumla; Markus Maeurer
Journal:  Semin Immunopathol       Date:  2020-06-09       Impact factor: 9.623

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.