Literature DB >> 27318512

Computational Tools for Stem Cell Biology.

Qin Bian1, Patrick Cahan2.   

Abstract

For over half a century, the field of developmental biology has leveraged computation to explore mechanisms of developmental processes. More recently, computational approaches have been critical in the translation of high throughput data into knowledge of both developmental and stem cell biology. In the past several years, a new subdiscipline of computational stem cell biology has emerged that synthesizes the modeling of systems-level aspects of stem cells with high-throughput molecular data. In this review, we provide an overview of this new field and pay particular attention to the impact that single cell transcriptomics is expected to have on our understanding of development and our ability to engineer cell fate.
Copyright © 2016 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  cell fate engineering; computational biology; network biology; single cell transcriptomics; stem cell biology

Mesh:

Year:  2016        PMID: 27318512      PMCID: PMC5116400          DOI: 10.1016/j.tibtech.2016.05.010

Source DB:  PubMed          Journal:  Trends Biotechnol        ISSN: 0167-7799            Impact factor:   19.536


  98 in total

1.  Core transcriptional regulatory circuitry in human embryonic stem cells.

Authors:  Laurie A Boyer; Tong Ihn Lee; Megan F Cole; Sarah E Johnstone; Stuart S Levine; Jacob P Zucker; Matthew G Guenther; Roshan M Kumar; Heather L Murray; Richard G Jenner; David K Gifford; Douglas A Melton; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2005-09-23       Impact factor: 41.582

Review 2.  Heterogeneity of embryonic and adult stem cells.

Authors:  Thomas Graf; Matthias Stadtfeld
Journal:  Cell Stem Cell       Date:  2008-11-06       Impact factor: 24.633

3.  m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells.

Authors:  Pedro J Batista; Benoit Molinie; Jinkai Wang; Kun Qu; Jiajing Zhang; Lingjie Li; Donna M Bouley; Ernesto Lujan; Bahareh Haddad; Kaveh Daneshvar; Ava C Carter; Ryan A Flynn; Chan Zhou; Kok-Seong Lim; Peter Dedon; Marius Wernig; Alan C Mullen; Yi Xing; Cosmas C Giallourakis; Howard Y Chang
Journal:  Cell Stem Cell       Date:  2014-10-16       Impact factor: 24.633

4.  Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming.

Authors:  Aaron R Quinlan; Michael J Boland; Mitchell L Leibowitz; Svetlana Shumilina; Sidney M Pehrson; Kristin K Baldwin; Ira M Hall
Journal:  Cell Stem Cell       Date:  2011-10-04       Impact factor: 24.633

5.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

6.  F-Seq: a feature density estimator for high-throughput sequence tags.

Authors:  Alan P Boyle; Justin Guinney; Gregory E Crawford; Terrence S Furey
Journal:  Bioinformatics       Date:  2008-09-10       Impact factor: 6.937

7.  Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells.

Authors:  Ilango Balakrishnan; Xiaodong Yang; Joseph Brown; Aravind Ramakrishnan; Beverly Torok-Storb; Peter Kabos; Jay R Hesselberth; Manoj M Pillai
Journal:  Stem Cells       Date:  2014-03       Impact factor: 6.277

8.  Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Authors:  Nicholas T Ingolia; Sina Ghaemmaghami; John R S Newman; Jonathan S Weissman
Journal:  Science       Date:  2009-02-12       Impact factor: 47.728

9.  Somatic coding mutations in human induced pluripotent stem cells.

Authors:  Athurva Gore; Zhe Li; Ho-Lim Fung; Jessica E Young; Suneet Agarwal; Jessica Antosiewicz-Bourget; Isabel Canto; Alessandra Giorgetti; Mason A Israel; Evangelos Kiskinis; Je-Hyuk Lee; Yuin-Han Loh; Philip D Manos; Nuria Montserrat; Athanasia D Panopoulos; Sergio Ruiz; Melissa L Wilbert; Junying Yu; Ewen F Kirkness; Juan Carlos Izpisua Belmonte; Derrick J Rossi; James A Thomson; Kevin Eggan; George Q Daley; Lawrence S B Goldstein; Kun Zhang
Journal:  Nature       Date:  2011-03-03       Impact factor: 49.962

10.  CellNet: network biology applied to stem cell engineering.

Authors:  Patrick Cahan; Hu Li; Samantha A Morris; Edroaldo Lummertz da Rocha; George Q Daley; James J Collins
Journal:  Cell       Date:  2014-08-14       Impact factor: 41.582

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  11 in total

Review 1.  Understanding development and stem cells using single cell-based analyses of gene expression.

Authors:  Pavithra Kumar; Yuqi Tan; Patrick Cahan
Journal:  Development       Date:  2017-01-01       Impact factor: 6.868

Review 2.  Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics.

Authors:  Sabyasachi Dasgupta; Gary D Bader; Sidhartha Goyal
Journal:  Biophys J       Date:  2018-07-11       Impact factor: 4.033

3.  Assessment of engineered cells using CellNet and RNA-seq.

Authors:  Arthur H Radley; Remy M Schwab; Yuqi Tan; Jeesoo Kim; Emily K W Lo; Patrick Cahan
Journal:  Nat Protoc       Date:  2017-04-27       Impact factor: 13.491

Review 4.  Functional and Biomimetic Materials for Engineering of the Three-Dimensional Cell Microenvironment.

Authors:  Guoyou Huang; Fei Li; Xin Zhao; Yufei Ma; Yuhui Li; Min Lin; Guorui Jin; Tian Jian Lu; Guy M Genin; Feng Xu
Journal:  Chem Rev       Date:  2017-10-09       Impact factor: 60.622

5.  Induced pluripotent stem cells derived from human amnion in chemically defined conditions.

Authors:  Jaroslav Slamecka; Steven McClellan; Anna Wilk; Javier Laurini; Elizabeth Manci; Simon P Hoerstrup; Benedikt Weber; Laurie Owen
Journal:  Cell Cycle       Date:  2018-02-07       Impact factor: 4.534

6.  Endothelial stem and progenitor cells (stem cells): (2017 Grover Conference Series).

Authors:  Mervin C Yoder
Journal:  Pulm Circ       Date:  2017-11-03       Impact factor: 3.017

7.  A stochastic and dynamical view of pluripotency in mouse embryonic stem cells.

Authors:  Yen Ting Lin; Peter G Hufton; Esther J Lee; Davit A Potoyan
Journal:  PLoS Comput Biol       Date:  2018-02-16       Impact factor: 4.475

8.  SeesawPred: A Web Application for Predicting Cell-fate Determinants in Cell Differentiation.

Authors:  András Hartmann; Satoshi Okawa; Gaia Zaffaroni; Antonio Del Sol
Journal:  Sci Rep       Date:  2018-09-06       Impact factor: 4.379

9.  DeepNEU: cellular reprogramming comes of age - a machine learning platform with application to rare diseases research.

Authors:  Wayne R Danter
Journal:  Orphanet J Rare Dis       Date:  2019-01-10       Impact factor: 4.123

Review 10.  Genomic and molecular control of cell type and cell type conversions.

Authors:  Xiuling Fu; Fangfang He; Yuhao Li; Allahverdi Shahveranov; Andrew Paul Hutchins
Journal:  Cell Regen (Lond)       Date:  2017-11-22
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