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Laying the Biological, Computational and Architectural Foundations for Human Cell Lineage Discovery


Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs

Author(s): Ofir Raz, Liming Tao, Tamir Biezuner, Tzipy Marx, Yaara Neumeier, Narek Tumanyan, Ehud Shapiro
Published in: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23116161

A generic, cost-effective, and scalable cell lineage analysis platform

Author(s): Tamir Biezuner, Adam Spiro, Ofir Raz, Shiran Amir, Lilach Milo, Rivka Adar, Noa Chapal-Ilani, Veronika Berman, Yael Fried, Elena Ainbinder, Galit Cohen, Haim M. Barr, Ruth Halaban, Ehud Shapiro
Published in: Genome Research, Issue 26/11, 2016, Page(s) 1588-1599, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.202903.115

eSTGt: a programming and simulation environment for population dynamics

Author(s): Adam Spiro, Ehud Shapiro
Published in: BMC Bioinformatics, Issue 17/1, 2016, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-016-1004-y

Erratum to: eSTGt: a programming and simulation environment for population dynamics

Author(s): Spiro, Adam; Shapiro, Ehud
Published in: BMC Bioinformatics, Issue 1, 2016, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-016-1155-x

Accuracy of Answers to Cell Lineage Questions Depends on Single-Cell Genomics Data Quality and Quantity

Author(s): Adam Spiro; Ehud Shapiro
Published in: PLoS Computational Biology, Issue 1, 2016, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1004983

On the journey from nematode to human, scientists dive by the zebrafish cell lineage tree

Author(s): Ehud Shapiro
Published in: Genome Biology, Issue 19/1, 2018, ISSN 1474-760X
Publisher: BMC
DOI: 10.1186/s13059-018-1453-x

Short tandem repeat stutter model inferred from direct measurement of in vitro stutter noise

Author(s): Ofir Raz, Tamir Biezuner, Adam Spiro, Shiran Amir, Lilach Milo, Alon Titelman, Amos Onn, Noa Chapal-Ilani, Liming Tao, Tzipy Marx, Uriel Feige, Ehud Shapiro
Published in: Nucleic Acids Research, Issue 47/5, 2019, Page(s) 2436-2445, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky1318

Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees

Author(s): W Gong, AA Granados, J Hu, MG Jones, O Raz, I Salvador-Martínez,…Ehud Shapiro, MichaelB.Elowitz, Pablo Meyer
Published in: Cell Systems, 2021, ISSN 2405-4712
Publisher: CellPress
DOI: 10.1016/j.cels.2021.05.008

Retrospective cell lineage reconstruction in humans by using short tandem repeats

Author(s): Liming Tao, Ofir Raz, Zipora Marx, Manjusha S Ghosh, Sandra Huber, Julia Greindl-Junghans, Tamir Biezuner, Shiran Amir, Lilach Milo, Rivka Adar, Ron Levy, Amos Onn, Noa Chapal-Ilani, Veronika Berman, Asaf Ben Arie, Guy Rom, Barak Oron, Ruth Halaban, Zbigniew T.Czyz, Melanie Warner-Klein, Christoph A. Klein, Ehud Shapiro
Published in: Cell reports methods, 2021, ISSN 2667-2375
Publisher: CellPress
DOI: 10.1016/j.crmeth.2021.100054

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