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List of works by Ehud Shapiro

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

scientific article published on 24 August 2016

A library of programmable DNAzymes that operate in a cellular environment

scientific article

A mechanical Turing machine: blueprint for a biomolecular computer ⬇️

scientific article published on March 21, 2012

A programmable NOR-based device for transcription profile analysis ⬇️

scientific article published on September 7, 2012

A synthetic biology approach for evaluating the functional contribution of designer cellulosome components to deconstruction of cellulosic substrates

scientific article

A universal mechanism ties genotype to phenotype in trinucleotide diseases

scientific article (publication date: November 2007)

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

scientific article

Accurate, model-based tuning of synthetic gene expression using introns in S. cerevisiae

scientific article

Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues

scientific article

An autonomous molecular computer for logical control of gene expression

scientific article

Application of a stochastic name-passing calculus to representation and simulation of molecular processes

article

BioAmbients: an abstraction for biological compartments

article

Biotechnology: logic goes in vitro

scientific article published in February 2007

Cell biology. RNA computing in a living cell

scientific article published in October 2008

Cell lineage analysis of a mouse tumor

scientific article

Cell lineage analysis of acute leukemia relapse uncovers the role of replication-rate heterogeneity and microsatellite instability ⬇️

scientific article published on May 29, 2012

Cell lineage analysis of the mammalian female germline

scientific article

Cells as computation

scientific article published on September 2002

Colon stem cell and crypt dynamics exposed by cell lineage reconstruction

scientific article published in July 2011

Comparing algorithms that reconstruct cell lineage trees utilizing information on microsatellite mutations

scientific article (publication date: 2013)

Computer-Aided High-Throughput Cloning of Bacteria in Liquid Medium ⬇️

scientific article published on February 1, 2011

Correcting the bias against interdisciplinary research

scientific article published on April 2014

DNA computing: Molecules reach consensus

scientific article published in October 2013

DNA molecule provides a computing machine with both data and fuel

scientific article

De novo DNA synthesis using single molecule PCR.

scientific article published on 30 July 2008

De novo DNA synthesis using single-molecule PCR.

scientific article published in January 2012

Detection of Multiple Disease Indicators by an Autonomous Biomolecular Computer ⬇️

scientific article published on June 23, 2011

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

scientific article published on 10 August 2016

Estimating cell depth from somatic mutations

scientific article

Genomic variability within an organism exposes its cell lineage tree

scientific article

Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive code

scholarly article

Heuristic for maximizing DNA reuse in synthetic DNA library assembly

scientific article

Identification of CTCF as a master regulator of the clustered protocadherin genes ⬇️

scientific article published on December 30, 2011

Lineage grammars: describing, simulating and analyzing population dynamics

scientific article

Mapping the translation initiation landscape of an S. cerevisiae gene using fluorescent proteins

scientific article published on 28 May 2013

Molecular implementation of simple logic programs

scientific article published on 2 August 2009

Muscle-bound primordial stem cells give rise to myofiber-associated myogenic and non-myogenic progenitors

scientific article (publication date: 2011)

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

scientific article published on 29 May 2018

Processing DNA molecules as text ⬇️

scientific article published on June 15, 2010

Programmable in vivo selection of arbitrary DNA sequences

scientific article

Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

scientific article published on 15 July 2015

Reconstruction of cell lineage trees in mice

scientific article

Recursive Construction and Error Correction of DNA Molecules and Libraries from Synthetic and Natural DNA

scientific article published on January 1, 2011

Recursive construction of perfect DNA molecules and libraries from imperfect oligonucleotides

scientific article

Recursive construction of perfect DNA molecules from imperfect oligonucleotides

scientific article

Single cell analysis exposes intratumor heterogeneity and suggests that FLT3-ITD is a late event in leukemogenesis.

scientific article

Single-cell sequencing-based technologies will revolutionize whole-organism science

scientific article

Stochastic computing with biomolecular automata

scholarly article

Synthesis and cell-free cloning of DNA libraries using programmable microfluidics

scientific article

Tapping the computing power of biological molecules gives rise to tiny machines that can speak directly to living cells.

scientific article published in May 2006

The Human Cell Atlas

The Human Cell Atlas White Paper ⬇️

journal article from 'arXiv:1810.05192 [q-bio]' published in 2018

The family of concurrent logic programming languages

scholarly article by Ehud Shapiro published 1 September 1989 in ACM Computing Surveys

Towards molecular computers that operate in a biological environment

Using expression profiles of Caenorhabditis elegans neurons to identify genes that mediate synaptic connectivity

scientific article

eSTGt: a programming and simulation environment for population dynamics

scientific article

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