Publications by authors named "John Reinitz"

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Characterizing the regulatory logic of transcriptional control at the DNA sequence level by ensembles of thermodynamic models.
Alan Utsuni Sabino, Drielly de Moraes Guerreiro, Ah-Ram Kim, Alexandre Ferreira Ramos, John Reinitz

Bioinformatics· October 2025

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Two-State Stochastic Model of In Vivo Observations of Transcriptional Bursts.
Luiz Guilherme S da Silva, Romain Yvinec, Guilherme Prata, Varshant Dhar, John Reinitz

Braz J Phys· May 2025

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Global repression by tailless during segmentation.
Lauro Hiroshi Pimentel Masuda, Alan Utsuni Sabino, John Reinitz, Alexandre Ferreira Ramos, Ariane Machado-Lima

Dev Biol· January 2024

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Evolution of biological cooperation: an algorithmic approach.
Ivan Sudakow, John Reinitz, Sergey A Vakulenko, Dima Grigoriev

Sci Rep· January 2024

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The effect of mutational robustness on the evolvability of multicellular organisms and eukaryotic cells.
Pengyao Jiang, Martin Kreitman, John Reinitz

J Evol Biol· June 2023

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Fully interpretable deep learning model of transcriptional control.
Yi Liu, Kenneth Barr, John Reinitz

Bioinformatics· July 2020

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Adaptation, fitness landscape learning and fast evolution.
John Reinitz, Sergey Vakulenko, Dmitri Grigoriev, Andreas Weber

F1000Res· June 2020

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An in silico analysis of robust but fragile gene regulation links enhancer length to robustness.
Kenneth Barr, John Reinitz, Ovidiu Radulescu

PLoS Comput Biol· November 2019

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Physical implications of so(2, 1) symmetry in exact solutions for a self-repressing gene.
Alexandre F Ramos, John Reinitz

J Chem Phys· July 2019

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Correction: A sequence level model of an intact locus predicts the location and function of nonadditive enhancers.
Kenneth A Barr, John Reinitz

PLoS One· May 2018

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Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation.
Kenneth A Barr, Carlos Martinez, Jennifer R Moran, Ah-Ram Kim, Alexandre F Ramos, John Reinitz

BMC Syst Biol· November 2017

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A sequence level model of an intact locus predicts the location and function of nonadditive enhancers.
Kenneth A Barr, John Reinitz

PLoS One· September 2017

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DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan.
C Matthew Hope, Ilaria Rebay, John Reinitz

Biophys J· January 2017

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Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations.
UnJin Lee, John J Skinner, John Reinitz, Marsha Rich Rosner, Eun-Jin Kim

PLoS One· May 2016

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The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification.
Eric Bertolino, John Reinitz, Manu

Dev Biol· May 2016

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Parallel Simulated Annealing Using an Adaptive Resampling Interval.
Zhihao Lou, John Reinitz

Parallel Comput· April 2016

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Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster.
Pengyao Jiang, Michael Z Ludwig, Martin Kreitman, John Reinitz

Dev Biol· September 2015

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Gene regulation and noise reduction by coupling of stochastic processes.
Alexandre F Ramos, José Eduardo M Hornos, John Reinitz

Phys Rev E Stat Nonlin Soft Matter Phys· February 2015

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A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients.
Unjin Lee, Casey Frankenberger, Jieun Yun, Elena Bevilacqua, Carlos Caldas, John Reinitz

PLoS One· October 2014

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Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.
Carlos Martinez, Joshua S Rest, Ah-Ram Kim, Michael Ludwig, Martin Kreitman, John Reinitz

Mol Biol Evol· April 2014

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A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design.
Carlos A Martinez, Kenneth A Barr, Ah-Ram Kim, John Reinitz

Methods· July 2013

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Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic.
Ah-Ram Kim, Carlos Martinez, John Ionides, Alexandre F Ramos, Michael Z Ludwig, John Reinitz

PLoS Genet· June 2013

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Preparation of Drosophila embryos for quantitative imaging of gene expression.
Svetlana Surkova, Ekaterina Myasnikova, Konstantin N Kozlov, Andrei Pisarev, John Reinitz

Cold Spring Harb Protoc· June 2013

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Quantitative imaging of gene expression in Drosophila embryos.
Svetlana Surkova, Ekaterina Myasnikova, Konstantin N Kozlov, Andrei Pisarev, John Reinitz

Cold Spring Harb Protoc· June 2013

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Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants.
Svetlana Surkova, Elena Golubkova, Manu, Lena Panok, Lyudmila Mamon, John Reinitz

Dev Biol· April 2013

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