John Reinitz

发表

Parallel simulated annealing using an adaptive resampling interval

Zhihao Lou, John Reinitz, J. Reinitz, 2016, Parallel Comput..

GCPReg package for registration of the segmentation gene expression data in Drosophila

John Reinitz, Konstantin N Kozlov, Ekaterina Myasnikova, 2009, Fly.

Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty

Perry L. Miller, John Reinitz, L. W. Wright, 1994, Comput. Appl. Biosci..

An in silico analysis of robust but fragile gene regulation links enhancer length to robustness

John Reinitz, Ovidiu Radulescu, Kenneth Barr, 2019, bioRxiv.

Using of Evolutionary Computations in Image Processing for Quantitative Atlas of Drosophila Genes Expression

Alexander V. Spirov, John Reinitz, Dmitry L. Timakin, 2001, EvoWorkshops.

Spatio-Temporal Registration of the Expression Patterns of Drosophila Segmentation Genes

John Reinitz, Maria Samsonova, David Kosman, 1999, ISMB.

Mechanisms of gap gene expression canalization in the Drosophila blastoderm

John Reinitz, Maria Samsonova, Manu, 2011, BMC Systems Biology.

Punctuated evolution and robustness in morphogenesis

Dima Grigoriev, John Reinitz, Andreas Weber, 2014, Biosyst..

Experimental Determination of Drosophila Embryonic Coordinates by Genetic Algorithms, the Simplex method, and Their Hybrid

Alexander V. Spirov, John Reinitz, Dmitry L. Timakin, 2000, EvoWorkshops.

A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ

John Reinitz, Maria Samsonova, Andrei Pisarev, 2002, Silico Biol..

Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila

John Reinitz, Svetlana Surkova, Maria Samsonova, 2009, Bioinform..

ImageServer, a Tool for On-line Processing and Analysis of Biological Images

John Reinitz, Ekaterina Myasnikova, Maria Samsonova, 2005, J. Integr. Bioinform..

Modeling the Connection Between Development and Evolution: Preliminary Report

Eric Mjolsness, David H. Sharp, John Reinitz, 1995, Evolution and Biocomputation.

Registration of the expression patterns of Drosophila segmentation genes by two independent methods

John Reinitz, Maria Samsonova, Konstantin Kozlov, 2001, Bioinform..

Reverse Engineering the Gap Gene Network of Drosophila melanogaster

Leon Glass, Theodore J. Perkins, Johannes Jaeger, 2006, PLoS Comput. Biol..

Reconstruction of the Dynamics of Drosophila Genes Expression from Sets of Images Sharing a Common Pattern

Alexander V. Spirov, John Reinitz, Dmitry L. Timakin, 2002, Real Time Imaging.

Master equation simulation analysis of immunostained Bicoid morphogen gradient

John Reinitz, Ekaterina M. Myasnikova, Yu Feng Wu, 2007, BMC Systems Biology.

Information and simulation systems for the analysis of gene regulation and metabolic pathways (Preface)

Ralf Hofestädt, Nikolay A. Kolchanov, John Reinitz, 2002, Silico Biol..

Fast redundant dyadic wavelet transform in application to spatial registration of the expression patterns of Drosophila segmentation genes

John Reinitz, Maria Samsonova, Konstantin Kozlov, 2000, Proceedings 15th International Conference on Pattern Recognition. ICPR-2000.

Support vector regression applied to the determination of the developmental age of a Drosophila embryo from its segmentation gene expression patterns

John Reinitz, Maria Samsonova, Ekaterina M. Myasnikova, 2002, ISMB.

HOX Pro: a specialized database for clusters and networks of homeobox genes

Alexander V. Spirov, John Reinitz, Timothy Bowler, 2000, Nucleic Acids Res..

Genetic algorithms for genetic neural nets. Research report

David H. Sharp, Eric Mjolsness, John Reinitz, 1991 .

Fully interpretable deep learning model of transcriptional control

Yi Liu, John Reinitz, Kenneth Barr, 2019, bioRxiv.

Parallel Simulated Annealing by Mixing of States

Yuefan Deng, John Reinitz, King-Wai Chu, 1999 .

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

David H. Sharp, Alexander V. Spirov, David H. Sharp, 2009, PLoS Comput. Biol..

Estimation of Errors in Gene Expression Data Introduced by Diffractive Blurring of Confocal Images

John Reinitz, Svetlana Surkova, Maria Samsonova, 2009, 2009 13th International Machine Vision and Image Processing Conference.

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

John Reinitz, Svetlana Surkova, Maria Samsonova, 2012, PLoS Comput. Biol..

FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

John Reinitz, Maria Samsonova, Andrei Pisarev, 2008, Nucleic Acids Res..

Design of the Integrated Atlas of Segmentation Gene Expression in Situ

John Reinitz, Maria Samsonova, Andrei Pisarev, 2000, German Conference on Bioinformatics.

ImageServer, a Tool for On-line Processing and Analysis of Biological Images

John Reinitz, Maria Samsonova, Andrei Pisarev, 2005, J. Integr. Bioinform..

A database for management of gene expression data in situ

John Reinitz, Maria Samsonova, Andrei Pisarev, 2004, Bioinform..

Looking at functional genomics from inside the Drosophila blastoderm

John Reinitz, 2001, German Conference on Bioinformatics.

Application of the Neural Networks Based on Multi-valued Neurons to Classification of the Images of Gene Expression Patterns

Igor N. Aizenberg, John Reinitz, Maria Samsonova, 2001, Fuzzy Days.

Classification of the images of gene expression patterns using neural networks based on multivalued neurons with the minimal number of inputs

Igor N. Aizenberg, Constantine Butakoff, John Reinitz, 2002, IS&T/SPIE Electronic Imaging.

Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene

David H. Sharp, Johannes Jaeger, John Reinitz, 2006, Nature Genetics.

Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants.

John Reinitz, Lena Panok, Manu, 2013, Developmental biology.

On the dynamic nature of positional information.

Johannes Jaeger, John Reinitz, J. Reinitz, 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

Size regulation in the segmentation of Drosophila: interacting interfaces between localized domains of gene expression ensure robust spatial patterning.

John Reinitz, Sergei Vakulenko, Ovidiu Radulescu, 2009, Physical review letters.

Removal of background signal from in situ data on the expression of segmentation genes in Drosophila

John Reinitz, Ekaterina Myasnikova, David Kosman, 2005, Development Genes and Evolution.

Model with asymptotically stable dynamics for Drosophila gap gene network

Alexander M. Samsonov, John Reinitz, Konstantin Kozlov, 2008 .

Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.

John Reinitz, Ah-Ram Kim, Kevin White, 2014, Molecular biology and evolution.

Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation

John Reinitz, Ah-Ram Kim, Alexandre F Ramos, 2017, BMC Systems Biology.

A high-throughput method for quantifying gene expression data from early Drosophila embryos

Johannes Jaeger, John Reinitz, Hilde Janssens, 2005, Development Genes and Evolution.

Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images

John Reinitz, Ekaterina Myasnikova, Hilde Janssens, 2008, Fly.

The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification.

John Reinitz, Manu, J. Reinitz, 2016, Developmental biology.

Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster

David H. Sharp, Johannes Jaeger, John Reinitz, 2007, Mechanisms of Development.

Developmental biology: A ten per cent solution

John Reinitz, J. Reinitz, 2007, Nature.

How gap genes make their domains: An analytical study based on data driven approximations.

Alexander M. Samsonov, John Reinitz, Vitaly V. Gursky, 2001, Chaos.

Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic

David H. Sharp, John Reinitz, Ah-Ram Kim, 2013, PLoS genetics.

A sequence level model of an intact locus predicts the location and function of nonadditive enhancers

John Reinitz, J. Reinitz, Kenneth A. Barr, 2017, PloS one.

Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila.

John Reinitz, Francisco J. P. Lopes, J. Reinitz, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Gene circuits and their uses

David H. Sharp, John Reinitz, 1996 .

Erratum to “Quantitative dynamics and increased variability of segmentation gene expression in the DrosophilaKrüppel and knirps mutants” [Dev. Biol. 376 (2013) 99–112]

John Reinitz, Lena Panok, Manu, 2013, Developmental Biology.

Pattern formation and nuclear divisions are uncoupled in Drosophila segmentation: comparison of spatially discrete and continuous models

Johannes Jaeger, Alexander M. Samsonov, John Reinitz, 2004 .

Sharp borders from fuzzy gradients.

John Reinitz, Alexander Spirov, David M Holloway, 2002, Trends in genetics : TIG.

Transcriptional Control in Drosophila

David H. Sharp, John Reinitz, D. Sharp, 2003, Complexus.

Optimal parallelization of simulated annealing by state mixing

John Reinitz, King-Wai Chu, 2001 .