J. Reinitz

发表

Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila.

M. Levine, J. Reinitz, M. Levine, 1990, Developmental biology.

A connectionist model of the Drosophila blastoderm

E. Mjolsness, D. Sharp, J. Reinitz, 1990 .

Dynamic control of positional information in the early Drosophila embryo

David H. Sharp, Manu, D. Sharp, 2004, Nature.

Prediction of mutant expression patterns using gene circuits.

David H. Sharp, D. Sharp, J. Reinitz, 1998, Bio Systems.

Genetic Algorithms for Genetic Neural Nets.

E. Mjolsness, D. Sharp, J. Reinitz, 1991 .

Modeling the Connection Between Development and Evolution: Preliminary Report

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

Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback.

David H. Sharp, E. Mjolsness, D. Sharp, 1995, The Journal of experimental zoology.

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

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

Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient.

J. Reinitz, D. Arnosti, D. Kosman, 1999, Development.

Mechanism of eve stripe formation

David H. Sharp, D. Sharp, J. Reinitz, 1995, Mechanisms of Development.

Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins

J. Reinitz, D. Kosman, S. Small, 1998, Development Genes and Evolution.

Stripe forming architecture of the gap gene system.

D. Sharp, J. Reinitz, D. Kosman, 1998, Developmental genetics.

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.

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

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

Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation

David H. Sharp, Manu, D. Sharp, 2009, PLoS biology.

Dynamical Analysis of Regulatory Interactions in the Gap Gene System of Drosophila melanogaster

David H. Sharp, Manu, D. Sharp, 2004, Genetics.

Characterization of the Drosophila segment determination morphome.

Manu, J. Reinitz, D. Kosman, 2008, Developmental biology.

Drosophila blastoderm patterning.

Manu, J. Reinitz, J. Jaeger, 2012, Current opinion in genetics & development.

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

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

Temporal classification of Drosophila segmentation gene expression patterns by the multi-valued neural recognition method.

J. Reinitz, I. Aizenberg, E. Myasnikova, 2002, Mathematical biosciences.

Adaptation, fitness landscape learning and fast evolution.

J. Reinitz, S. Vakulenko, D. Grigoriev, 2019, F1000Research.

Adaptation, fitness landscape learning and fast evolution

J. Reinitz, S. Vakulenko, D. Grigoriev, 2019, F1000Research.

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.

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

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

Cell divisions as a mechanism for selection in stable steady states of multi-stationary gene circuits

J. Reinitz, K. Kozlov, V. Gursky, 2006 .

Fully interpretable deep learning model of transcriptional control

J. Reinitz, Kenneth A. Barr, Yi Liu, 2020, Bioinformatics.

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

J. Reinitz, O. Radulescu, Kenneth A. Barr, 2019, PLoS computational biology.

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.

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.

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.

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.

Thoracic patterning by the Drosophila gap gene hunchback.

D Kosman, J Reinitz, J. Reinitz, 2001, Developmental biology.

Transcriptional Control in Drosophila

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

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.

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.

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 .

Study of stability mechanisms of embryonic development in fruit fly Drosophila

J. Reinitz, M. Samsonova, S. Surkova, 2011, Russian Journal of Developmental Biology.

Model with asymptotically stable dynamics for Drosophila gap gene network

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

The Whitham principle for multikink solutions of reaction-diffusion equations

J. Reinitz, O. Radulescu, S. Vakulenko, 2009 .

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.

Developmental biology: A ten per cent solution

John Reinitz, J. Reinitz, 2007, Nature.

Dynamic filtration of the expression pattern variability of Drosophila zygotic segmentation genes

J. Reinitz, E. Myasnikova, M. Samsonova, 2008 .

The Center for Data Intensive Computing Center for Data Intensive Computing Table 2. Cdic Affiliates Name Affiliation Expertise Carl Anderson Bnl/biology Protein Structures Carmen Benkovitz Bnl/environmental Sciences Atmospheric Transport Michael Creutz Bnl/physics Lattice Gauge Theory Yuefan Deng S

Applied, J. Glimm, J. Reinitz, 2002 .

Gene networks accelerate evolution by fitness landscape learning

J. Reinitz, S. Vakulenko, D. Grigoriev, 2016, 1609.08784.

Gene regulation and noise reduction by coupling of stochastic processes.

J. Reinitz, J. Hornos, A. F. Ramos, 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient.

J. Reinitz, D. Arnosti, D. Kosman, 1999, Development.

Important advances in understanding the molecular mechanisms of development have stemmed from genetic analysis of Drosophila embryogenesis. Regulation of gene expression in the early embryo is critical for determining specification of regional and segmental identity (Nüsslein-

J. Reinitz, D. Arnosti, D. Kosman, 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..

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

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

S1 Text : sequence level model of the gene regulation

J. Reinitz, O. Radulescu, Kenneth A. Barr, 2019 .

Methods for acquisition of quantitative data from confocal images of gene expression in situ

K. N. Kozlov, E. M. Myasnikova, M. G. Samsonova, 2008, Cell and Tissue Biology.

A Prognostic Gene Signature for Metastasis-Free Survival of Triple Negative Breast Cancer Patients

J. Reinitz, S. Chin, C. Caldas, 2013, PloS one.

DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan.

J. Reinitz, I. Rebay, C. Hope, 2017, Biophysical journal.

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

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

Natural variation of the expression pattern of the segmentation gene even-skipped in melanogaster.

J. Reinitz, M. Kreitman, M. Ludwig, 2015, Developmental biology.

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

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

Quantitative imaging of gene expression in Drosophila embryos.

J. Reinitz, K. Kozlov, E. Myasnikova, 2013, Cold Spring Harbor protocols.

The effect of mutational robustness on the evolvability of multicellular organisms and eukaryotic cells

J. Reinitz, M. Kreitman, Pengyao Jiang, 2021, bioRxiv.

The relationship between robustness and evolution

J. Reinitz, M. Kreitman, Pengyao Jiang, 2018 .

Punctuated evolution and robustness in morphogenesis

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

Reverse Engineering the Gap Gene Network of Drosophila melanogaster

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

Theoretical and experimental analysis of the phage lambda genetic switch implies missing levels of co-operativity.

J Reinitz, J. Reinitz, J. Vaisnys, 1990, Journal of theoretical biology.

Master equation simulation analysis of immunostained Bicoid morphogen gradient

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

A connectionist model of development.

David H. Sharp, D H Sharp, E Mjolsness, 1991, Journal of theoretical biology.

Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations

J. Reinitz, M. Rosner, John J. Skinner, 2015, PloS one.

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

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

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

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

A database for management of gene expression data in situ

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

Automated assay of gene expression at cellular resolution.

D Kosman, J Reinitz, D H Sharp, 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Biological implications of $\mathfrak{so}(2,1)$ symmetry in exact solutions for a self-repressing gene

J. Reinitz, A. F. Ramos, 2017, 1707.04365.

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

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

Fully interpretable deep learning model of transcriptional control

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

On the dynamic nature of positional information.

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

Multiscale modeling of developmental processes

David H. Sharp, Eric Mjolsness, John Reinitz, 1993 .

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

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

Parallel Simulated Annealing by Mixing of States

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

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.

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.

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

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

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..

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

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

Hybrid Reductions of Computational Models of Ion Channels Coupled to Cellular Biochemistry

Ovidiu Radulescu, Jasha Sommer-Simpson, John Reinitz, 2016, CMSB.

Robust morphogenesis by chaotic dynamics

J. Reinitz, S. Vakulenko, D. Grigoriev, 2023, Scientific reports.

A synthetic biology approach to the development of transcriptional regulatory models and custom enhancer design.

J. Reinitz, Ah-Ram Kim, Kenneth A. Barr, 2013, Methods.

Mechanisms of gap gene expression canalization in the Drosophila blastoderm

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

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

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

Parallel simulated annealing using an adaptive resampling interval

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

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..

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

J. Reinitz, A. F. Ramos, 2019, The Journal of chemical physics.

Noise reduction by coupling of stochastic processes and canalization in biology

J. Reinitz, J. Hornos, A. F. Ramos, 2013, 1302.1909.

Bursting on a two state stochastic model for gene transcription in Drosophila embryos

J. Reinitz, R. Yvinec, G. N. Prata, 2017, bioRxiv.