D. Pervouchine

发表

Gene-specific patterns of expression variation across organs and species

Dmitri D. Pervouchine, R. Guigó, T. Gingeras, 2016, Genome Biology.

The human transcriptome across tissues and individuals

Dmitri D. Pervouchine, Ayellet V. Segrè, Pedro G. Ferreira, 2015, Science.

A comparative encyclopedia of DNA elements in the mouse genome

Shane J. Neph, Dmitri D. Pervouchine, Matthew D. Rasmussen, 2014, Nature.

Comparative Analysis of the Transcriptome across Distant Species

Peter J. Bickel, Raymond K. Auerbach, Peter J. Park, 2014, Nature.

Networka Theta Rhythm in a Model of CA1 Interneuron Slow and Fast Inhibition and an H-Current Interact to

Corey D. Acker, M. Whittington, N. Kopell, 2016 .

Slow and fast inhibition and an H-current interact to create a theta rhythm in a model of CA1 interneuron network.

Nancy Kopell, Dmitri D. Pervouchine, Horacio G Rotstein, 2005, Journal of neurophysiology.

IRIS: intermolecular RNA interaction search.

D. Pervouchine, 2004, Genome informatics. International Conference on Genome Informatics.

Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes

M. Gerstein, Andrea Tanzer, S. Balasubramanian, 2014, bioRxiv.

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression

Dmitri D. Pervouchine, Michael A. Beer, M. Gerstein, 2014, Nature Communications.

Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay

Dmitri D. Pervouchine, A. Frankish, R. Guigó, 2019, Nucleic acids research.

Novel autoregulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay

Dmitri D. Pervouchine, A. Frankish, R. Guigó, 2018 .

A benchmark for RNA-seq quantification pipelines

Dmitri D. Pervouchine, C. Mason, R. Irizarry, 2016, Genome Biology.

Engineered riboregulators enable post-transcriptional control of gene expression

Farren J. Isaacs, Dmitri D. Pervouchine, J. Collins, 2004, Nature Biotechnology.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction

Nuno A. Fonseca, Jonathan M. Mudge, J. Harrow, 2015, BMC Genomics.

Neuronal metabolism governs cortical network response state.

Dmitri D. Pervouchine, R. Traub, M. Whittington, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Conserved long-range base pairings are associated with pre-mRNA processing of human genes

Dmitri D. Pervouchine, R. Guigó, D. Pervouchine, 2020, Nature Communications.

JN-00957-2004 : Final Accepted Version Title : Slow and fast inhibition and an h-current interact to create a theta rhythm in a model of CA 1 interneuron network

Miles A. Whittington, Horacio G. Rotstein, Nancy Kopell, 2005 .

On the normalization of RNA equilibrium free energy to the length of the sequence.

Simon Kasif, S. Kasif, J. Graber, 2003, Nucleic acids research.

A limited set of transcriptional programs define major cell types

Dmitri D. Pervouchine, R. Guigó, T. Gingeras, 2019, Genome research.

Erratum: A benchmark for RNA-seq quantification pipelines [Genome Biol. (2016), 17, 74], DOI: 10.1186/s13059-016-0940-1

Xintao Wei, Mingxiang Teng, Rafael A. Irizarry, 2016 .

Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA

Andrey A. Mironov, Dmitri D. Pervouchine, Alexander V. Favorov, 2006, J. Bioinform. Comput. Biol..

Modulation of alternative splicing by long-range RNA structures in Drosophila

Mikhail S. Gelfand, Dmitri D. Pervouchine, M. Gelfand, 2009, Nucleic acids research.

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes

Dmitri D. Pervouchine, D. Pervouchine, 2018, Genes.

An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons

Dmitri D. Pervouchine, D. Pervouchine, T. Ivanov, 2018, Genes.

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes

Dmitri D. Pervouchine, O. Kalinina, D. Pervouchine, 2020, bioRxiv.

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

Jonathan M. Mudge, Dmitri D. Pervouchine, J. Harrow, 2019, npj Genomic Medicine.

Systematic re-annotation of 191 genes associated with early-onset epilepsy unmasks de novo variants linked to Dravet syndrome in novel SCN1A exons

Jonathan M. Mudge, Dmitri D. Pervouchine, J. Harrow, 2019, bioRxiv.

Neurons to Transient Inputs Phase-Response Curves Give the Responses of

G. Ermentrout, A. Reyes, K. Aihara, 2006 .

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Dmitri D. Pervouchine, Pedro G. Ferreira, Marta R. Hidalgo, 2018, Nature Communications.

Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs

D. Papatsenko, D. Pervouchine, M. Granovskaya, 2022, PloS one.

A benchmark for RNAseq quantification pipelines

C. Mason, R. Irizarry, S. Djebali, 2016 .

Multiple competing RNA structures dynamically control alternative splicing in human ATE1 gene

Dmitri D. Pervouchine, O. Dontsova, D. Pervouchine, 2020, bioRxiv.

Tissue-specific regulation of gene expression via unproductive splicing

A. Mironov, D. Pervouchine, Alexey Mironov, 2022, bioRxiv.

TransCistor reveals the landscape of cis -regulatory long noncoding 1 RNAs 2

Dmitri D. Pervouchine, Hugo A. Guillen-Ramirez, Rory Johnson, 2022 .

Transcriptome sequencing suggests that pre-mRNA splicing counteracts premature intronic polyadenylation

D. Pervouchine, Sergei Margasyuk, Mariia Vlasenok, 2022, bioRxiv.

Tandem Exon Duplications Expanding the Alternative Splicing Repertoire

D. Pervouchine, Timofei Ivanov, 2022, Acta naturae.

A limited set of transcriptional programs define major histological types and provide the molecular basis for a cellular taxonomy of the human body

Dmitri D. Pervouchine, R. Guigó, T. Gingeras, 2019, bioRxiv.

Tissue-specific regulation of gene expression via unproductive splicing

Dmitri D. Pervouchine, A. Mironov, D. Pervouchine, 2023, bioRxiv.

Intron-centric estimation of alternative splicing from RNA-seq data

Roderic Guigó, Dmitri D. Pervouchine, David G. Knowles, 2012, Bioinform..

Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs

Dmitri D. Pervouchine, D. Papatsenko, D. Pervouchine, 2021, bioRxiv.

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Pedro G. Ferreira, Marta R. Hidalgo, R. Guigó, 2018, Nature Communications.

Circular exonic RNAs: When RNA structure meets topology.

Dmitri D. Pervouchine, D. Pervouchine, 2019, Biochimica et biophysica acta. Gene regulatory mechanisms.

RNAcontacts, a pipeline for predicting contacts from RNA proximity ligation assays

D. Pervouchine, Changchang Cao, Guo Li, 2022, bioRxiv.

Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation

Dmitri D. Pervouchine, D. Pervouchine, Mariia Vlasenok, 2023, bioRxiv.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

Jonathan M. Mudge, J. Harrow, A. Frankish, 2019, npj Genomic Medicine.

Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures

Mikhail S. Gelfand, Andrey A. Mironov, Dmitri D. Pervouchine, 2012, RECOMB.

conserved long-range RNA structures Evidence for widespread association of mammalian splicing and Material Supplemental

Dmitri D. Pervouchine, M. Gelfand, A. Mironov, 2011 .

Gene-specific patterns of expression variation across organs and species

Dmitri D. Pervouchine, R. Guigó, T. Gingeras, 2016, Genome Biology.

Erratum to: A benchmark for RNA-seq quantification pipelines

C. Mason, R. Irizarry, S. Djebali, 2016, Genome Biology.

MULTIPLE RHYTHMS AND SWITCHES IN THE NERVOUS SYSTEM

M. Whittington, T. Gloveli, N. Kopell, 2007 .

Gamma and Theta Rhythms in Biophysical Models of Hippocampal Circuits

Nancy Kopell, Dmitri D. Pervouchine, Paola Malerba, 2010 .

Low-Dimensional Maps Encoding Dynamics in Entorhinal Cortex and Hippocampus

Miles A. Whittington, Horacio G. Rotstein, Nancy Kopell, 2006, Neural Computation.

IRBIS: a systematic search for conserved complementarity

Dmitri D. Pervouchine, D. Pervouchine, Dmitri D Pervouchine, 2014, RNA.

Supplemental Material References

M. Gelfand, A. Mironov, D. Cooper, 2012 .

Comparative Analysis of the Transcriptome across Distant Species

Dmitri D. Pervouchine, Gennifer E. Merrihew, Benjamin W. Booth, 2014, Nature.

A comparative encyclopedia of DNA elements in the mouse genome

Mukul S. Bansal, Shane J. Neph, Dmitri D. Pervouchine, 2014, Nature.

Hierarchy of Closures of Matrix Pencils

D. Pervouchine, 2004 .

RNAcontacts: A Pipeline for Predicting Contacts from RNA Proximity Ligation Assays

D. Pervouchine, Changchang Cao, Sergei Margasyuk, 2023, Acta naturae.

Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay

Dmitri D. Pervouchine, A. Frankish, R. Guigó, 2019, Nucleic acids research.