Mirny, Leonid: search on Z-Library

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1

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization

Nora, Elphège P., Goloborodko, Anton, Valton, Anne-Laure, Gibcus, Johan H., Uebersohn, Alec, Abdennur, Nezar, Dekker, Job, Mirny, Leonid A., Bruneau, Benoit G.

Journal:

Year:

2017

Language:

english

File:

PDF, 8.54 MB

english, 2017

2

The 3D Genome as Moderator of Chromosomal Communication

Dekker, Job, Mirny, Leonid

Journal:

Year:

2016

Language:

english

File:

PDF, 1017 KB

english, 2016

3

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

Flyamer, Ilya M., Gassler, Johanna, Imakaev, Maxim, Brandão, Hugo B., Ulianov, Sergey V., Abdennur, Nezar, Razin, Sergey V., Mirny, Leonid A., Tachibana-Konwalski, Kikuë

Journal:

Year:

2017

Language:

english

File:

PDF, 10.75 MB

english, 2017

4

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

van Berkum, Nynke L., Lieberman-Aiden, Erez, Williams, Louise, Imakaev, Maxim, Gnirke, Andreas, Mirny, Leonid A., Dekker, Job, Lander, Eric S.

Journal:

Journal of Visualized Experiments

Year:

2010

Language:

english

File:

PDF, 415 KB

english, 2010

5

Monte Carlo modeling of epidemiological studies

Shlyakhter, Alexander, Mirny, Leonid, Vlasov, Alexander, Wilson, Richard

Journal:

Human and Ecological Risk Assessment An International Journal

Year:

1996

Language:

english

File:

PDF, 919 KB

english, 1996

6

The fractal globule as a model of chromatin architecture in the cell

Leonid A. Mirny

Journal:

Chromosome Research

Year:

2011

Language:

english

File:

PDF, 583 KB

english, 2011

7

Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score

Michele Vendruscolo, Leonid A. Mirny, Eugene I. Shakhnovich, Eytan Domany

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 222 KB

english, 2000

8

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Boettiger, Alistair N., Bintu, Bogdan, Moffitt, Jeffrey R., Wang, Siyuan, Beliveau, Brian J., Fudenberg, Geoffrey, Imakaev, Maxim, Mirny, Leonid A., Wu, Chao-ting, Zhuang, Xiaowei

Journal:

Year:

2016

Language:

english

File:

PDF, 1.54 MB

english, 2016

9

Formation of Chromosomal Domains by Loop Extrusion

Fudenberg, Geoffrey, Imakaev, Maxim, Lu, Carolyn, Goloborodko, Anton, Abdennur, Nezar, Mirny, Leonid A.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.92 MB

english, 2016

10

An optimized energy potential can predict SH2 domain-peptide interactions

Wunderlich, Zeba, Mirny, Leonid

Journal:

Nature Precedings

Year:

2008

File:

PDF, 1.06 MB

2008

11

10.1038/74111

Shakhnovich, Eugene I., Li, Lewyn, Mirny, Leonid A.

Journal:

Natural Structural Biology

Year:

2000

Language:

english

File:

PDF, 333 KB

english, 2000

12

Kinetics of Protein-DNA Interaction: Facilitated Target Location in Sequence-Dependent Potential

Slutsky, Michael, Mirny, Leonid A.

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 344 KB

english, 2004

13

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

Marti-Renom, Marc A., Mirny, Leonid A., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 630 KB

english, 2011

14

High-order chromatin architecture determines the landscape of chromosomal alterations in cancer

Fudenberg, Geoffrey, Getz, Gad, Meyerson, Matthew, Mirny, Leonid

Journal:

Nature Precedings

Year:

2011

File:

PDF, 2.89 MB

2011

15

10.1038/74122

Shakhnovich, Eugene I., Li, Lewyn, Mirny, Leonid A.

Journal:

Nature Genetics

Year:

2000

Language:

english

File:

PDF, 252 KB

english, 2000

16

Zfx Controls the Self-Renewal of Embryonic and Hematopoietic Stem Cells

Jose M. Galan-Caridad, Sivan Harel, Teresita L. Arenzana, Z. Esther Hou, Fiona K. Doetsch, Leonid A. Mirny, Boris Reizis

Journal:

Year:

2007

Language:

english

File:

PDF, 1.65 MB

english, 2007

17

Using the Topology of Metabolic Networks to Predict Viability of Mutant Strains

Wunderlich, Zeba, Mirny, Leonid A.

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 204 KB

english, 2006

18

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

Imakaev, Maxim, Fudenberg, Geoffrey, McCord, Rachel Patton, Naumova, Natalia, Goloborodko, Anton, Lajoie, Bryan R, Dekker, Job, Mirny, Leonid A

Journal:

Year:

2012

Language:

english

File:

PDF, 1.17 MB

english, 2012

19

A pathway for mitotic chromosome formation

Gibcus, Johan H., Samejima, Kumiko, Goloborodko, Anton, Samejima, Itaru, Naumova, Natalia, Nuebler, Johannes, Kanemaki, Masato T., Xie, Linfeng, Paulson, James R., Earnshaw, William C., Mirny, Leonid

Journal:

Year:

2018

Language:

english

File:

PDF, 8.68 MB

english, 2018

20

Cooler: scalable storage for Hi-C data and other genomically-labeled arrays

Abdennur, Nezar, Mirny, Leonid, Wren, Jonathan

Journal:

Year:

2019

Language:

english

File:

PDF, 8.73 MB

english, 2019

21

Highly structured homolog pairing reflects functional organization of the Drosophila genome

AlHaj Abed, Jumana, Erceg, Jelena, Goloborodko, Anton, Nguyen, Son C., McCole, Ruth B., Saylor, Wren, Fudenberg, Geoffrey, Lajoie, Bryan R., Dekker, Job, Mirny, Leonid A., Wu, C.-ting

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 4.43 MB

english, 2019

22

Ultrastructural Details of Mammalian Chromosome Architecture

Krietenstein, Nils, Abraham, Sameer, Venev, Sergey V., Abdennur, Nezar, Gibcus, Johan, Hsieh, Tsung-Han S., Parsi, Krishna Mohan, Yang, Liyan, Maehr, RenÃ©, Mirny, Leonid A., Dekker, Job, Rando, Olive

Journal:

Year:

2020

Language:

english

File:

PDF, 8.21 MB

english, 2020

23

Diffusion in correlated random potentials, with applications to DNA

Slutsky, Michael, Kardar, Mehran, Mirny, Leonid

Journal:

Physical Review E

Year:

2004

Language:

english

File:

PDF, 391 KB

english, 2004

24

Biophysics: Cell commuters avoid delays

Journal:

Year:

2008

Language:

english

File:

PDF, 341 KB

english, 2008

25

Universality and diversity of the protein folding scenarios:a comprehensive analysis with the aid of a lattice model

Leonid A Mirny, Victor Abkevich, Eugene I Shakhnovich

Journal:

Folding and Design

Year:

1996

Language:

english

File:

PDF, 948 KB

english, 1996

26

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

Doyle, Boryana, Fudenberg, Geoffrey, Imakaev, Maxim, Mirny, Leonid A., Marti-Renom, Marc A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.07 MB

english, 2014

27

Isoform-Specific Expression and Feedback Regulation of E Protein TCF4 Control Dendritic Cell Lineage Specification

Grajkowska, Lucja T., Ceribelli, Michele, Lau, Colleen M., Warren, Margaret E., Tiniakou, Ioanna, Nakandakari Higa, Sandra, Bunin, Anna, Haecker, Hans, Mirny, Leonid A., Staudt, Louis M., Reizis, Bori

Journal:

Year:

2017

Language:

english

File:

PDF, 3.58 MB

english, 2017

28

A Ligand-Based Approach to Understanding Selectivity of Nuclear Hormone Receptors PXR, CAR, FXR, LXRα, and LXRβ

Sean Ekins, Leonid Mirny, Erin G. Schuetz

Journal:

Pharmaceutical Research

Year:

2002

Language:

english

File:

PDF, 747 KB

english, 2002

29

A mechanism of cohesin‐dependent loop extrusion organizes zygotic genome architecture

Gassler, Johanna, Brandão, Hugo B, Imakaev, Maxim, Flyamer, Ilya M, Ladstätter, Sabrina, Bickmore, Wendy A, Peters, Jan‐Michael, Mirny, Leonid A, Tachibana, Kikuë

Journal:

The EMBO Journal

Year:

2017

Language:

english

File:

PDF, 3.58 MB

english, 2017

30

Chromatin organization by an interplay of loop extrusion and compartmental segregation

Nuebler, Johannes, Fudenberg, Geoffrey, Imakaev, Maxim, Abdennur, Nezar, Mirny, Leonid A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 2.55 MB

english, 2018

31

Limits of Chromosome Compaction by Loop-Extruding Motors

Banigan, Edward J., Mirny, Leonid A.

Journal:

Physical Review X

Year:

2019

Language:

english

File:

PDF, 590 KB

english, 2019

32

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs

Mirny, Leonid, Wunderlich, Zeba

Journal:

Nature Precedings

Year:

2008

Language:

english

File:

PDF, 288 KB

english, 2008

33

Higher-order chromatin structure: bridging physics and biology

Geoffrey Fudenberg, Leonid A Mirny

Journal:

Current Opinion in Genetics & Development

Year:

2012

Language:

english

File:

PDF, 701 KB

english, 2012

34

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs

Wunderlich, Zeba, Mirny, Leonid

Journal:

Nature Precedings

Year:

2008

Language:

english

File:

PDF, 288 KB

english, 2008

35

Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals

Feodorova, Yana, Falk, Martin, Mirny, Leonid A., Solovei, Irina

Journal:

Trends in Cell Biology

Year:

2020

File:

PDF, 2.10 MB

2020

36

Using Orthologous and Paralogous Proteins to Identify Specificity-determining Residues in Bacterial Transcription Factors

Leonid A. Mirny, Mikhail S. Gelfand

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 645 KB

english, 2002

37

Compaction and Segregation of Sister Chromatids by Loop-Extruding Enzymes

Goloborodko, Anton, Imakaev, Maxim, Marko, John F., Mirny, Leonid

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 41 KB

english, 2017

38

Different gene regulation strategies revealed by analysis of binding motifs

Zeba Wunderlich, Leonid A. Mirny

Journal:

Trends in Genetics

Year:

2009

Language:

english

File:

PDF, 700 KB

english, 2009

39

Chromosomal architecture changes upon cell differentiation

Maxim Imakaev, Geoffrey Fudenberg, Leonid Mirny

Journal:

Epigenetics & Chromatin

Year:

2013

Language:

english

File:

PDF, 77 KB

english, 2013

40

Polymer Models of Yeast S. Cerevisiae Genome Organization

Goloborodko, Anton, Fudenberg, Geoffrey, Belton, Jon-Matthew, Imakaev, Maxim, Dekker, Job, Mirny, Leonid¯

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 77 KB

english, 2013

41

Modeling chromosomes: Beyond pretty pictures

Imakaev, Maxim V., Fudenberg, Geoffrey, Mirny, Leonid A.

Journal:

Year:

2015

Language:

english

File:

PDF, 674 KB

english, 2015

42

Nucleosome-mediated cooperativity between transcription factors

Journal:

Nature Precedings

Year:

2009

Language:

english

File:

PDF, 5.05 MB

english, 2009

43

Evolutionary conservation of the folding nucleus

Leonid Mirny, Eugene Shakhnovich

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 267 KB

english, 2001

44

Using Topology of the Metabolic Network to Predict Viability of Mutant Strains

Zeba Wunderlich, Leonid Mirny

Journal:

Year:

2005

Language:

english

File:

PDF, 2.99 MB

english, 2005

45

Detection of α/β-hydrolase fold in the cell surface esterases of Acinetobacter species using an analysis of 3D profiles

Rinat N. Alon, Leonid Mirny, Joel L. Sussman, David L. Gutnick

Journal:

Year:

1995

Language:

english

File:

PDF, 1013 KB

english, 1995

46

Erratum: Diffusion in correlated random potentials, with applications to DNA [Phys. Rev. E 69 , 061903 (2004)]

Slutsky, Michael, Kardar, Mehran, Mirny, Leonid A.

Journal:

Physical Review E

Year:

2004

Language:

english

File:

PDF, 11 KB

english, 2004

47

Virus shapes and buckling transitions in spherical shells

Lidmar, Jack, Mirny, Leonid, Nelson, David R.

Journal:

Physical Review E

Year:

2003

Language:

english

File:

PDF, 1.04 MB

english, 2003

48

[Methods in Cell Biology] Microtubules, in vitro Volume 95 || Quantitative Characterization of Filament Dynamics by Single-Molecule Lifetime Measurements

Mirny, Leonid A.

Year:

2010

Language:

english

File:

PDF, 995 KB

english, 2010

49

Polymer Models Integrate Inverted Nuclear Geometry with Conventional HI-C Compartmentalization

Falk, Martin J., Naumova, Natalia M., Fudenberg, Geoffrey, Feodorova, Yana N., Dekker, Job, Mirny, Leonid A., Solovei, Irina

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

50

Corrigendum: The 4D nucleome project

Dekker, Job, Belmont, Andrew S., Guttman, Mitchell, Leshyk, Victor O., Lis, John T., Lomvardas, Stavros, Mirny, Leonid A., O’Shea, Clodagh C., Park, Peter J., Ren, Bing, Politz, Joan C. Ritland, Shend

Journal:

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

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