Publications
Nuebler
J,
Fudenberg
G,
Imakaev
M,
Abdennur
N,
Mirny
L
(2017). Chromatin organization by an interplay of loop extrusion and compartmental segregation
bioRxiv
Gibcus
JH,
Samejima
K,
Goloborodko
A,
Samejima
I,
Naumova
N,
Kanemaki
M,
Xie
L,
Paulson
JR,
Earnshaw
WC,
Mirny
LA,
Dekker
J
(2017). Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays
bioRxiv
Gassler
J,
Brandao
HB,
Imakaev
M,
Flyamer
IM,
Ladstatter
S,
Bickmore
WA,
Peters
J,
Mirny
LA,
Tachibana-Konwalski
K
(2017). A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture
The EMBO Journal
e201798083
[bioRxiv (August, 2017)]
Finn
E,
Pegoraro
G,
Brandao
HB,
Valton
A,
Oomen
ME,
Dekker
J,
Mirny
L,
Misteli
T
(2017). Heterogeneity and intrinsic variation in spatial genome organization
bioRxiv
Kerpedjiev
P,
Abdennur
N,
Lekschas
F,
McCallum
C,
Dinkla
K,
Strobelt
H,
Luber
JM,
Ouellette
SB,
Ahzir
A,
Kumar
N,
Hwang
J,
Alver
B,
Pfister
H,
Mirny
LA,
Park
PJ,
Gehlenborg
N
(2017). HiGlass: Web-based visual comparison and exploration of genome interaction maps
bioRxiv
Schwarzer
W,
Abdennur
N,
Goloborodko
A,
Pekowska
A,
Fudenberg
G,
Loe-Mie
Y,
Fonseca
NA,
Huber
W,
H. Haering
C,
Mirny
L,
Spitz
F
(2017). Two independent modes of chromatin organization revealed by cohesin removal
Nature
551(7678):51-56
[bioRxiv (Dec, 2016)]
Dekker
J,
Belmont
AS,
Guttman
M,
Leshyk
VO,
Lis
JT,
Lomvardas
S,
Mirny
LA,
O’Shea
CC,
Park
PJ,
Ren
B,
et al.
(2017). The 4D nucleome project
Nature
549(7671):219-226
Phillips
AM,
Gonzalez
LO,
Nekongo
EE,
Ponomarenko
AI,
McHugh
SM,
Butty
VL,
Levine
SS,
Lin
Y,
Mirny
LA,
Shoulders
MD
(2017). Host proteostasis modulates influenza evolution
eLife
6
Schalbetter
SA,
Goloborodko
A,
Fudenberg
G,
Belton
J,
Miles
C,
Yu
M,
Dekker
J,
Mirny
L,
Baxter
J
(2017). SMC complexes differentially compact mitotic chromosomes according to genomic context
Nature Cell Biology
19(9):1071-1080
[bioRxiv (Dec, 2016)]
Nora
EP,
Goloborodko
A,
Valton
A,
Gibcus
JH,
Uebersohn
A,
Abdennur
N,
Dekker
J,
Mirny
LA,
Bruneau
BG
(2017). Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization
Cell
169(5):930-944.e22
[bioRxiv (Dec, 2016)]
McFarland
CD,
Yaglom
JA,
Wojtkowiak
JW,
Scott
JG,
Morse
DL,
Sherman
MY,
Mirny
LA
(2017). The damaging effect of passenger mutations on cancer progression
Cancer Research
Flyamer
IM,
Gassler
J,
Imakaev
M,
Brandão
HB,
Ulianov
SV,
Abdennur
N,
Razin
SV,
Mirny
LA,
Tachibana-Konwalski
K
(2017). Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Nature
544(7648):110-114
Grajkowska
LT,
Ceribelli
M,
Lau
CM,
Warren
ME,
Tiniakou
I,
Nakandakari Higa
S,
Bunin
A,
Haecker
H,
Mirny
LA,
Staudt
LM,
Reizis
B
(2017). Isoform-specific expression and feedback regulation of E protein TCF4 control dendritic cell lineage specification
Immunity
46(1):65-77
Sawai
CM,
Babovic
S,
Upadhaya
S,
Knapp
DJ,
Lavin
Y,
Lau
CM,
Goloborodko
A,
Feng
J,
Fujisaki
J,
Ding
L,
Mirny
L,
Merad
M,
Eaves
CJ,
Reizis
B
(2016). Hematopoietic stem cells are the major source of multilineage hematopoiesis in adult animals
Immunity
45(3):597-609
Goloborodko
A,
Marko
JF,
Mirny
LA
(2016). Chromosome compaction by active loop extrusion
Biophysical Journal
110(10):2162-2168
[bioRxiv (Jun, 2015)]
Fudenberg
G,
Imakaev
M,
Lu
C,
Goloborodko
A,
Abdennur
N,
Mirny
LA
(2016). Formation of chromosomal domains by loop extrusion
Cell Reports
15(9):2038-2049
[bioRxiv (Aug, 2015)]
Goloborodko
A,
Imakaev
MV,
Marko
JF,
Mirny
L
(2016). Compaction and segregation of sister chromatids via active loop extrusion
eLife
5
[bioRxiv (Jan, 2016)]
Dekker
J,
Mirny
L
(2016). The 3D genome as moderator of chromosomal communication
Cell
164(6):1110-1121
Boettiger
AN,
Bintu
B,
Moffitt
JR,
Wang
S,
Beliveau
BJ,
Fudenberg
G,
Imakaev
M,
Mirny
LA,
Wu
C,
Zhuang
X
(2016). Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
Nature
529(7586):418-422
Imakaev
MV,
Fudenberg
G,
Mirny
LA
(2015). Modeling chromosomes: Beyond pretty pictures
FEBS Letters
589(20PartA):3031-3036
Kind
J,
Pagie
L,
Vries
SS,
Nahidiazar
L,
Dey
SS,
Bienko
M,
Zhan
Y,
Lajoie
B,
Graaf
CA,
Amendola
M,
Fudenberg
G,
Imakaev
M,
Mirny
L,
Jalink
K,
Dekker
J,
van Oudenaarden
A,
van Steensel
B
(2015). Genome-wide maps of nuclear lamina interactions in single human cells
Cell
163(1):134-147
McFarland
CD,
Yaglom
JA,
Wojtkowiak
JW,
Scott
JG,
Morse
DL,
Sherman
MY,
Mirny
LA
(2015). Passenger DNA alterations reduce cancer fitness in cell culture and mouse models
bioRxiv
Imakaev
MV,
Tchourine
KM,
Nechaev
SK,
Mirny
LA
(2015). Effects of topological constraints on globular polymers
Soft Matter
11(4):665-671
Mizuguchi
T,
Fudenberg
G,
Mehta
S,
Belton
J,
Taneja
N,
Folco
HD,
FitzGerald
P,
Dekker
J,
Mirny
L,
Barrowman
J,
Grewal
S
(2014). Cohesin-dependent globules and heterochromatin shape 3D genome architecture in s. pombe
Nature
516(7531):432-435
Dolmatova
E,
Tucker
NR,
Lin
H,
Cooper
RR,
Ye
J,
Sinner
MF,
Imakaev
M,
Lubitz
SA,
Leyton-Mange
J,
Vlahakes
G,
et al.
(2014). Identification of a functional SNP regulating pRRX1 at the 1q24 locus for atrial fibrillation
Circulation
130(Suppl 2):A18865-A18865
Doyle
B,
Fudenberg
G,
Imakaev
M,
Mirny
LA
(2014). Chromatin loops as allosteric modulators of enhancer-promoter interactions
PLoS Computational Biology
10(10):e1003867
[bioRxiv (Nov, 2014)]
McFarland
CD,
Mirny
LA,
Korolev
KS
(2014). Tug-of-war between driver and passenger mutations in cancer and other adaptive processes
Proceedings of the National Academy of Sciences
111(42):15138-15143
[bioRxiv (Feb, 2014)]
Yaglom
JA,
McFarland
C,
Mirny
L,
Sherman
MY
(2014). Oncogene-triggered suppression of DNA repair leads to DNA instability in cancer
Oncotarget
5(18):8367-8378
Weisberg
SP,
Smith-Raska
MR,
Esquilin
JM,
Zhang
J,
Arenzana
TL,
Lau
CM,
Churchill
M,
Pan
H,
Klinakis
A,
Dixon
JE,
et al.
(2014). ZFX controls propagation and prevents differentiation of acute t-lymphoblastic and myeloid leukemia
Cell Reports
6(3):528-540
Naumova
N,
Imakaev
M,
Fudenberg
G,
Zhan
Y,
Lajoie
BR,
Mirny
LA,
Dekker
J
(2013). Organization of the mitotic chromosome
Science
342(6161):948-953
McFarland
CD,
Korolev
KS,
Kryukov
GV,
Sunyaev
SR,
Mirny
LA
(2013). Impact of deleterious passenger mutations on cancer progression
Proceedings of the National Academy of Sciences
110(8):2910-2915
Le
TBK,
Imakaev
MV,
Mirny
LA,
Laub
MT
(2013). High-resolution mapping of the spatial organization of a bacterial chromosome
Science
342(6159):731-734
Dekker
J,
Mirny
L
(2013). Biological techniques: Chromosomes captured one by one
Nature
502(7469):45-46
Dekker
J,
Marti-Renom
MA,
Mirny
LA
(2013). Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
Nature Reviews Genetics
14(6):390-403
Leith
JS,
Tafvizi
A,
Huang
F,
Uspal
WE,
Doyle
PS,
Fersht
AR,
Mirny
LA,
Oijen
AM
(2012). Sequence-dependent sliding kinetics of p53
Proceedings of the National Academy of Sciences
109(41):16552-16557
Imakaev
M,
Fudenberg
G,
McCord
RP,
Naumova
N,
Goloborodko
A,
Lajoie
BR,
Dekker
J,
Mirny
LA
(2012). Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Nature Methods
9(10):999-1003
Engreitz
JM,
Agarwala
V,
Mirny
LA
(2012). Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease
PLoS ONE
7(9):e44196
Fudenberg
G,
Mirny
LA
(2012). Higher-order chromatin structure: Bridging physics and biology
Current Opinion in Genetics & Development
22(2):115-124
Fudenberg
G,
Getz
G,
Meyerson
M,
Mirny
LA
(2011). High order chromatin architecture shapes the landscape of chromosomal alterations in cancer
Nature Biotechnology
29(12):1109-1113
Marti-Renom
MA,
Mirny
LA
(2011). Bridging the resolution gap in structural modeling of 3D genome organization
PLoS Computational Biology
7(7):e1002125
Tafvizi
A,
Mirny
LA,
Oijen
AM
(2011). Dancing on DNA: Kinetic aspects of search processes on DNA
ChemPhysChem
12(8):1481-1489
Tafvizi
A,
Huang
F,
Fersht
AR,
Mirny
LA,
Oijen
AM
(2011). A single-molecule characterization of p53 search on DNA
Proceedings of the National Academy of Sciences
108(2):563-568
Mirny
LA
(2011). The fractal globule as a model of chromatin architecture in the cell
Chromosome Research
19(1):37-51
Mirny
LA
(2010). Nucleosome-mediated cooperativity between transcription factors
Proceedings of the National Academy of Sciences
107(52):22534-22539
Mirny
LA,
Needleman
DJ
(2010). Quantitative characterization of filament dynamics by single-molecule lifetime measurements
Microtubules, in vitro
Berkum
NL,
Lieberman-Aiden
E,
Williams
L,
Imakaev
M,
Gnirke
A,
Mirny
LA,
Dekker
J,
Lander
ES
(2010). Hi-C: A method to study the three-dimensional architecture of genomes.
Journal of Visualized Experiments
Bölinger
D,
Sułkowska
JI,
Hsu
H,
Mirny
LA,
Kardar
M,
Onuchic
JN,
Virnau
P
(2010). A stevedore’s protein knot
PLoS Computational Biology
6(4):e1000731
Needleman
DJ,
Groen
A,
Ohi
R,
Maresca
T,
Mirny
L,
Mitchison
T
(2009). Fast microtubule dynamics in meiotic spindles measured by single molecule imaging: Evidence that the spindle environment does not stabilize microtubules
Molecular Biology of the Cell
21(2):323-333
Wunderlich
Z,
Mirny
LA
(2009). Using genome-wide measurements for computational prediction of SH2-peptide interactions
Nucleic Acids Research
37(14):4629-4641
Lieberman-Aiden
E,
Berkum
NL,
Williams
L,
Imakaev
M,
Ragoczy
T,
Telling
A,
Amit
I,
Lajoie
BR,
Sabo
PJ,
Dorschner
MO,
et al.
(2009). Comprehensive mapping of long-range interactions reveals folding principles of the human genome
Science
326(5950):289-293
Wunderlich
Z,
Mirny
LA
(2009). Different gene regulation strategies revealed by analysis of binding motifs
Trends in Genetics
25(10):434-440
Mirny
L,
Slutsky
M,
Wunderlich
Z,
Tafvizi
A,
Leith
J,
Kosmrlj
A
(2009). How a protein searches for its site on DNA: The mechanism of facilitated diffusion
Journal of Physics A: Mathematical and Theoretical
42(43):434013
Leith
JS,
Tafvizi
A,
Huang
F,
Fersht
AR,
Mirny
LA,
Oijen
AM
(2009). Sequence-dependent kinetics of one-dimensional diffusion of p53 on DNA
Biophysical Journal
96(3):416a
Kolesov
G,
Mirny
LA
(2009). Using evolutionary information to find specificity-determining and co-evolving residues
Computational Systems Biology
Jamal Rahi
S,
Virnau
P,
Mirny
LA,
Kardar
M
(2008). Predicting transcription factor specificity with all-atom models
Nucleic Acids Research
36(19):6209-6217
Tafvizi
A,
Huang
F,
Leith
JS,
Fersht
AR,
Mirny
LA,
Oijen
AM
(2008). Tumor suppressor p53 slides on DNA with low friction and high stability
Biophysical Journal
95(1):L01-L03
Wunderlich
Z,
Mirny
LA
(2008). Spatial effects on the speed and reliability of protein-DNA search
Nucleic Acids Research
36(11):3570-3578
Mirny
L
(2008). Biophysics: Cell commuters avoid delays
Nature Physics
4(2):93-95
Gomez-Uribe
C,
Verghese
GC,
Mirny
LA
(2007). Operating regimes of signaling cycles: Statics, dynamics, and noise filtering
PLoS Computational Biology
3(12):e246
Kolesov
G,
Wunderlich
Z,
Laikova
ON,
Gelfand
MS,
Mirny
LA
(2007). How gene order is influenced by the biophysics of transcription regulation
Proceedings of the National Academy of Sciences
104(35):13948-13953
Kolesov
G,
Virnau
P,
Kardar
M,
Mirny
LA
(2007). Protein knot server: Detection of knots in protein structures
Nucleic Acids Research
35(Web Server):W425-W428
Levine
J,
Kueh
HY,
Mirny
L
(2007). Intrinsic fluctuations, robustness, and tunability in signaling cycles
Biophysical Journal
92(12):4473-4481
Galan-Caridad
JM,
Harel
S,
Arenzana
TL,
Hou
ZE,
Doetsch
FK,
Mirny
LA,
Reizis
B
(2007). Zfx controls the self-renewal of embryonic and hematopoietic stem cells
Cell
129(2):345-357
Wunderlich
Z,
Mirny
LA
(2006). Using the topology of metabolic networks to predict viability of mutant strains
Biophysical Journal
91(6):2304-2311
Virnau
P,
Mirny
LA,
Kardar
M
(2006). Intricate knots in proteins: Function and evolution
PLoS Computational Biology
2(9):e122
Spirin
V,
Gelfand
MS,
Mironov
AA,
Mirny
LA
(2006). A metabolic network in the evolutionary context: Multiscale structure and modularity
Proceedings of the National Academy of Sciences
103(23):8774-8779
Donald
JE,
Hubner
IA,
Rotemberg
VM,
Shakhnovich
EI,
Mirny
LA
(2005). CoC: A database of universally conserved residues in protein folds
Bioinformatics
21(10):2539-2540
Slutsky
M,
Mirny
LA
(2004). Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential
Biophysical Journal
87(6):4021-4035
Slutsky
M,
Kardar
M,
Mirny
L
(2004). Diffusion in correlated random potentials, with applications to DNA
Physical Review E
69(6)
Lidmar
J,
Mirny
L,
Nelson
DR
(2003). Virus shapes and buckling transitions in spherical shells
Physical Review E
68(5)
Spirin
V,
Mirny
LA
(2003). Protein complexes and functional modules in molecular networks
Proceedings of the National Academy of Sciences
100(21):12123-12128
Spirin
V,
Gelfand
M,
Mirny
L
(2003). Computational analysis of metabolic modules and pathways in E. coli metabolic network
ISCB
4
Chen
W,
Mirny
L,
Shakhnovich
EI
(2003). Fold recognition with minimal gaps
Proteins: Structure, Function, and Bioinformatics
51(4):531-543
Li
L,
Shakhnovich
EI,
Mirny
LA
(2003). Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases
Proceedings of the National Academy of Sciences
100(8):4463-4468
Ekins
S,
Mirny
L,
Schuetz
EG
(2002). A Ligand-Based Approach to Understanding Selectivity of Nuclear Hormone Receptors PXR, CAR, FXR, LXRα, and LXRβ
Pharmaceutical Research
19(12):1788-1800
Dokholyan
NV,
Mirny
LA,
Shakhnovich
EI
(2002). Understanding conserved amino acids in proteins
Physica A: Statistical Mechanics and its Applications
314(1-4):600-606
Mirny
LA,
Gelfand
MS
(2002). Using orthologous and paralogous proteins to identify specificity determining residues
Genome Biology
3(3):preprint0002.1
Mirny
LA
(2002). Structural analysis of conserved base pairs in protein-DNA complexes
Nucleic Acids Research
30(7):1704-1711
Mirny
L,
Shakhnovich
E
(2001). Protein folding theory: From lattice to all-atom models
Annual Review of Biophysics and Biomolecular Structure
30(1):361-396
Mirny
L,
Shakhnovich
E
(2001). Evolutionary conservation of the folding nucleus
Journal of Molecular Biology
308(2):123-129
Mirny
L,
Gelfand
M
(2001). What evolution can tell us about protein-DNA interactions
Proceedings of the International School of Physics "Enrico Fermi"
145
Mirny
L,
Shakhnovich
E
(2001). Protein folding: Matching theory and experiment
Proceedings of the International School of Physics "Enrico Fermi"
145
Vendruscolo
M,
Mirny
LA,
Shakhnovich
EI,
Domany
E
(2000). Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score
3.0.CO;2-3>Proteins: Structure, Function, and Genetics
41(2):192-201
Mirny
LA,
Finkelstein
AV,
Shakhnovich
EI
(2000). Statistical significance of protein structure prediction by threading
Proceedings of the National Academy of Sciences
97(18):9978-9983
Li
L,
Mirny
LA,
Shakhnovich
EI
(2000). Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
Nature Structural Biology
7(4):336-342
Mirny
LA,
Shakhnovich
EI
(1999). Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
Journal of Molecular Biology
291(1):177-196
Finkelstein
A,
Rykunov
D,
Lobanov
MY,
Badretdinov
AY,
Reva
B,
Skolnick
J,
Mirny
L,
Shakhnovich
E
(1999). Molecular biophysics-overcoming the crudeness of energy estimates in protein 3D structure prediction by homologs: The when and the how.
Biophysics
44(6):946-956
Mirny
LA,
Shakhnovich
EI
(1998). Protein structure prediction by threading. Why it works and why it does not.
Journal of Molecular Biology
283(2):507-526
Mirny
LA,
Abkevich
VI,
Shakhnovich
EI
(1998). How evolution makes proteins fold quickly
Proceedings of the National Academy of Sciences
95(9):4976-4981
Mirny
LA
(1998). Protein folding: From lattice models to real proteins
Harvard University, Ph.D. Thesis.
Mirny
LA,
Shakhnovich
EI
(1996). How to derive a protein folding potential? A new approach to an old problem
Journal of Molecular Biology
264(5):1164-1179
Shlyakhter
A,
Mirny
L,
Vlasov
A,
Wilson
R
(1996). Monte carlo modeling of epidemiological studies
Human and Ecological Risk Assessment: An International Journal
2(4):920-938
Mirny
L,
Domany
E
(1996). Protein fold recognition and dynamics in the space of contact maps
Proteins: Structure, Function, and Genetics
26(4):391-410
Mirny
LA,
Abkevich
V,
Shakhnovich
EI
(1996). Universality and diversity of the protein folding scenarios:a comprehensive analysis with the aid of a lattice model
Folding and Design
1(2):103-116
Alon
RN,
Mirny
L,
Sussman
JL,
Gutnick
DL
(1995). Detection of alpha/beta-hydrolase fold in the cell surface esterases of acinetobacter species using an analysis of 3D profiles
FEBS letters
371(3):231-235
Chepel
VY,
Khvostunov
I,
Mirny
L,
Talyzina
T,
Andreev
S
(1994). 3-D computer modelling of chromatin fibres for radiation damage simulation
Radiation Protection Dosimetry
52(1):259-264