Ioshikhes, I. P. : rechercher sur Z-Library

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1

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I., Pugh, B. F.

Journal:

Genome Research

Année:

2008

Langue:

english

Fichier:

PDF, 760 KB

english, 2008

2

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties

Ouma, Wilberforce Zachary, Pogacar, Katja, Grotewold, Erich, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 3.59 MB

english, 2018

3

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

Margarido, Gabriel R. A., Heckerman, David, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2015

Langue:

english

Fichier:

PDF, 1.53 MB

english, 2015

4

A Markov chain for numerical chromosomal instability in clonally expanding populations

Elizalde, Sergi, Laughney, Ashley M., Bakhoum, Samuel F., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 11.22 MB

english, 2018

5

A novel riboswitch classification based on imbalanced sequences achieved by machine learning

Beyene, Solomon Shiferaw, Ling, Tianyi, Ristevski, Blagoj, Chen, Ming, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2020

Fichier:

PDF, 6.80 MB

2020

6

Discovering functional sequences with RELICS, an analysis method for CRISPR screens

Fiaux, Patrick C., Chen, Hsiuyi V., Chen, Poshen B., Chen, Aaron R., McVicker, Graham, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2020

Fichier:

PDF, 2.61 MB

2020

7

Global dynamics of newly constructed oligonucleosomes of conventional and variant H2A.Z histone

Amutha Ramaswamy, Ilya Ioshikhes

Journal:

BMC Structural Biology

Année:

2007

Langue:

english

Fichier:

PDF, 6.96 MB

english, 2007

8

Structural dynamics of nucleosome core particle: Comparison with nucleosomes containing histone variants

Amutha Ramaswamy, Ivet Bahar, Ilya Ioshikhes

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 1.66 MB

english, 2005

9

10.1038/79189

Zhang, Michael Q., Ioshikhes, Ilya P.

Journal:

Nature Genetics

Année:

2000

Langue:

english

Fichier:

PDF, 77 KB

english, 2000

10

Nucleosome organization in the Drosophila genome

Mavrich, Travis N., Jiang, Cizhong, Ioshikhes, Ilya P., Li, Xiaoyong, Venters, Bryan J., Zanton, Sara J., Tomsho, Lynn P., Qi, Ji, Glaser, Robert L., Schuster, Stephan C.

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 1.60 MB

english, 2008

11

Nucleosome positions predicted through comparative genomics

Ioshikhes, Ilya P, Albert, Istvan, Zanton, Sara J, Pugh, B Franklin

Journal:

Nature Genetics

Année:

2006

Langue:

english

Fichier:

PDF, 341 KB

english, 2006

12

The features ofDrosophilacore promoters revealed by statistical analysis

Naum I Gershenzon, Edward N Trifonov, Ilya P Ioshikhes

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 478 KB

english, 2006

13

Nucleosome DNA Sequence Pattern Revealed by Multiple Alignment of Experimentally Mapped Sequences

Ilya Ioshikhes, Alex Bolshoy, Konstantin Derenshteyn, Mark Borodovsky, Edward N. Trifonov

Journal:

Journal of Molecular Biology

Année:

1996

Langue:

english

Fichier:

PDF, 199 KB

english, 1996

14

Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites

Nandi, Soumyadeep, Ioshikhes, Ilya

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 1.16 MB

english, 2012

15

Human milk metagenome: a functional capacity analysis

Tonya L Ward, Sergey Hosid, Ilya Ioshikhes, Illimar Altosaar

Journal:

BMC Microbiology

Année:

2013

Langue:

english

Fichier:

PDF, 877 KB

english, 2013

16

Promoter Classifier

Naum I. Gershenzon, Dr Ilya P. Ioshikhes

Journal:

Applied Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 438 KB

english, 2005

17

Periodical Distribution of Transcription Factor Sites in Promoter Regions and Connection with Chromatin Structure

Ilya Ioshikhes, Edward N. Trifonov and Michael Q. Zhang

Journal:

Proceedings of the National Academy of Sciences

Année:

1999

Langue:

english

Fichier:

PDF, 1.14 MB

english, 1999

18

[IEEE Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05) - Minneapolis, MN, USA (19-21 Oct. 2005)] Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05) - Global Dynamics of Nucleosome Arrays: Influence of Variant Histone H2A.Z

Li Wang,, Ramaswamy, A., Ioshikhes, I.

Année:

2005

Langue:

english

Fichier:

PDF, 590 KB

english, 2005

19

Algorithms for Mapping of mRNA Targets for MicroRNA

Ioshikhes, Ilya, Roy, Sashwati, Sen, Chandan K.

Journal:

DNA and Cell Biology

Année:

2007

Langue:

english

Fichier:

PDF, 694 KB

english, 2007

20

Preferred Positions of AA and TT Dinucleotides in Aligned Nucleosomal DNA Sequences

Ioshikhes, I., Bolshoy, A., Trifonov, E. N.

Journal:

Journal of Biomolecular Structure and Dynamics

Année:

1992

Langue:

english

Fichier:

PDF, 354 KB

english, 1992

21

A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder

Kaminsky, Z, Tochigi, M, Jia, P, Pal, M, Mill, J, Kwan, A, Ioshikhes, I, Vincent, J B, Kennedy, J L, Strauss, J, Pai, S, Wang, S-C, Petronis, A

Journal:

Molecular Psychiatry

Année:

2012

Langue:

english

Fichier:

PDF, 629 KB

english, 2012

22

Synergy of human Pol II core promoter elements revealed by statistical sequence analysis

Gershenzon, N. I., Ioshikhes, I. P.

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 164 KB

english, 2005

23

Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1

Lee, D.-H., Gershenzon, N., Gupta, M., Ioshikhes, I. P., Reinberg, D., Lewis, B. A.

Journal:

Molecular and Cellular Biology

Année:

2005

Langue:

english

Fichier:

PDF, 738 KB

english, 2005

24

Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor

Liu, Y., Nandi, S., Martel, A., Antoun, A., Ioshikhes, I., Blais, A.

Journal:

Nucleic Acids Research

Année:

2012

Langue:

english

Fichier:

PDF, 2.65 MB

english, 2012

25

Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1

Lee, D.-H., Gershenzon, N., Gupta, M., Ioshikhes, I. P., Reinberg, D., Lewis, B. A.

Journal:

Molecular and Cellular Biology

Année:

2005

Fichier:

PDF, 19 KB

2005

26

Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure

Ioshikhes, I., Trifonov, E. N., Zhang, M. Q.

Journal:

Proceedings of the National Academy of Sciences

Année:

1999

Langue:

english

Fichier:

PDF, 99 KB

english, 1999

27

Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors

Nandi, S., Blais, A., Ioshikhes, I.

Journal:

Nucleic Acids Research

Année:

2013

Langue:

english

Fichier:

PDF, 4.12 MB

english, 2013

28

Interdependence between DNA template secondary structure and priming efficiencies of short primers

Lvovsky, L., Ioshikhes, I., Raja, M. C., Zevin-Sonkin, D., Sobolev, I. A., Liberzon, A., Shwartzburd, J., Ulanovsky, L. E.

Journal:

Nucleic Acids Research

Année:

1998

Langue:

english

Fichier:

PDF, 103 KB

english, 1998

29

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

Zhabinskaya, Dina, Benham, Craig J., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2012

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2012

30

Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters

Hosid, Sergey, Ioshikhes, Ilya, Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.19 MB

english, 2014

31

Reconstruction of the Gene Regulatory Network Involved in the Sonic Hedgehog Pathway with a Potential Role in Early Development of the Mouse Brain

Liu, Jinhua, Wang, Xuelong, Li, Juan, Wang, Haifang, Wei, Gang, Yan, Jun, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2014

32

Comparison of Insertional RNA Editing in Myxomycetes

Chen, Cai, Frankhouser, David, Bundschuh, Ralf, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2012

Langue:

english

Fichier:

PDF, 670 KB

english, 2012

33

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism

Rybakova, Katja N., Bruggeman, Frank J., Tomaszewska, Aleksandra, Moné, Martijn J., Carlberg, Carsten, Westerhoff, Hans V., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2015

Langue:

english

Fichier:

PDF, 4.07 MB

english, 2015

34

A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase

Da, Lin-Tai, Pardo Avila, Fátima, Wang, Dong, Huang, Xuhui, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2013

Langue:

english

Fichier:

PDF, 1.97 MB

english, 2013

35

How MicroRNA and Transcription Factor Co-regulatory Networks Affect Osteosarcoma Cell Proliferation

Poos, Kathrin, Smida, Jan, Nathrath, Michaela, Maugg, Doris, Baumhoer, Daniel, Korsching, Eberhard, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2013

Langue:

english

Fichier:

PDF, 763 KB

english, 2013

36

Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data

Xing, Haipeng, Mo, Yifan, Liao, Will, Zhang, Michael Q., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2012

Langue:

english

Fichier:

PDF, 804 KB

english, 2012

37

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells

Markowetz, Florian, Mulder, Klaas W., Airoldi, Edoardo M., Lemischka, Ihor R., Troyanskaya, Olga G., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2010

Langue:

english

Fichier:

PDF, 1.45 MB

english, 2010

38

Conformation Regulation of the X Chromosome Inactivation Center: A Model

Scialdone, Antonio, Cataudella, Ilaria, Barbieri, Mariano, Prisco, Antonella, Nicodemi, Mario, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2011

Langue:

english

Fichier:

PDF, 361 KB

english, 2011

39

Suppressed Expression of T-Box Transcription Factors Is Involved in Senescence in Chronic Obstructive Pulmonary Disease

Acquaah-Mensah, George K., Malhotra, Deepti, Vulimiri, Madhulika, McDermott, Jason E., Biswal, Shyam, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2012

Langue:

english

Fichier:

PDF, 467 KB

english, 2012

40

A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data

Xie, Qing, Liu, Qi, Mao, Fengbiao, Cai, Wanshi, Wu, Honghu, You, Mingcong, Wang, Zhen, Chen, Bingyu, Sun, Zhong Sheng, Wu, Jinyu, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.72 MB

english, 2014

41

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers

Ozonov, Evgeniy A., van Nimwegen, Erik, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2013

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2013

42

Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions

Beshnova, Daria A., Cherstvy, Andrey G., Vainshtein, Yevhen, Teif, Vladimir B., Ioshikhes,

Journal:

PLoS Computational Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2014

43

The Next Generation of Transcription Factor Binding Site Prediction

Mathelier, Anthony, Wasserman, Wyeth W., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2013

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2013

44

The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis

Teschendorff, Andrew E., Liu, Xiaoping, Caren, Helena, Pollard, Steve M., Beck, Stephan, Widschwendter, Martin, Chen, Luonan, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2014

45

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Mahony, Shaun, Edwards, Matthew D., Mazzoni, Esteban O., Sherwood, Richard I., Kakumanu, Akshay, Morrison, Carolyn A., Wichterle, Hynek, Gifford, David K., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2014

Langue:

english

Fichier:

PDF, 2.17 MB

english, 2014

46

Variety of genomic DNA patterns for nucleosome positioning

Ioshikhes, I., Hosid, S., Pugh, B. F.

Journal:

Genome Research

Année:

2011

Langue:

english

Fichier:

PDF, 1.26 MB

english, 2011

47

Voluntary Running Triggers VGF-Mediated Oligodendrogenesis to Prolong the Lifespan of Snf2h-Null Ataxic Mice

Alvarez-Saavedra, Matías, De Repentigny, Yves, Yang, Doo, O’Meara, Ryan W., Yan, Keqin, Hashem, Lukas E., Racacho, Lemuel, Ioshikhes, Ilya, Bulman, Dennis E., Parks, Robin J., Kothary, Rashmi, Pickett

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 7.65 MB

english, 2016

48

Structural dynamics of nucleosome mediated by acetylations at H3K56 and H3K115,122

Rajagopalan, Muthukumaran, Balasubramanian, Sangeetha, Ioshikhes, Ilya, Ramaswamy, Amutha

Journal:

European Biophysics Journal

Année:

2017

Langue:

english

Fichier:

PDF, 2.23 MB

english, 2017

49

Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns

Yang, Doo, Ioshikhes, Ilya

Journal:

Journal of Computational Biology

Année:

2017

Langue:

english

Fichier:

PDF, 575 KB

english, 2017

50

Insights into interplay between rexinoid signaling and myogenic regulatory factor-associated chromatin state in myogenic differentiation

Hamed, Munerah, Khilji, Saadia, Dixon, Katherine, Blais, Alexandre, Ioshikhes, Ilya, Chen, Jihong, Li, Qiao

Journal:

Nucleic Acids Research

Année:

2017

Langue:

english

Fichier:

PDF, 4.84 MB

english, 2017