Ioshikhes, Ilya P : rechercher sur Z-Library

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1

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

2

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

3

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

4

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

5

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

6

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

7

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

8

10.1038/79189

Zhang, Michael Q., Ioshikhes, Ilya P.

Journal:

Nature Genetics

Année:

2000

Langue:

english

Fichier:

PDF, 77 KB

english, 2000

9

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

10

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

11

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

12

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

13

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

14

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

15

Promoter Classifier

Naum I. Gershenzon, Dr Ilya P. Ioshikhes

Journal:

Applied Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 438 KB

english, 2005

16

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

17

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

18

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

19

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

20

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

21

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

22

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

23

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

24

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

25

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

26

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

27

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

28

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

29

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

30

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

31

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

32

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

33

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

34

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

35

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

36

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

37

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

38

Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes

Hassan, Junaid, Qu, Zhi, Bergaust, Linda L., Bakken, Lars R., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2016

Langue:

english

Fichier:

PDF, 3.45 MB

english, 2016

39

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks

Zhang, Song-Yao, Zhang, Shao-Wu, Liu, Lian, Meng, Jia, Huang, Yufei, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2016

Langue:

english

Fichier:

PDF, 9.62 MB

english, 2016

40

Imputation for transcription factor binding predictions based on deep learning

Qin, Qian, Feng, Jianxing, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2017

Langue:

english

Fichier:

PDF, 1.87 MB

english, 2017

41

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast

Tsai, Zing Tsung-Yeh, Shiu, Shin-Han, Tsai, Huai-Kuang, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2015

Langue:

english

Fichier:

PDF, 1.39 MB

english, 2015

42

Maximum entropy methods for extracting the learned features of deep neural networks

Finnegan, Alex, Song, Jun S., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2017

Langue:

english

Fichier:

PDF, 4.03 MB

english, 2017

43

The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects

Kamola, Piotr J., Nakano, Yuko, Takahashi, Tomoko, Wilson, Paul A., Ui-Tei, Kumiko, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2015

Langue:

english

Fichier:

PDF, 878 KB

english, 2015

44

Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations

Kenzaki, Hiroo, Takada, Shoji, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2015

Langue:

english

Fichier:

PDF, 6.12 MB

english, 2015

45

PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse

Reuter, Kerstin, Biehl, Alexander, Koch, Laurena, Helms, Volkhard, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2016

Langue:

english

Fichier:

PDF, 4.73 MB

english, 2016

46

Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA

Rossi, Nicholas A., Dunlop, Mary J., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2017

Langue:

english

Fichier:

PDF, 1.68 MB

english, 2017

47

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

Pulido-Quetglas, Carlos, Aparicio-Prat, Estel, Arnan, Carme, Polidori, Taisia, Hermoso, Toni, Palumbo, Emilio, Ponomarenko, Julia, Guigo, Roderic, Johnson, Rory, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2017

Langue:

english

Fichier:

PDF, 2.16 MB

english, 2017

48

Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns

Huska, Matthew, Vingron, Martin, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2016

Langue:

english

Fichier:

PDF, 2.86 MB

english, 2016

49

Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells

Luo, Yanting, He, Jianlin, Xu, Xiguang, Sun, Ming-an, Wu, Xiaowei, Lu, Xuemei, Xie, Hehuang, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 6.25 MB

english, 2018

50

Optimized Position Weight Matrices in Prediction of Novel Putative Binding Sites for Transcription Factors in the Drosophila melanogaster Genome

Morozov, Vyacheslav Y., Ioshikhes, Ilya P., Nurminsky, Dmitry I.

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 1.43 MB

english, 2013