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1

Activities and Sensitivities in Boolean Network Models

Shmulevich, Ilya, Kauffman, Stuart A.

Journal:

Physical Review Letters

Année:

2004

Langue:

english

Fichier:

PDF, 159 KB

english, 2004

2

Learning the structure of dynamic Bayesian networks from

Harri Lähdesmäki, Ilya Shmulevich

Journal:

Machine Learning

Année:

2008

Langue:

english

Fichier:

PDF, 1.09 MB

english, 2008

3

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Saltz, Joel, Gupta, Rajarsi, Hou, Le, Kurc, Tahsin, Singh, Pankaj, Nguyen, Vu, Samaras, Dimitris, Shroyer, Kenneth R., Zhao, Tianhao, Batiste, Rebecca, Van Arnam, John, Shmulevich, Ilya, Rao, Arvind U

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 4.00 MB

english, 2018

4

Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis

Xishan Hao, Baocun Sun, Limei Hu, Harri Lähdesmäki, Valerie Dunmire, Yumei Feng, Shi-Wu Zhang, Huamin Wang, Chunlei Wu, Hua Wang, Gregory N. Fuller, W. Fraser Symmans, Ilya Shmulevich, Wei Zhang

Journal:

Année:

2004

Langue:

english

Fichier:

PDF, 272 KB

english, 2004

5

Kernel density estimation with adaptive varying window size

Vladimir Katkovnik, Ilya Shmulevich

Journal:

Pattern Recognition Letters

Année:

2002

Langue:

english

Fichier:

PDF, 228 KB

english, 2002

6

Propagating organization: an enquiry

Stuart Kauffman, Robert K. Logan, Robert Este, Randy Goebel, David Hobill, Ilya Shmulevich

Journal:

Biology & Philosophy

Année:

2008

Langue:

english

Fichier:

PDF, 168 KB

english, 2008

7

Classifieds

Lin, Jake, Kreisberg, Richard, Kallio, Aleksi, Dudley, Aimée M, Nykter, Matti, Shmulevich, Ilya, May, Patrick, Autio, Reija

Journal:

JOM Journal of the Minerals, Metals and Materials Society

Année:

2014

Langue:

english

Fichier:

PDF, 318 KB

english, 2014

8

Meet a member

Lin, Jake, Kreisberg, Richard, Kallio, Aleksi, Dudley, Aimée M, Nykter, Matti, Shmulevich, Ilya, May, Patrick, Autio, Reija

Journal:

JOM Journal of the Minerals, Metals and Materials Society

Année:

2014

Langue:

english

Fichier:

PDF, 359 KB

english, 2014

9

Comprehensive molecular characterization of gastric adenocarcinoma

Bass, Adam J., Thorsson, Vesteinn, Shmulevich, Ilya, Reynolds, Sheila M., Miller, Michael, Bernard, Brady, Hinoue, Toshinori, Laird, Peter W., Curtis, Christina, Shen, Hui, Weisenberger, Daniel J., Sc

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 3.69 MB

english, 2014

10

Genomic Signal Processing: The Salient Issues

Dougherty, Edward R., Shmulevich, Ilya, Bittner, Michael L.

Journal:

EURASIP Journal on Advances in Signal Processing

Année:

2004

Langue:

english

Fichier:

PDF, 641 KB

english, 2004

11

Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis

Peterson, Eliza J.R., Abidi, Abrar A., Arrieta-Ortiz, Mario L., Aguilar, Boris, Yurkovich, James T., Kaur, Amardeep, Pan, Min, Srinivas, Vivek, Shmulevich, Ilya, Baliga, Nitin S.

Journal:

Année:

2020

Fichier:

PDF, 2.14 MB

2020

12

Steady-state analysis of genetic regulatory networks modelled by probabilistic Boolean networks

Ilya Shmulevich, Ilya Gluhovsky, Ronaldo F. Hashimoto, Edward R. Dougherty, Wei Zhang

Journal:

Comparative and Functional Genomics

Année:

2003

Langue:

english

Fichier:

PDF, 146 KB

english, 2003

13

Tumor specific gene expression profiles in human leiomyosarcoma : An evaluation of intratumor heterogeneity

Ilya Shmulevich, Kelly Hunt, Adel El-Naggar, Ellen Taylor, Latha Ramdas, Pilar Labordé, Kenneth R. Hess, Raphael Pollock, Wei Zhang

Journal:

Année:

2002

Langue:

english

Fichier:

PDF, 751 KB

english, 2002

14

Noise in a small genetic circuit that undergoes bifurcation

Trent Toulouse, Ping Ao, Ilya Shmulevich, Stuart Kauffman

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 334 KB

english, 2005

15

Book review

Ilya Shmulevich

Journal:

Bulletin of Mathematical Biology

Année:

2004

Langue:

english

Fichier:

PDF, 27 KB

english, 2004

16

Biochemical and statistical network models for systems biology

Nathan D Price, Ilya Shmulevich

Journal:

Current Opinion in Biotechnology

Année:

2007

Langue:

english

Fichier:

PDF, 333 KB

english, 2007

17

The number and probability of canalizing functions

Winfried Just, Ilya Shmulevich, John Konvalina

Journal:

Physica D: Nonlinear Phenomena

Année:

2004

Langue:

english

Fichier:

PDF, 119 KB

english, 2004

18

Steady-state probabilities for attractors in probabilistic Boolean networks

Marcel Brun, Edward R. Dougherty, Ilya Shmulevich

Journal:

Signal Processing

Année:

2005

Langue:

english

Fichier:

PDF, 532 KB

english, 2005

19

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

Harri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja

Journal:

Signal Processing

Année:

2006

Langue:

english

Fichier:

PDF, 424 KB

english, 2006

20

Almost all monotone Boolean functions are polynomially learnable using membership queries

Ilya Shmulevich, Aleksey D. Korshunov, Jaakko Astola

Journal:

Information Processing Letters

Année:

2001

Langue:

english

Fichier:

PDF, 42 KB

english, 2001

21

Breakdown probabilities of recursive stack filters

Pertti Koivisto, Olli Yli-Harja, Antti Niemistö, Ilya Shmulevich

Journal:

Signal Processing

Année:

2001

Langue:

english

Fichier:

PDF, 127 KB

english, 2001

22

Genomic signal processing

Jaakko Astola, Edward Dougherty, Ilya Shmulevich, Ioan Tabus

Journal:

Signal Processing

Année:

2003

Langue:

english

Fichier:

PDF, 79 KB

english, 2003

23

Mappings between probabilistic Boolean networks

Edward R. Dougherty, Ilya Shmulevich

Journal:

Signal Processing

Année:

2003

Langue:

english

Fichier:

PDF, 181 KB

english, 2003

24

Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays

Rongcai Jiang, Cristian Mircean, Ilya Shmulevich, David Cogdell, Yu Jia, Ioan Tabus, Kenneth Aldape, Raymond Sawaya, Janet M. Bruner, Gregory N. Fuller, Wei Zhang

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 448 KB

english, 2006

25

A Data Integration Framework for Prediction of Transcription Factor Targets : A BCL6 Case Study

Matti Nykter, Harri Lähdesmäki, Alistair Rust, Vesteinn Thorsson, Ilya Shmulevich

Journal:

Annals of the New York Academy of Sciences

Année:

2009

Langue:

english

Fichier:

PDF, 375 KB

english, 2009

26

NGAL decreases E-cadherin-mediated cell–cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells

Hu, Limei, Hittelman, Walter, Lu, Tao, Ji, Ping, Arlinghaus, Ralph, Shmulevich, Ilya, Hamilton, Stanley R, Zhang, Wei

Journal:

Laboratory Investigation

Année:

2009

Langue:

english

Fichier:

PDF, 709 KB

english, 2009

27

Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding

Ilya Shmulevich, Olli Yli-Harja, Edward Coyle, Dirk-Jan Povel, Kjell Lemström

Journal:

Language Resources and Evaluation

Année:

2001

Langue:

english

Fichier:

PDF, 88 KB

english, 2001

28

Markov Random Field Modeling in Median Pyramidal Transform Domain for Denoising Applications

Ilya Gluhovsky, Vladimir Melnik, Ilya Shmulevich

Journal:

Journal of Mathematical Imaging and Vision

Année:

2002

Langue:

english

Fichier:

PDF, 342 KB

english, 2002

29

An inhibition-based stochastic countable-time decision model

Ilya Shmulevich, A. H. G. S. Van der Ven

Journal:

British Journal of Mathematical and Statistical Psychology

Année:

2002

Langue:

english

Fichier:

PDF, 173 KB

english, 2002

30

Adaptable data management for systems biology investigations

John Boyle, Hector Rovira, Chris Cavnor, David Burdick, Sarah Killcoyne, Ilya Shmulevich

Journal:

BMC Bioinformatics

Année:

2009

Langue:

english

Fichier:

PDF, 1.00 MB

english, 2009

31

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

David B Burdick, Chris C Cavnor, Jeremy Handcock, Sarah Killcoyne, Jake Lin, Bruz Marzolf, Stephen A Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich, John Boyle

Journal:

BMC Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 2.51 MB

english, 2010

32

EPEPT: A web service for enhanced P-value estimation in permutation tests

Theo A Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich

Journal:

BMC Bioinformatics

Année:

2011

Langue:

english

Fichier:

PDF, 461 KB

english, 2011

33

Simcluster: clustering enumeration gene expression data on the simplex space

Ricardo ZN Vêncio, Leonardo Varuzza, Carlos A de B Pereira, Helena Brentani, Ilya Shmulevich

Journal:

BMC Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 475 KB

english, 2007

34

ProbCD: enrichment analysis accounting for categorization uncertainty

Ricardo ZN Vêncio, Ilya Shmulevich

Journal:

BMC Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 308 KB

english, 2007

35

Systems biology driven software design for the research enterprise

John Boyle, Christopher Cavnor, Sarah Killcoyne, Ilya Shmulevich

Journal:

BMC Bioinformatics

Année:

2008

Langue:

english

Fichier:

PDF, 532 KB

english, 2008

36

Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation

Albert C Huang, Limei Hu, Stuart A Kauffman, Wei Zhang, Ilya Shmulevich

Journal:

BMC Systems Biology

Année:

2009

Langue:

english

Fichier:

PDF, 370 KB

english, 2009

37

Probabilistic Boolean Networks Volume 1104 (The Modeling and Control of Gene Regulatory Networks) || 1. Boolean Networks

Shmulevich, Ilya, Dougherty, Edward R.

Année:

2010

Langue:

english

Fichier:

PDF, 829 KB

english, 2010

38

Probabilistic Boolean Networks Volume 1104 (The Modeling and Control of Gene Regulatory Networks) || 6. Asynchronous Networks

Shmulevich, Ilya, Dougherty, Edward R.

Année:

2010

Langue:

english

Fichier:

PDF, 333 KB

english, 2010

39

Probabilistic Boolean Networks Volume 1104 (The Modeling and Control of Gene Regulatory Networks) || Front Matter

Shmulevich, Ilya, Dougherty, Edward R.

Année:

2010

Langue:

english

Fichier:

PDF, 135 KB

english, 2010

40

Probabilistic Boolean Networks Volume 1104 (The Modeling and Control of Gene Regulatory Networks) || 4. Structural Intervention

Shmulevich, Ilya, Dougherty, Edward R.

Année:

2010

Langue:

english

Fichier:

PDF, 411 KB

english, 2010

41

Probabilistic Boolean Networks Volume 1104 (The Modeling and Control of Gene Regulatory Networks) || 5. External Control

Shmulevich, Ilya, Dougherty, Edward R.

Année:

2010

Langue:

english

Fichier:

PDF, 873 KB

english, 2010

42

Probabilistic Boolean Networks Volume 1104 (The Modeling and Control of Gene Regulatory Networks) || 2. Structure and Dynamics of Probabilistic Boolean Networks

Shmulevich, Ilya, Dougherty, Edward R.

Année:

2010

Langue:

english

Fichier:

PDF, 675 KB

english, 2010

43

Probabilistic Boolean Networks Volume 1104 (The Modeling and Control of Gene Regulatory Networks) || Back Matter

Shmulevich, Ilya, Dougherty, Edward R.

Année:

2010

Langue:

english

Fichier:

PDF, 191 KB

english, 2010

44

Probabilistic Boolean Networks Volume 1104 (The Modeling and Control of Gene Regulatory Networks) || 3. Inference of Model Structure

Shmulevich, Ilya, Dougherty, Edward R.

Année:

2010

Langue:

english

Fichier:

PDF, 465 KB

english, 2010

45

Taming Data

Alan Aderem, Ilya Shmulevich

Journal:

Cell Host & Microbe

Année:

2008

Langue:

english

Fichier:

PDF, 88 KB

english, 2008

46

Association of BRCA1 and BRCA2 Mutations With Survival, Chemotherapy Sensitivity, and Gene Mutator Phenotype in Patients With Ovarian Cancer

Yang, Da, Khan, Sofia, Sun, Yan, Hess, Kenneth, Shmulevich, Ilya, Sood, Anil K., Zhang, Wei

Journal:

JAMA The Journal of the American Medical Association

Année:

2011

Langue:

english

Fichier:

PDF, 486 KB

english, 2011

47

Function of C/EBPδ in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals

Litvak, Vladimir, Ramsey, Stephen A, Rust, Alistair G, Zak, Daniel E, Kennedy, Kathleen A, Lampano, Aaron E, Nykter, Matti, Shmulevich, Ilya, Aderem, Alan

Journal:

Nature Immunology

Année:

2009

Langue:

english

Fichier:

PDF, 586 KB

english, 2009

48

Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma

Moore, Lynette M, Kivinen, Virpi, Liu, Yuexin, Annala, Matti, Cogdell, David, Liu, Xiuping, Liu, Chang-Gong, Sawaya, Raymond, Yli-Harja, Olli, Shmulevich, Ilya, Fuller, Gregory N, Zhang, Wei, Nykter,

Journal:

The Journal of Pathology

Année:

2013

Langue:

english

Fichier:

PDF, 483 KB

english, 2013

49

Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion

Eun-Ju Lee, Cristian Mircean, Ilya Shmulevich, Huamin Wang, Jinsong Liu, Antti Niemistö, John J Kavanagh, Je-Ho Lee, Wei Zhang

Journal:

Molecular Cancer

Année:

2005

Langue:

english

Fichier:

PDF, 852 KB

english, 2005

50

Gene-pair expression signatures reveal lineage control

Heinäniemi, Merja, Nykter, Matti, Kramer, Roger, Wienecke-Baldacchino, Anke, Sinkkonen, Lasse, Zhou, Joseph Xu, Kreisberg, Richard, Kauffman, Stuart A, Huang, Sui, Shmulevich, Ilya

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 2.44 MB

english, 2013