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1

Evaluating Network Inference Methods in Terms of Their Ability to Preserve the Topology and Complexity of Genetic Networks

Kiani, Narsis A., Zenil, Hector, Olczak, Jakub, Tegnér, Jesper

Journal:

Seminars in Cell & Developmental Biology

Year:

2016

Language:

english

File:

PDF, 1.58 MB

english, 2016

2

Causal deconvolution by algorithmic generative models

Zenil, Hector, Kiani, Narsis A., Zea, Allan A., Tegnér, Jesper

Journal:

Nature Machine Intelligence

Year:

2019

Language:

english

File:

PDF, 2.33 MB

english, 2019

3

Neuronal firing rates account for distractor effects on mnemonic accuracy in a visuo-spatial working memory task

Julian Macoveanu, Torkel Klingberg, Jesper Tegnér

Journal:

Biological Cybernetics

Year:

2007

Language:

english

File:

PDF, 600 KB

english, 2007

4

Quantifying loss of information in network-based dimensionality reduction techniques

Zenil, Hector, Kiani, Narsis A., Tegnér, Jesper

Journal:

Journal of Complex Networks

Year:

2015

Language:

english

File:

PDF, 1.55 MB

english, 2015

5

A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

Tegnér, Jesper, Zenil, Hector, Kiani, Narsis A., Ball, Gordon, Gomez-Cabrero, David

Journal:

Philosophical Transactions Mathematical Physical & Engineering Sciences

Year:

2016

Language:

english

File:

PDF, 435 KB

english, 2016

6

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

Hofmann-Apitius, Martin, Ball, Gordon, Gebel, Stephan, Bagewadi, Shweta, de Bono, Bernard, Schneider, Reinhard, Page, Matt, Kodamullil, Alpha, Younesi, Erfan, Ebeling, Christian, Tegnér, Jesper, Canar

Journal:

International Journal of Molecular Sciences

Year:

2015

Language:

english

File:

PDF, 5.02 MB

english, 2015

7

A Review of Graph and Network Complexity from an Algorithmic Information Perspective

Zenil, Hector, Kiani, Narsis, Tegnér, Jesper

Journal:

Year:

2018

Language:

english

File:

PDF, 457 KB

english, 2018

8

An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems

Zenil, Hector, Kiani, Narsis A., Marabita, Francesco, Deng, Yue, Elias, Szabolcs, Schmidt, Angelika, Ball, Gordon, Tegnér, Jesper

Journal:

Year:

2019

Language:

english

File:

PDF, 7.00 MB

english, 2019

9

[IEEE 2020 IEEE Congress on Evolutionary Computation (CEC) - Glasgow, United Kingdom (2020.7.19-2020.7.24)] 2020 IEEE Congress on Evolutionary Computation (CEC) - Evolving Neural Networks through a Reverse Encoding Tree

Zhang, Haoling, Yang, Chao-Han Huck, Zenil, Hector, Kiani, Narsis A., Shen, Yue, Tegner, Jesper N.

Year:

2020

File:

PDF, 2.99 MB

2020

10

Towards scalable and data efficient learning of Markov boundaries

Jose M. Peña, Roland Nilsson, Johan Björkegren, Jesper Tegnér

Journal:

International Journal of Approximate Reasoning

Year:

2007

Language:

english

File:

PDF, 339 KB

english, 2007

11

Learning dynamic Bayesian network models via cross-validation

Jose M. Peña, Johan Björkegren, Jesper Tegnér

Journal:

Pattern Recognition Letters

Year:

2005

Language:

english

File:

PDF, 410 KB

english, 2005

12

Epigenetic alterations in autoimmune disease

Esteban Ballestar, Biola M Javierre, Lorenzo de la Rica, David Gómez-Cabrero, Jesper Tegnér, Carmen Gomez-Vaquero, Javier Narvaez, Henar Hernando, Virginia C Rodriguez, Roser Vento, Laura Ciudad, Javi

Journal:

Journal of Translational Medicine

Year:

2011

Language:

english

File:

PDF, 88 KB

english, 2011

13

Decoding complex biological networks - tracing essential and modulatory parameters in complex and simplified models of the cell cycle

Olivia Eriksson, Tom Andersson, Yishao Zhou, Jesper Tegnér

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 506 KB

english, 2011

14

Can modular analysis identify disease-associated candidate genes for therapeutics?

Journal:

Journal of Biology

Year:

2009

Language:

english

File:

PDF, 101 KB

english, 2009

15

The dynamical stability of reverberatory neural circuits

Jesper Tegnér, Albert Compte, Xiao-Jing Wang

Journal:

Biological Cybernetics

Year:

2002

Language:

english

File:

PDF, 266 KB

english, 2002

16

Spike-timing-dependent plasticity: common themes and divergent vistas

Adam Kepecs, Mark C.W. van Rossum, Sen Song, Jesper Tegner

Journal:

Biological Cybernetics

Year:

2002

Language:

english

File:

PDF, 248 KB

english, 2002

17

Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions

Mika Gustafsson, Michael Hörnquist, Jesper Lundström, Johan Björkegren, Jesper Tegnér

Journal:

Annals of the New York Academy of Sciences

Year:

2009

Language:

english

File:

PDF, 428 KB

english, 2009

18

Modulation of Burst Frequency by Calcium-Dependent Potassium Channels in the Lamprey Locomotor System: Dependence of the Activity Level

Jesper Tegnér, Anders Lansner, Sten Grillner

Journal:

Journal of Computational Neuroscience

Year:

1998

Language:

english

File:

PDF, 2.85 MB

english, 1998

19

Systems biology of innate immunity

Jesper Tegnér, Roland Nilsson, Vladimir B. Bajic, Johan Björkegren, Timothy Ravasi

Journal:

Cellular Immunology

Year:

2006

Language:

english

File:

PDF, 545 KB

english, 2006

20

Perturbations to uncover gene networks

Jesper Tegnér, Johan Björkegren

Journal:

Trends in Genetics

Year:

2007

Language:

english

File:

PDF, 643 KB

english, 2007

21

GABAB-ergic modulation of burst rate and intersegmental coordination in lamprey: experiments and simulations

Jesper Tegnér, Sten Grillner

Journal:

Year:

2000

Language:

english

File:

PDF, 239 KB

english, 2000

22

An adaptive spike-timing-dependent plasticity rule

Jesper Tegnér, Ádám Kepecs

Journal:

Year:

2002

Language:

english

File:

PDF, 197 KB

english, 2002

23

The synaptic NMDA component desynchronizes neural bursters

Jesper Tegnér, Jeanette Hellgren-Kotaleski

Journal:

Year:

1999

Language:

english

File:

PDF, 255 KB

english, 1999

24

Control of burst proportion and frequency range by drive-dependent modulation of adaptation

Jeanette Hellgren Kotaleski, Jesper Tegnér, Sten Grillner, Anders Lansner

Journal:

Year:

1999

Language:

english

File:

PDF, 301 KB

english, 1999

25

On reliable discovery of molecular signatures

Roland Nilsson, Johan Björkegren, Jesper Tegnér

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 706 KB

english, 2009

26

Detection of compound mode of action by computational integration of whole-genome measurements and genetic perturbations

Kristofer Hallén, Johan Björkegren, Jesper Tegnér

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 392 KB

english, 2006

27

Detecting multivariate differentially expressed genes

Roland Nilsson, José M Peña, Johan Björkegren, Jesper Tegnér

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 483 KB

english, 2007

28

Computational disease modeling – fact or fiction?

Jesper N Tegnér, Albert Compte, Charles Auffray, Gary An, Gunnar Cedersund, Gilles Clermont, Boris Gutkin, Zoltán N Oltvai, Klaas Enno Stephan, Randy Thomas, Pablo Villoslada

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 179 KB

english, 2009

29

Integrated approaches to uncovering transcription regulatory networks in mammalian cells

Kai Tan, Jesper Tegner, Timothy Ravasi

Journal:

Year:

2008

Language:

english

File:

PDF, 798 KB

english, 2008

30

Intrinsic function of a neuronal network — a vertebrate central pattern generator

Sten Grillner, Örjan Ekeberg, Abdeljabbar El Manira, Anders Lansner, David Parker, Jesper Tegnér, Peter Wallén

Journal:

Brain Research Reviews

Year:

1998

Language:

english

File:

PDF, 964 KB

english, 1998

31

Pediatric systems medicine: evaluating needs and opportunities using congenital heart block as a case study

Tegnér, Jesper, Abugessaisa, Imad

Journal:

Pediatric Research

Year:

2013

Language:

english

File:

PDF, 500 KB

english, 2013

32

Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression

de la Rica, Lorenzo, Urquiza, José M., Gómez-Cabrero, David, Islam, Abul B.M.M.K., López-Bigas, Nuria, Tegnér, Jesper, Toes, René E.M., Ballestar, Esteban

Journal:

Journal of Autoimmunity

Year:

2013

Language:

english

File:

PDF, 1.28 MB

english, 2013

33

Data integration in the era of omics: current and future challenges

Gomez-Cabrero, David, Abugessaisa, Imad, Maier, Dieter, Teschendorff, Andrew, Merkenschlager, Matthias, Gisel, Andreas, Ballestar, Esteban, Bongcam-Rudloff, Erik, Conesa, Ana, Tegnér, Jesper

Journal:

BMC Systems Biology

Year:

2014

Language:

english

File:

PDF, 911 KB

english, 2014

34

STATegra EMS: an Experiment Management System for complex next-generation omics experiments

Hernández-de-Diego, Rafael, Boix-Chova, Noemi, Gómez-Cabrero, David, Tegner, Jesper, Abugessaisa, Imad, Conesa, Ana

Journal:

BMC Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.21 MB

english, 2014

35

Methylome characterization of CD4+ T cells in multiple sclerosis — Establishing a role for miR-21 in autoimmune disease

Ruhrmann, Sabrina, Piket, Eliane, Bergman, Petra, Kular, Lara, Lorenzi, Julio Cesar Cetrulo, Aeinehband, Shahin, Parsa, Roham, Gomez-cabrero, David, Tegnér, Jesper, Piehl, Fredrik, Jagodic, Maja

Journal:

Journal of Neuroimmunology

Year:

2014

Language:

english

File:

PDF, 52 KB

english, 2014

36

[IEEE 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Shanghai, China (2013.12.18-2013.12.21)] 2013 IEEE International Conference on Bioinformatics and Biomedicine - Algorithmic complexity of motifs clusters superfamilies of networks

Zenil, Hector, Kiani, Narsis A., Tegner, Jesper

Year:

2013

Language:

english

File:

PDF, 219 KB

english, 2013

37

An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training

Lindholm, Maléne E, Marabita, Francesco, Gomez-Cabrero, David, Rundqvist, Helene, Ekström, Tomas J, Tegnér, Jesper, Sundberg, Carl Johan

Journal:

Year:

2014

Language:

english

File:

PDF, 945 KB

english, 2014

38

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

Marabita, Francesco, Almgren, Malin, Lindholm, Maléne E., Ruhrmann, Sabrina, Fagerström-Billai, Fredrik, Jagodic, Maja, Sundberg, Carl J., Ekström, Tomas J., Teschendorff, Andrew E., Tegnér, Jesper, G

Journal:

Year:

2013

Language:

english

File:

PDF, 7.12 MB

english, 2013

39

Stronger Synaptic Connectivity as a Mechanism behind Development of Working Memory-related Brain Activity during Childhood

Edin, Fredrik, Macoveanu, Julian, Olesen, Pernille, Tegnér, Jesper, Klingberg, Torkel

Journal:

Journal of Cognitive Neuroscience

Year:

2007

Language:

english

File:

PDF, 340 KB

english, 2007

40

VEGF-B promotes cancer metastasis through a VEGF-A–independent mechanism and serves as a marker of poor prognosis for cancer patients

Yang, Xiaojuan, Zhang, Yin, Hosaka, Kayoko, Andersson, Patrik, Wang, Jian, Tholander, Fredrik, Cao, Ziquan, Morikawa, Hiromasa, Tegnér, Jesper, Yang, Yunlong, Iwamoto, Hideki, Lim, Sharon, Cao, Yihai

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 3.13 MB

english, 2015

41

FRONTO-PARIETAL CONNECTION ASYMMETRY REGULATES WORKING MEMORY DISTRACTIBILITY

EDIN, FREDRIK, KLINGBERG, TORKEL, STÖDBERG, TOMMY, TEGNÉR, JESPER

Journal:

Journal of Integrative Neuroscience

Year:

2007

Language:

english

File:

PDF, 508 KB

english, 2007

42

Laboratory biomarkers and frailty: presentation of the FRAILOMIC initiative

Lippi, Giuseppe, Jansen-Duerr, Pidder, Viña, Jose, Durrance-Bagale, Anna, Abugessaisa, Imad, Gomez-Cabrero, David, Tegnér, Jesper, Grillari, Johannes, Erusalimsky, Jorge, Sinclair, Alan, Rodriguez-Man

Journal:

Clinical Chemistry and Laboratory Medicine

Year:

2015

Language:

english

File:

PDF, 116 KB

english, 2015

43

Transcriptional Profiling Uncovers a Network of Cholesterol-Responsive Atherosclerosis Target Genes

Skogsberg, Josefin, Lundström, Jesper, Kovacs, Alexander, Nilsson, Roland, Noori, Peri, Maleki, Shohreh, Köhler, Marina, Hamsten, Anders, Tegnér, Jesper, Björkegren, Johan, Frankel, Wayne N.

Journal:

Year:

2008

Language:

english

File:

PDF, 566 KB

english, 2008

44

Electrotonic Signals along Intracellular Membranes May Interconnect Dendritic Spines and Nucleus

Shemer, Isaac, Brinne, Björn, Tegnér, Jesper, Grillner, Sten, Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 916 KB

english, 2008

45

Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR

Marabita, Francesco, de Candia, Paola, Torri, Anna, Tegnér, Jesper, Abrignani, Sergio, Rossi, Riccardo L.

Journal:

Briefings in Bioinformatics

Year:

2015

Language:

english

File:

PDF, 793 KB

english, 2015

46

Monozygotic twins discordant for common variable immunodeficiency reveal impaired DNA demethylation during naïve-to-memory B-cell transition

Rodríguez-Cortez, Virginia C., del Pino-Molina, Lucia, Rodríguez-Ubreva, Javier, Ciudad, Laura, Gómez-Cabrero, David, Company, Carlos, Urquiza, José M., Tegnér, Jesper, Rodríguez-Gallego, Carlos, Lópe

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 702 KB

english, 2015

47

Methods of Information Theory and Algorithmic Complexity for Network Biology

Zenil, Hector, Kiani, Narsis A., Tegnér, Jesper

Journal:

Seminars in Cell & Developmental Biology

Year:

2016

Language:

english

File:

PDF, 1.34 MB

english, 2016

48

[IEEE 2015 11th International Conference on Signal-Image Technology & Internet-Based Systems (SITIS) - Bangkok, Thailand (2015.11.23-2015.11.27)] 2015 11th International Conference on Signal-Image Technology & Internet-Based Systems (SITIS) - Topological Evaluation of Methods for Reconstruction of Genetic Regulatory Networks

Olczak, Jakub, Kiani, Narsis A., Zenil, Hector, Tegner, Jesper

Year:

2015

Language:

english

File:

PDF, 478 KB

english, 2015

49

Human macrophages induce CD4+Foxp3+ regulatory T cells via binding and re-release of TGF-β

Schmidt, Angelika, Zhang, Xing-Mei, Joshi, Rubin N, Iqbal, Shasina, Wahlund, Casper, Gabrielsson, Susanne, Harris, Robert A, Tegnér, Jesper

Journal:

Immunology & Cell Biology

Year:

2016

Language:

english

File:

PDF, 3.22 MB

english, 2016

50

IL-1β promotes Th17 differentiation by inducing alternative splicing of FOXP3

Mailer, Reiner K. W., Joly, Anne-Laure, Liu, Sang, Elias, Szabolcs, Tegner, Jesper, Andersson, John

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 1.13 MB

english, 2015

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