Yan, Koon-Kiu: search on Z-Library

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1

Comparing Technological Development and Biological Evolution from a Network Perspective

Yan, Koon-Kiu, Wang, Daifeng, Xiong, Kun, Gerstein, Mark

Journal:

Year:

2020

File:

PDF, 1.20 MB

2020

2

Architecture of the human regulatory network derived from ENCODE data

Gerstein, Mark B., Kundaje, Anshul, Hariharan, Manoj, Landt, Stephen G., Yan, Koon-Kiu, Cheng, Chao, Mu, Xinmeng Jasmine, Khurana, Ekta, Rozowsky, Joel, Alexander, Roger, Min, Renqiang, Alves, Pedro,

Journal:

Year:

2012

Language:

english

File:

PDF, 15.53 MB

english, 2012

3

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

Chao Cheng, Koon-Kiu Yan, Kevin Y Yip, Joel Rozowsky, Roger Alexander…

Journal:

Year:

2011

Language:

english

File:

PDF, 3.82 MB

english, 2011

4

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

Cheng, Chao, Yan, Koon-Kiu, Hwang, Woochang, Qian, Jiang, Bhardwaj, Nitin, Rozowsky, Joel, Lu, Zhi John, Niu, Wei, Alves, Pedro, Kato, Masaomi, Snyder, Michael, Gerstein, Mark, Price, Nathan D.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.65 MB

english, 2011

5

Measuring the Evolutionary Rewiring of Biological Networks

Shou, Chong, Bhardwaj, Nitin, Lam, Hugo Y. K., Yan, Koon-Kiu, Kim, Philip M., Snyder, Michael, Gerstein, Mark B., Snel, Berend

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 682 KB

english, 2011

6

OrthoClust: an orthology-based network framework for clustering data across multiple species

Yan, Koon-Kiu, Wang, Daifeng, Rozowsky, Joel, Zheng, Henry, Cheng, Chao, Gerstein, Mark

Journal:

Year:

2014

Language:

english

File:

PDF, 1.99 MB

english, 2014

7

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

Yan, Koon-Kiu, Lou, Shaoke, Gerstein, Mark, Zhong, Sheng

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 5.46 MB

english, 2017

8

Optimal ranking in networks with community structure

Huafeng Xie, Koon-Kiu Yan, Sergei Maslov

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2007

Language:

english

File:

PDF, 228 KB

english, 2007

9

Cross-Disciplinary Network Comparison: Matchmaking between Hairballs

Yan, Koon-Kiu, Wang, Daifeng, Sethi, Anurag, Muir, Paul, Kitchen, Robert, Cheng, Chao, Gerstein, Mark

Journal:

Year:

2016

Language:

english

File:

PDF, 1.32 MB

english, 2016

10

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data

Yip, Kevin Y., Alexander, Roger P., Yan, Koon-Kiu, Gerstein, Mark, Rattray, Magnus

Journal:

Year:

2010

Language:

english

File:

PDF, 419 KB

english, 2010

11

Upstream plasticity and downstream robustness in evolution of molecular networks

Sergei Maslov, Kim Sneppen, Kasper Astrup Eriksen, Koon-Kiu Yan

Journal:

BMC Evolutionary Biology

Year:

2004

Language:

english

File:

PDF, 317 KB

english, 2004

12

An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome

Cheng, Chao, Andrews, Erik, Yan, Koon-Kiu, Ung, Matthew, Wang, Daifeng, Gerstein, Mark

Journal:

Year:

2015

Language:

english

File:

PDF, 1.71 MB

english, 2015

13

Network Approaches for Dissecting the Immune System

Hao Shi,, Yan, Koon-Kiu, Ding, Liang, Qian, Chenxi, Chi, Hongbo, Yu, Jiyang

Journal:

Year:

2020

File:

PDF, 21.24 MB

2020

14

Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

Jacob Bock Axelsen, Koon-Kiu Yan, Sergei Maslov

Journal:

Year:

2007

Language:

english

File:

PDF, 546 KB

english, 2007

15

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps

Yan, Koon-Kiu, Yardımcı, Galip Gürkan, Yan, Chengfei, Noble, William S., Gerstein, Mark

Journal:

Year:

2017

Language:

english

File:

PDF, 285 KB

english, 2017

16

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Sethi, Anurag, Gu, Mengting, Gumusgoz, Emrah, Chan, Landon, Yan, Koon-Kiu, Rozowsky, Joel, Barozzi, Iros, Afzal, Veena, Akiyama, Jennifer A., Plajzer-Frick, Ingrid, Yan, Chengfei, Novak, Catherine S.,

Journal:

Year:

2020

File:

PDF, 5.27 MB

2020

17

Ranking scientific publications using a model of network traffic

Walker, Dylan, Xie, Huafeng, Yan, Koon-Kiu, Maslov, Sergei

Journal:

Journal of Statistical Mechanics Theory and Experiment

Year:

2007

Language:

english

File:

PDF, 606 KB

english, 2007

18

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia

Wang, Daifeng, Yan, Koon-Kiu, Rozowsky, Joel, Pan, Eric, Gerstein, Mark

Journal:

Trends in Genetics

Year:

2016

Language:

english

File:

PDF, 1.04 MB

english, 2016

19

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks

Koon-Kiu Yan, Gang Fang, Nitin Bhardwaj, Roger P. Alexander, Mark Gerstein and Gregory A. Petsko

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.44 MB

english, 2010

20

Cross-talk between GLI transcription factors and FOXC1 promotes T-cell acute lymphoblastic leukemia dissemination

Tosello, Valeria, Bongiovanni, Deborah, Liu, Jingjing, Pan, Qingfei, Yan, Koon-kiu, Saccomani, Valentina, Van Trimpont, Maaike, Pizzi, Marco, Mazzoni, Martina, Dei Tos, Angelo Paolo, Amadori, Alberto,

Journal:

Year:

2020

File:

PDF, 4.60 MB

2020

21

[IEEE 2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) - Cold Spring Harbor, NY (2010.11.10-2010.11.12)] 2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) - Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph

Koon-Kiu Yan,, Gerstein, M

Year:

2010

Language:

english

File:

PDF, 576 KB

english, 2010

22

Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets

Bhardwaj, Nitin, Carson, Matthew B., Abyzov, Alexej, Yan, Koon-Kiu, Lu, Hui, Gerstein, Mark B., Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.07 MB

english, 2010

23

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

Wang, Daifeng, Yan, Koon-Kiu, Sisu, Cristina, Cheng, Chao, Rozowsky, Joel, Meyerson, William, Gerstein, Mark B., Morozov, Alexandre V

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.29 MB

english, 2015

24

Comparative analysis of the transcriptome across distant species

Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A., Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O.,

Journal:

Year:

2014

Language:

english

File:

PDF, 4.03 MB

english, 2014

25

The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data

Ye, Cheng, Paccanaro, Alberto, Gerstein, Mark, Yan, Koon-Kiu

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.94 MB

2020

26

Fluctuations in Mass-Action Equilibrium of Protein Binding Networks

Yan, Koon-Kiu, Walker, Dylan, Maslov, Sergei

Journal:

Physical Review Letters

Year:

2008

Language:

english

File:

PDF, 244 KB

english, 2008

27

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels

Nitin Bhardwaj, Koon-Kiu Yan, Mark B. Gerstein and Peter J. Bickel

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.48 MB

english, 2010

28

Cellular Superspreaders: An Epidemiological Perspective on HIV Infection inside the Body

Talbert-Slagle, Kristina, Atkins, Katherine E., Yan, Koon-Kiu, Khurana, Ekta, Gerstein, Mark, Bradley, Elizabeth H., Berg, David, Galvani, Alison P., Townsend, Jeffrey P., Rall, Glenn F.

Journal:

Year:

2014

Language:

english

File:

PDF, 723 KB

english, 2014

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