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1

Ribosomal RNA Genes Contribute to the Formation of Pseudogenes and Junk DNA in the Human Genome

Robicheau, Brent M., Susko, Edward, Harrigan, Amye M., Snyder, Marlene

Journal:

Genome Biology and Evolution

Year:

2017

Language:

english

File:

PDF, 1.66 MB

english, 2017

2

Estimating mortality of Atlantic bluefin tuna (Thunnus thynnus) in an experimental recreational catch-and-release fishery

Michael J.W. Stokesbury, John D. Neilson, Edward Susko, Steven J. Cooke

Journal:

Biological Conservation

Year:

2011

Language:

english

File:

PDF, 536 KB

english, 2011

3

Molecular clocks provide little information to date methanogenic Archaea

Roger, Andrew J., Susko, Edward

Journal:

Nature Ecology & Evolution

Year:

2018

Language:

english

File:

PDF, 681 KB

english, 2018

4

An Annealed Sequential Monte Carlo Method for Bayesian Phylogenetics

Wang, Liangliang, Wang, Shijia, Bouchard-Côté, Alexandre, Susko, Edward

Journal:

Systematic Biology

Year:

2019

Language:

english

File:

PDF, 1.12 MB

english, 2019

5

An independent heterotachy model and its implications for phylogeny and divergence time estimation

Jihua Wu, Edward Susko, Andrew J. Roger

Journal:

Molecular Phylogenetics and Evolution

Year:

2008

Language:

english

File:

PDF, 144 KB

english, 2008

6

Weighted tests of homogeneity for testing the number of components in a mixture

Journal:

Computational Statistics & Data Analysis

Year:

2003

Language:

english

File:

PDF, 114 KB

english, 2003

7

Biases in Phylogenetic Estimation Can Be Caused by Random Sequence Segments

Edward Susko, Mathew Spencer, Andrew J. Roger

Journal:

Journal of Molecular Evolution

Year:

2005

Language:

english

File:

PDF, 224 KB

english, 2005

8

Topological Estimation Biases with Covarion Evolution

Huai-Chun Wang, Edward Susko, Matthew Spencer, Andrew J. Roger

Journal:

Journal of Molecular Evolution

Year:

2008

Language:

english

File:

PDF, 479 KB

english, 2008

9

Rate-variation need not defeat phylogenetic inference through pairwise sequence comparisons

Jihua Wu, Edward Susko

Journal:

Journal of Theoretical Biology

Year:

2010

Language:

english

File:

PDF, 124 KB

english, 2010

10

Statistical informatics: software tools for statistical inference about expression arrays

Nadon, Robert, Shi, Peide, Susko, Edward, Ramm, Peter

Journal:

Nature Genetics

Year:

1999

Language:

english

File:

PDF, 91 KB

english, 1999

11

Estimation of Relaxation Time Distributions in Magnetic Resonance Imaging

Edward Susko, Michael J. Bronskill, Simon J. Graham and Robert J. Tibshirani

Journal:

Canadian Journal of Statistics

Year:

2001

Language:

english

File:

PDF, 902 KB

english, 2001

12

Estimation of a Residual Distribution with Small Numbers of Repeated Measurements

Edward Susko and Robert Nadon

Journal:

Canadian Journal of Statistics

Year:

2002

Language:

english

File:

PDF, 950 KB

english, 2002

13

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

Huai-Chun Wang, Karen Li, Edward Susko, Andrew J Roger

Journal:

BMC Evolutionary Biology

Year:

2008

Language:

english

File:

PDF, 1.04 MB

english, 2008

14

PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

Huai-Chun Wang, Edward Susko, Andrew J Roger

Journal:

BMC Evolutionary Biology

Year:

2009

Language:

english

File:

PDF, 843 KB

english, 2009

15

On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: Data quality and confounding factors

Huai-Chun Wang, Edward Susko, Andrew J. Roger

Journal:

Biochemical and Biophysical Research Communications

Year:

2006

Language:

english

File:

PDF, 162 KB

english, 2006

16

Testing Congruence in Phylogenomic Analysis

Jessica W. Leigh, Edward Susko, Manuela Baumgartner and Andrew J. Roger

Journal:

Systematic Biology

Year:

2008

Language:

english

File:

PDF, 2.08 MB

english, 2008

17

On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations

Ajanthah Sangaralingam, Edward Susko, David Bryant, Matthew Spencer

Journal:

BMC Evolutionary Biology

Year:

2010

Language:

english

File:

PDF, 1002 KB

english, 2010

18

The Site-Wise Log-Likelihood Score is a Good Predictor of Genes under Positive Selection

Wang, Huai-Chun, Susko, Edward, Roger, Andrew J.

Journal:

Journal of Molecular Evolution

Year:

2013

Language:

english

File:

PDF, 615 KB

english, 2013

19

A SUF Fe-S Cluster Biogenesis System in the Mitochondrion-Related Organelles of the Anaerobic Protist Pygsuia

Stairs, Courtney W., Eme, Laura, Brown, Matthew W., Mutsaers, Cornelis, Susko, Edward, Dellaire, Graham, Soanes, Darren M., van der Giezen, Mark, Roger, Andrew J.

Journal:

Current Biology

Year:

2014

Language:

english

File:

PDF, 2.50 MB

english, 2014

20

Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture

Jose Sergio Hleap,Edward Susko,Christian Blouin

Journal:

BMC Structural Biology

Year:

2013

Language:

english

File:

PDF, 675 KB

english, 2013

21

A diagnostic tool for mixture models

Susko, Edward., Chen, Jiahua., Kalbfleisch, J.D.

Journal:

Journal of Statistical Computation and Simulation

Year:

2001

Language:

english

File:

PDF, 1.41 MB

english, 2001

22

Large Sample Approximations of Probabilities of Correct Evolutionary Tree Estimation and Biases of Maximum Likelihood Estimation

Journal:

Statistical Applications in Genetics and Molecular Biology

Year:

2011

Language:

english

File:

PDF, 1.05 MB

english, 2011

23

CONTINUOUS-TIME MARKOV MODELS FOR SPECIES INTERACTIONS

Spencer, Matthew, Susko, Edward

Journal:

Year:

2005

Language:

english

File:

PDF, 65 KB

english, 2005

24

On the Distributions of Bootstrap Support and Posterior Distributions for a Star Tree

Journal:

Systematic Biology

Year:

2008

Language:

english

File:

PDF, 521 KB

english, 2008

25

Conditioned Genome Reconstruction: How to Avoid Choosing the Conditioning Genome

Spencer, Matthew, Bryant, David, Susko, Edward

Journal:

Systematic Biology

Year:

2007

Language:

english

File:

PDF, 2.46 MB

english, 2007

26

Estimation of Rates-Across-Sites Distributions in Phylogenetic Substitution Models

Susko, Edward, Field, Chris, Blouin, Christian, Roger, Andrew J.

Journal:

Systematic Biology

Year:

2003

Language:

english

File:

PDF, 137 KB

english, 2003

27

[Integrated Likelihood Methods for Eliminating Nuisance Parameters]: Comment

Journal:

Statistical Science

Year:

1999

Language:

english

File:

PDF, 358 KB

english, 1999

28

Conditioned Genome Reconstruction: How to Avoid Choosing the Conditioning Genome

Matthew Spencer, David Bryant and Edward Susko

Journal:

Systematic Biology

Year:

2007

Language:

english

File:

PDF, 3.05 MB

english, 2007

29

SPIE Proceedings [SPIE BiOS 2001 The International Symposium on Biomedical Optics - San Jose, CA (Saturday 20 January 2001)] Microarrays: Optical Technologies and Informatics - Statistical inference methods for gene expression arrays

Nadon, Robert, Shi, Peide, Skandalis, Adonis, Woody, Erik, Hubschle, Hermann, Susko, Edward, Rghei, Nezar, Ramm, Peter, Bittner, Michael L., Chen, Yidong, Dorsel, Andreas N., Dougherty, Edward R.

Year:

2001

Language:

english

File:

PDF, 849 KB

english, 2001

30

On the Distributions of Bootstrap Support and Posterior Distributions for a Star Tree

Journal:

Systematic Biology

Year:

2008

Language:

english

File:

PDF, 1.89 MB

english, 2008

31

Split-specific Bootstrap Measures for Quantifying Phylogenetic Stability and the Influence of Taxon Selection

Wang, Huai-Chun, Susko, Edward, Roger, Andrew J.

Journal:

Molecular Phylogenetics and Evolution

Year:

2016

Language:

english

File:

PDF, 902 KB

english, 2016

32

Bootstrap Supports Is Not First-Order Correct

Journal:

Systematic Biology

Year:

2009

Language:

english

File:

PDF, 1.97 MB

english, 2009

33

Smoothed Bootstrap Aggregation for Assessing Selection Pressure at Amino Acid Sites

Mingrone, Joseph, Susko, Edward, Bielawski, Joseph

Journal:

Molecular Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 657 KB

english, 2016

34

The Parameters of the Barry and Hartigan General Markov Model Are Statistically NonIdentifiable

Liwen Zou, Edward Susko, Chris Field and Andrew J. Roger

Journal:

Systematic Biology

Year:

2011

Language:

english

File:

PDF, 741 KB

english, 2011

35

Estimation of Rates-across-Sites Distributions in Phylogenetic Substitution Models

Edward Susko, Chris Field, Christian Blouin and Andrew J. Roger

Journal:

Systematic Biology

Year:

2003

Language:

english

File:

PDF, 1.43 MB

english, 2003

36

Improved Least Squares Topology Testing and Estimation

Journal:

Systematic Biology

Year:

2011

Language:

english

File:

PDF, 1.28 MB

english, 2011

37

Continuous-Time Markov Models for Species Interactions

Matthew Spencer and Edward Susko

Journal:

Year:

2005

Language:

english

File:

PDF, 1.24 MB

english, 2005

38

The Probability of Correctly Resolving a Split as an Experimental Design Criterion in Phylogenetics

Edward Susko and Andrew J. Roger

Journal:

Systematic Biology

Year:

2012

Language:

english

File:

PDF, 1.92 MB

english, 2012

39

Fitting Nonstationary General-Time-Reversible Models to Obtain Edge-Lengths and Frequencies for the Barry-Hartigan Model

Liwen Zou, Edward Susko, Chris Field and Andrew J. Roger

Journal:

Systematic Biology

Year:

2012

Language:

english

File:

PDF, 2.24 MB

english, 2012

40

Low-level arsenic exposure via drinking water consumption and female fecundity - A preliminary investigation

Susko, Michele L., Bloom, Michael S., Neamtiu, Iulia A., Appleton, Allison A., Surdu, Simona, Pop, Cristian, Fitzgerald, Edward F., Anastasiu, Doru, Gurzau, Eugen S.

Journal:

Environmental Research

Year:

2017

Language:

english

File:

PDF, 227 KB

english, 2017

41

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

Wang, Huai-Chun, Minh, Bui Quang, Susko, Edward, Roger, Andrew J.

Journal:

Systematic Biology

Year:

2017

Language:

english

File:

PDF, 1.22 MB

english, 2017

42

Bayes factor biases for non-nested models and corrections

Journal:

Canadian Journal of Statistics

Year:

2017

Language:

english

File:

PDF, 639 KB

english, 2017

43

Modelling Prokaryote Gene Content

Spencer, Matthew, Susko, Edward, Roger, Andrew J.

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 607 KB

english, 2006

44

Using Minimum Bootstrap support for Splits to Construct Confidence Regions for Trees

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 1.14 MB

english, 2006

45

Accelerated Estimation of Frequency Classes in Site-heterogeneous Profile Mixture Models

Susko, Edward, Lincker, Léa, Roger, Andrew J

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 465 KB

english, 2018

46

ModL: exploring and restoring regularity when testing for positive selection

Mingrone, Joseph, Susko, Edward, Bielawski, Joseph, Hancock, John

Journal:

Year:

2018

Language:

english

File:

PDF, 1.42 MB

english, 2018

47

The Relative Importance of Modeling Site Pattern Heterogeneity versus Partition-wise Heterotachy in Phylogenomic Inference

Wang, Huai-Chun, Susko, Edward, Roger, Andrew J

Journal:

Systematic Biology

Year:

2019

Language:

english

File:

PDF, 404 KB

english, 2019

48

The Relative Importance of Modeling Site Pattern Heterogeneity versus Partition-wise Heterotachy in Phylogenomic Inference

Wang, Huai-Chun, Susko, Edward, Roger, Andrew J

Journal:

Systematic Biology

Year:

2019

File:

PDF, 404 KB

2019

49

On the Use of Information Criteria for Model Selection in Phylogenetics

Susko, Edward, Roger, Andrew J, Saitou, Naruya

Journal:

Molecular Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 375 KB

english, 2019

50

A phenotype-genotype codon model for detecting adaptive evolution

Jones, Christopher T, Youssef, Noor, Susko, Edward, Bielawski, Joseph P

Journal:

Systematic Biology

Year:

2019

Language:

english

File:

PDF, 1.58 MB

english, 2019