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1

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

Fukushima, Kenji, Fang, Xiaodong, Alvarez-Ponce, David, Cai, Huimin, Carretero-Paulet, Lorenzo, Chen, Cui, Chang, Tien-Hao, Farr, Kimberly M., Fujita, Tomomichi, Hiwatashi, Yuji, Hoshi, Yoshikazu, Ima

Journal:

Nature Ecology & Evolution

Year:

2017

Language:

english

File:

PDF, 1.54 MB

english, 2017

2

High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise

Weitzman, Chava L., Tillett, Richard L., Sandmeier, Franziska C., Tracy, C. Richard, Alvarez-Ponce, David

Journal:

Standards in Genomic Sciences

Year:

2018

Language:

english

File:

PDF, 3.01 MB

english, 2018

3

Evolutionary Rate and Duplicability in the Arabidopsis thaliana Protein-Protein Interaction Network

Alvarez-Ponce, D., Fares, M. A.

Journal:

Genome Biology and Evolution

Year:

2012

Language:

english

File:

PDF, 5.57 MB

english, 2012

4

The relationship between the hierarchical position of proteins in the human signal transduction network and their rate of evolution

David Alvarez-Ponce

Journal:

BMC Evolutionary Biology

Year:

2012

Language:

english

File:

PDF, 314 KB

english, 2012

5

Gene similarity networks provide tools for understanding eukaryote origins and evolution

Alvarez-Ponce, D., Lopez, P., Bapteste, E., McInerney, J. O.

Journal:

Proceedings of the National Academy of Sciences

Year:

2013

Language:

english

File:

PDF, 744 KB

english, 2013

6

Network-Level and Population Genetics Analysis of the Insulin/TOR Signal Transduction Pathway Across Human Populations

Luisi, P., Alvarez-Ponce, D., Dall'Olio, G. M., Sikora, M., Bertranpetit, J., Laayouni, H.

Journal:

Molecular Biology and Evolution

Year:

2012

Language:

english

File:

PDF, 453 KB

english, 2012

7

Comment on “The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway”

Rozas,, Alvarez-Ponce, David, Aguade, Montserrat

Journal:

Evolutionary Bioinformatics

Year:

2013

Language:

english

File:

PDF, 452 KB

english, 2013

8

Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes

Alvarez-Ponce, D., Aguade, M., Rozas, J.

Journal:

Genome Research

Year:

2008

Language:

english

File:

PDF, 846 KB

english, 2008

9

Recent Positive Selection Has Acted on Genes Encoding Proteins with More Interactions within the Whole Human Interactome

Luisi, P., Alvarez-Ponce, D., Pybus, M., Fares, M. A., Bertranpetit, J., Laayouni, H.

Journal:

Genome Biology and Evolution

Year:

2015

Language:

english

File:

PDF, 705 KB

english, 2015

10

Molecular Population Genetics of the Insulin/TOR Signal Transduction Pathway: A Network-Level Analysis in Drosophila melanogaster

Alvarez-Ponce, D., Guirao-Rico, S., Orengo, D. J., Segarra, C., Rozas, J., Aguade, M.

Journal:

Molecular Biology and Evolution

Year:

2012

Language:

english

File:

PDF, 386 KB

english, 2012

11

Integration of Two Ancestral Chaperone Systems into One: The Evolution of Eukaryotic Molecular Chaperones in Light of Eukaryogenesis

Bogumil, D., Alvarez-Ponce, D., Landan, G., McInerney, J. O., Dagan, T.

Journal:

Molecular Biology and Evolution

Year:

2014

Language:

english

File:

PDF, 644 KB

english, 2014

12

Increased Genome Sampling Reveals a Dynamic Relationship between Gene Duplicability and the Structure of the Primate Protein-Protein Interaction Network

A. Doherty, D. Alvarez-ponce, J. O. Mcinerney

Year:

2012

Language:

english

File:

PDF, 405 KB

english, 2012

13

Obscure gastrointestinal bleeding due to multifocal intestinal angiosarcoma

Navarro-Chagoya, Dolores, Figueroa-Ruiz, Marco, López-Gómez, Javier, Nava-Leyva, Héctor, Álvarez-Ponce, Carlos Eduardo, Guzmán-Sombrero, Gustavo, Velazquez-Garcia, José

Journal:

International Journal of Surgery Case Reports

Year:

2015

Language:

english

File:

PDF, 832 KB

english, 2015

14

Chemical modification of keratin biofibres by graft polymerisation of methyl methacrylate using redox initiation

Martínez-Hernández, A. L., Santiago-Valtierra, A. L., Alvarez-Ponce, M. J.

Journal:

Materials Research Innovations

Year:

2008

Language:

english

File:

PDF, 424 KB

english, 2008

15

Comparative Genomics of the Vertebrate Insulin/TOR Signal Transduction Pathway: A Network-Level Analysis of Selective Pressures

Alvarez-Ponce, D., Aguade, M., Rozas, J.

Journal:

Genome Biology and Evolution

Year:

2011

Language:

english

File:

PDF, 599 KB

english, 2011

16

Recording negative results of protein–protein interaction assays: an easy way to deal with the biases and errors of interactomic data sets

Alvarez-Ponce, David

Journal:

Briefings in Bioinformatics

Year:

2016

Language:

english

File:

PDF, 130 KB

english, 2016

17

Essentiality Is a Strong Determinant of Protein Rates of Evolution during Mutation Accumulation Experiments in Escherichia coli

Alvarez-Ponce, David, Sabater-Muñoz, Beatriz, Toft, Christina, Ruiz-González, Mario X., Fares, Mario A.

Journal:

Genome Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 887 KB

english, 2016

18

The molecular chaperone DnaK is a source of mutational robustness

Aguilar-Rodríguez, José, Sabater-Muñoz, Beatriz, Montagud-Martínez, Roser, Berlanga, Víctor, Alvarez-Ponce, David, Wagner, Andreas, Fares, Mario A.

Journal:

Genome Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 1.63 MB

english, 2016

19

Secreted proteins defy the expression level–evolutionary rate anticorrelation

Feyertag, Felix, Berninsone, Patricia M., Alvarez-Ponce, David

Journal:

Molecular Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 3.55 MB

english, 2016

20

Chance and necessity in the genome evolution of endosymbiotic bacteria of insects

Sabater-Muñoz, Beatriz, Toft, Christina, Alvarez-Ponce, David, Fares, Mario A

Journal:

The ISME Journal

Year:

2017

Language:

english

File:

PDF, 1.89 MB

english, 2017

21

Intrinsic protein disorder reduces small-scale gene duplicability

Banerjee, Sanghita, Feyertag, Felix, Alvarez-Ponce, David

Journal:

Year:

2017

Language:

english

File:

PDF, 690 KB

english, 2017

22

Disulfide Bonds Enable Accelerated Protein Evolution

Feyertag, Felix, Alvarez-Ponce, David

Journal:

Molecular Biology and Evolution

Year:

2017

Language:

english

File:

PDF, 162 KB

english, 2017

23

Position Matters: Network Centrality Considerably Impacts Rates of Protein Evolution in the Human Protein–Protein Interaction Network

Alvarez-Ponce, David, Feyertag, Felix, Chakraborty, Sandip

Journal:

Genome Biology and Evolution

Year:

2017

Language:

english

File:

PDF, 1.77 MB

english, 2017

24

Phylogenetic Distribution of CMP-Neu5Ac Hydroxylase (CMAH), the Enzyme Synthetizing the Proinflammatory Human Xenoantigen Neu5Gc

Peri, Sateesh, Kulkarni, Asmita, Feyertag, Felix, Berninsone, Patricia M, Alvarez-Ponce, David

Journal:

Genome Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 507 KB

english, 2018

25

Maternal Serum Interleukin-6: A Non-Invasive Predictor of Histological Chorioamnionitis in Women with Preterm-Prelabor Rupture of Membranes

Martinez-Portilla, Raigam Jafet, Hawkins-Villarreal, Ameth, Alvarez-Ponce, Pamela, Chinolla-Arellano, Zarela Lizbeth, Moreno-Espinosa, Ana Lisbeth, Sandoval-Mejia, Ana Lilia, Moreno-Uribe, Nallely

Journal:

Fetal Diagnosis and Therapy

Year:

2018

Language:

english

File:

PDF, 236 KB

english, 2018

26

High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease

Alvarez-Ponce, David, Weitzman, Chava L., Tillett, Richard L., Sandmeier, Franziska C., Tracy, C. Richard

Journal:

Standards in Genomic Sciences

Year:

2018

Language:

english

File:

PDF, 2.99 MB

english, 2018

27

Higher Rates of Protein Evolution in the Self-Fertilizing Plant Arabidopsis thaliana than in the Out-Crossers Arabidopsis lyrata and Arabidopsis halleri

Payne, Bryan L, Alvarez-Ponce, David

Journal:

Genome Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 153 KB

english, 2018

28

Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks

Chakraborty, Sandip, Alvarez-Ponce, David

Journal:

BioMed Research International

Year:

2016

Language:

english

File:

PDF, 2.33 MB

english, 2016

29

Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection

Alvarez-Ponce, David, Torres-Sánchez, María, Feyertag, Felix, Kulkarni, Asmita, Nappi, Taylen, Jeltsch, Albert

Journal:

Year:

2018

Language:

english

File:

PDF, 1.43 MB

english, 2018

30

Arabidopsis Heat Stress-Induced Proteins Are Enriched in Electrostatically Charged Amino Acids and Intrinsically Disordered Regions

Alvarez-Ponce, David, Ruiz-González, Mario, Vera-Sirera, Francisco, Feyertag, Felix, Perez-Amador, Miguel, Fares, Mario

Journal:

International Journal of Molecular Sciences

Year:

2018

Language:

english

File:

PDF, 1.84 MB

english, 2018

31

Management of a borderline ovarian tumor in a pregnant woman in a rural hospital: a case report

Alvarez-Ponce, Carlos Eduardo, López-Gómez, Javier, Figueroa-Ruiz, Marco, Nava-Leyva, Hector, Aleman-Rojas, Fernando, Sandoval-Mejía, Analilia

Journal:

Case Reports in Clinical Pathology

Year:

2015

Language:

english

File:

PDF, 531 KB

english, 2015

32

The Human Genome Retains Relics of Its Prokaryotic Ancestry: Human Genes of Archaebacterial and Eubacterial Origin Exhibit Remarkable Differences

Alvarez-Ponce, David, McInerney, James O.

Journal:

Genome Biology and Evolution

Year:

2011

Language:

english

File:

PDF, 220 KB

english, 2011

33

N-glycoproteins exhibit a positive expression level-evolutionary rate correlation

Feyertag, Felix, Berninsone, Patricia M, Alvarez-Ponce, David

Journal:

Journal of Evolutionary Biology

Year:

2019

File:

PDF, 713 KB

2019

34

N-glycoproteins exhibit a positive expression level-evolutionary rate correlation

Feyertag, Felix, Berninsone, Patricia M, Alvarez-Ponce, David

Journal:

Journal of Evolutionary Biology

Year:

2019

Language:

english

File:

PDF, 713 KB

english, 2019

35

Emergency Surgical Treatment of Upper Airway Obstruction in Oncological Patients: Bibliographic Review and Proposal for Management Algorithm

J, Lopez-Gomez, A, Gomez-Pedraza, M, Granados-Garcia, E, Barrios, G, Ferretiz-Lopez, N, Cardenas-Herrera, C, Alvarez-Ponce

Journal:

Head and Neck Cancer Research

Year:

2018

Language:

english

File:

PDF, 415 KB

english, 2018

36

What lies beneath? Molecular evolution during the radiation of caecilian amphibians

Torres-Sánchez, María, Gower, David J., Alvarez-Ponce, David, Creevey, Christopher J., Wilkinson, Mark, San Mauro, Diego

Journal:

Year:

2019

Language:

english

File:

PDF, 3.44 MB

english, 2019

37

What lies beneath? Molecular evolution during the radiation of caecilian amphibians

Torres-Sánchez, María, Gower, David J., Alvarez-Ponce, David, Creevey, Christopher J., Wilkinson, Mark, San Mauro, Diego

Journal:

Year:

2019

File:

PDF, 3.44 MB

2019

38

Molecular chaperones accelerate the evolution of their protein clients in yeast

Alvarez-Ponce, David, Aguilar-Rodríguez, José, Fares, Mario A, Papp, Balazs

Journal:

Genome Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 5.55 MB

english, 2019

39

Emerging Priorities for Microbiome Research

Cullen, Chad M., Aneja, Kawalpreet K., Beyhan, Sinem, Cho, Clara E., Woloszynek, Stephen, Convertino, Matteo, McCoy, Sophie J., Zhang, Yanyan, Anderson, Matthew Z., Alvarez-Ponce, David, Smirnova, Eka

Journal:

Frontiers in Microbiology

Year:

2020

Language:

english

File:

PDF, 2.76 MB

english, 2020

40

Richard Dickerson, Molecular Clocks, and Rates of Protein Evolution

Alvarez-Ponce, David

Journal:

Journal of Molecular Evolution

Year:

2020

File:

PDF, 907 KB

2020

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