Guoqing Lu

2019

Age-related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus)

Zhang, M., Gaughan, S., Chang, Q., Chen, H., Lu, G., Wang, X., Xu, L., Zhu, L. & Jiang, J., Jul 2019, In : MicrobiologyOpen. 8, 7, e00778.

Research output: Contribution to journal › Article

Open Access

Urodela

Gastrointestinal Tract

Bacteroidetes

Proteobacteria

Ileum

Are the gut microbial systems of giant pandas unstable?

Yao, R., Yang, Z., Zhang, Z., Hu, T., Chen, H., Huang, F., Gu, X., Yang, X., Lu, G. & Zhu, L., Sep 2019, In : Heliyon. 5, 9, e02480.

Research output: Contribution to journal › Article

Open Access

Ailuropoda melanoleuca

intestinal microorganisms

digestive system

Clostridiaceae

Pseudomonadaceae

1 Citation (Scopus)

Comparative skin transcriptome of two Oujiang color common carp (Cyprinus carpio var. color) varieties

Du, J., Chen, X., Wang, J., Chen, H., Yue, W., Lu, G. & Wang, C., Feb 15 2019, In : Fish Physiology and Biochemistry. 45, 1, p. 177-185 9 p.

Research output: Contribution to journal › Article

colored varieties

Carps

Cyprinus carpio

Transcriptome

skin (animal)

Differential gene expression in chronic wasting disease-positive white-tailed deer (Odocoileus virginianus)

Trone-Launer, E. K., Wang, J., Lu, G., Mateus-Pinilla, N. E., Zick, P. R., Lamer, J. T., Shelton, P. A. & Jacques, C. N., Nov 1 2019, In : Ecology and Evolution. 9, 22, p. 12600-12612 13 p.

Research output: Contribution to journal › Article

Open Access

chronic wasting disease

Odocoileus virginianus

deer

gene expression

gene

Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation

Yao, R., Xu, L., Lu, G. & Zhu, L., May 1 2019, In : Evolutionary Bioinformatics. 15

Research output: Contribution to journal › Comment/debate

Open Access

Wild Animals

bioinformatics

Bioinformatics

wild animals

Nutrition

Habitat use and population structure of the shoal chub (Macrhybopsis hyostoma) in the upper Mississippi River basin

Gaughan, S., Steffensen, K. & Lu, G., Jun 15 2019, In : Environmental Biology of Fishes. 102, 6, p. 901-914 14 p.

Research output: Contribution to journal › Article

Mississippi River

habitat use

population structure

river basin

field survey

Resolving the genetic paradox of invasions: Preadapted genomes and postintroduction hybridization of bigheaded carps in the Mississippi River Basin

Wang, J., Gaughan, S., Lamer, J. T., Deng, C., Hu, W., Wachholtz, M., Qin, S., Nie, H., Liao, X., Ling, Q., Li, W., Zhu, L., Bernatchez, L., Wang, C. & Lu, G., Jan 1 2019, (Accepted/In press) In : Evolutionary Applications.

Research output: Contribution to journal › Article

Open Access

Mississippi

Carps

Mississippi River

Hypophthalmichthys molitrix

Rivers

2018

4 Citations (Scopus)

Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes

Zhu, L., Wu, Q., Deng, C., Zhang, M., Zhang, C., Chen, H., Lu, G. & Wei, F., May 2018, In : Environmental microbiology. 20, 5, p. 1711-1722 12 p.

Research output: Contribution to journal › Article

Carnivora

High Fat Diet

purines

fat

Felidae

2 Citations (Scopus)

Endangered Père David’s deer genome provides insights into population recovering

Zhu, L., Deng, C., Zhao, X., Ding, J., Huang, H., Zhu, S., Wang, Z., Qin, S., Ding, Y., Lu, G. & Yang, Z., Dec 2018, In : Evolutionary Applications. 11, 10, p. 2040-2053 14 p.

Research output: Contribution to journal › Article

Deer

deer

genome

Genome

gene

2017

2 Citations (Scopus)

An integrated and comprehensive transcriptome reveals immune-related genes and signal pathways in topmouth culter (Culter alburnus)

Lei, S., Chen, X., Wang, J., Zhou, L., Zhang, Y., Zhang, G., Lu, G. & Wang, C., May 1 2017, In : Aquaculture Research. 48, 5, p. 2231-2242 12 p.

Research output: Contribution to journal › Article

transcriptome

signal transduction

disease resistance

gene

health and disease

1 Citation (Scopus)

A systems biology approach for modeling microbiomes using split graphs

Kim, S., Thapa, I., Lu, G., Zhu, L. & Ali, H. H., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2062-2068 7 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Systems Biology

Microbiota

Fish

Fishes

Chemical analysis

4 Citations (Scopus)

Complete genome sequences of Pseudomonas fluorescens bacteriophages isolated from freshwater samples in Omaha, Nebraska

Lu, G., Luhr, J., Stoecklein, A., Warner, P. & Tapprich, W. E., Jan 1 2017, In : Genome Announcements. 5, 12, e01501-16.

Research output: Contribution to journal › Article

Pseudomonas Phages

Pseudomonas fluorescens

Fresh Water

Genome

Regulator Genes

Evolutionary relationship of three mitten crabs (Eriocheir sp)revealed by mitogenome and 5S ribosomal DNA analysis

Chen, X., Wang, J., Huang, L., Yue, W., Zou, J., Yuan, C., Lu, G. & Wang, C., Nov 2017, In : Aquaculture and Fisheries. 2, 6, p. 256-261 6 p.

Research output: Contribution to journal › Article

Open Access

Eriocheir

ribosomal DNA

crab

crabs

Eriocheir sinensis

5 Citations (Scopus)

Insect and plant-derived miRNAs in greenbug (Schizaphis graminum) and yellow sugarcane aphid (Sipha flava) revealed by deep sequencing

Wang, H., Zhang, C., Dou, Y., Yu, B., Liu, Y., Heng-Moss, T. M., Lu, G., Wachholtz, M., Bradshaw, J. D., Twigg, P., Scully, E., Palmer, N. & Sarath, G., Jan 30 2017, In : Gene. 599, p. 68-77 10 p.

Research output: Contribution to journal › Article

High-Throughput Nucleotide Sequencing

Saccharum

Aphids

MicroRNAs

Insects

2 Citations (Scopus)

Selection of appropriate reference genes for qPCR in the Chinese mitten crab, Eriocheir sinensis (Decapoda, Varunidae)

Huang, S., Chen, X., Wang, J., Chen, J., Yue, W., Lu, W., Lu, G. & Wang, C., Jan 1 2017, In : Crustaceana. 90, 3, p. 275-296 22 p.

Research output: Contribution to journal › Article

Varunidae

Eriocheir sinensis

Decapoda

crab

gene

2016

6 Citations (Scopus)

Characterization of pikeperch (Sander lucioperca) transcriptome and development of SSR markers

Han, X., Ling, Q., Li, C., Wang, G., Xu, Z. & Lu, G., Jun 1 2016, In : Biochemical Systematics and Ecology. 66, p. 188-195 8 p.

Research output: Contribution to journal › Article

Sanders

Sander lucioperca

Transcriptome

transcriptome

Genes

6 Citations (Scopus)

Complete mitochondrial genomes of three mitten crabs, Eriocheir sinensis, E. Hepuensis, and E. Japonica

Wang, J., Huang, L., Cheng, Q., Lu, G. & Wang, C. H., Jan 1 2016, In : Mitochondrial DNA. 27, 2, p. 1175-1176 2 p.

Research output: Contribution to journal › Article

Mitochondrial Genome

Genes

Minisatellite Repeats

Transfer RNA

rRNA Genes

1 Citation (Scopus)

Model-based clustering with certainty estimation: Implication for clade assignment of influenza viruses

Zhang, S., Li, Z., Beland, K. & Lu, G., Jul 21 2016, In : BMC bioinformatics. 17, 1, 287.

Research output: Contribution to journal › Article

Model-based Clustering

Influenza

Hemagglutinins

Orthomyxoviridae

Viruses

The complete mitochondrial genome of the shoal chub, Macrhybopsis hyostoma

Gaughan, S., Johnson, R., Wang, J., Wachholtz, M., Steffensen, K., King, T. & Lu, G., Jan 1 2016, In : Mitochondrial DNA Part B: Resources. 1, 1, p. 911-912 2 p.

Research output: Contribution to journal › Article

Cyprinidae

Mitochondrial Genome

Base Composition

Phylogeny

Transfer RNA

The complete mitochondrial genome of the silver chub, Macrhybopsis storeriana

Gaughan, S., Johnson, R., Wang, J., Wachholtz, M., Steffensen, K., King, T. & Lu, G., Jan 1 2016, In : Mitochondrial DNA Part B: Resources. 1, 1, p. 789-790 2 p.

Research output: Contribution to journal › Article

Cyprinidae

Mitochondrial Genome

Silver

Base Composition

Phylogeny

3 Citations (Scopus)

Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids

Wang, J., Lamer, J. T., Gaughan, S., Wachholtz, M., Wang, C. & Lu, G., Dec 1 2016, In : Ecology and Evolution. 6, 23, p. 8452-8459 8 p.

Research output: Contribution to journal › Article

Hypophthalmichthys nobilis

Hypophthalmichthys molitrix

transcriptomics

carp

transcriptome

2015

30 Citations (Scopus)

Genetic diversity in oxytocin ligands and receptors in New World monkeys

Ren, D., Lu, G., Moriyama, H., Mustoe, A. C., Harrison, E. B. & French, J. A., May 4 2015, In : PloS one. 10, 5, e0125775.

Research output: Contribution to journal › Article

Platyrrhini

Oxytocin Receptors

Cebidae

oxytocin

Oxytocin

34 Citations (Scopus)

Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis

Huang, S., Wang, J., Yue, W., Chen, J., Gaughan, S., Lu, W., Lu, G. & Wang, C., Sep 15 2015, In : Scientific reports. 5, 14015.

Research output: Contribution to journal › Article

Hepatopancreas

Biological Phenomena

Molting

Energy Metabolism

Genes

2014

23 Citations (Scopus)

Analysis of the skin transcriptome in two Oujiang color varieties of common carp

Wang, C., Wachholtz, M., Wang, J., Liao, X. & Lu, G., Mar 6 2014, In : PloS one. 9, 3, e90074.

Research output: Contribution to journal › Article

colored varieties

Carps

Gene Expression Profiling

Cyprinus carpio

transcriptome

9 Citations (Scopus)

Molecular phylogeny and evolutionary dynamics of influenza A nonstructural (NS) gene

Xu, J., Zhong, H. A., Madrahimov, A., Helikar, T. & Lu, G., Mar 1 2014, In : Infection, Genetics and Evolution. 22, p. 192-200 9 p.

Research output: Contribution to journal › Article

influenza

Phylogeny

Human Influenza

phylogeny

Swine

2013

15 Citations (Scopus)

Dynamics of Influenza Virus and Human Host Interactions During Infection and Replication Cycle

Madrahimov, A., Helikar, T., Kowal, B., Lu, G. & Rogers, J. A., Jun 1 2013, In : Bulletin of Mathematical Biology. 75, 6, p. 988-1011 24 p.

Research output: Contribution to journal › Article

influenza

Influenza

Orthomyxoviridae

Viruses

Replication

427 Citations (Scopus)

The Tree of Life and a New Classification of Bony Fishes

Betancur-R, R., Broughton, R. E., Wiley, E. O., Carpenter, K., López, J. A., Li, C., Holcroft, N. I., Arcila, D., Sanciangco, M., Cureton, J. C., Zhang, F., Buser, T., Campbell, M. A., Ballesteros, J. A., Roa-Varon, A., Willis, S., Borden, W. C., Rowley, T., Reneau, P. C., Hough, D. J. & 4 others, Lu, G., Grande, T., Arratia, G. & Ortí, G., Apr 29 2013, In : PLoS Currents. APR 2013, ecurrents.tol.53ba26640df0ccaee75bb165c8c26288.

Research output: Contribution to journal › Article

Fishes

Phylogeny

Perciformes

Uncertainty

Communication

52 Citations (Scopus)

Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species

Liao, X., Cheng, L., Xu, P., Lu, G., Wachholtz, M., Sun, X. & Chen, S., Apr 22 2013, In : PloS one. 8, 4, e62308.

Research output: Contribution to journal › Article

Carassius

Aquaculture

unigenes

Goldfish

Carps

11 Citations (Scopus)

Transcriptome analysis of two buffalograss cultivars

Wachholtz, M., Heng-Moss, T., Twigg, P., Baird, L., Lu, G. & Amundsen, K., Sep 11 2013, In : BMC genomics. 14, 1, 613.

Research output: Contribution to journal › Article

Gene Expression Profiling

Protein-Serine-Threonine Kinases

Transferases

Poaceae

Titanium

2012

11 Citations (Scopus)

Complete mitogenome sequence of black carp (Mylopharyngodon piceus) and its use for molecular phylogeny of leuciscine fishes

Chenghui, W., Wang, J., Yang, J., Lu, G., Song, X., Chen, Q., Xu, J., Yang, Q. & Li, S., May 1 2012, In : Molecular Biology Reports. 39, 5, p. 6337-6342 6 p.

Research output: Contribution to journal › Article

Carps

Phylogeny

Fishes

Mitochondrial Genome

Genes

3 Citations (Scopus)

Computational analysis of adaptive antigenic mutations of the human influenza hemagglutinin for vaccine strain selection

Rickert, J. D., Herpy, T. A., Zhong, H. A. & Lu, G., Mar 1 2012, In : International Journal of Bioinformatics Research and Applications. 8, 1-2, p. 81-98 18 p.

Research output: Contribution to journal › Article

Site selection

Vaccines

Influenza Vaccines

Hemagglutinins

Viruses

24 Citations (Scopus)

Evolutionary history and phylodynamics of influenza A and B neuraminidase (NA) genes inferred from large-scale sequence analyses

Xu, J., Davis, C. T., Christman, M. C., Rivailler, P., Zhong, H. A., Donis, R. O. & Lu, G., Jul 11 2012, In : PloS one. 7, 7, e38665.

Research output: Contribution to journal › Article

sialidase

Neuraminidase

influenza

Human Influenza

Sequence Analysis

8 Citations (Scopus)

Microsatellite genetic diversity and differentiation of native and introduced grass carp populations in three continents

Chen, Q., Wang, C., Lu, G., Zhao, J., Chapman, D. C., Zsigmond, J. & Li, S., Jun 1 2012, In : Genetica. 140, 4-6, p. 115-123 9 p.

Research output: Contribution to journal › Article

Ctenopharyngodon idella

Carps

Microsatellite Repeats

microsatellite repeats

Rivers

5 Citations (Scopus)

PhyloMarker–-A Tool for Mining Phylogenetic Markers through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Lei, R., Rowley, T. W., Zhu, L., Bailey, C. A., Engberg, S. E., Wood, M. L., Christman, M. C., Perry, G. H., Louis, E. E. & Lu, G., Jan 1 2012, In : Evolutionary Bioinformatics. 8

Research output: Contribution to journal › Review article

Open Access

Cheirogaleidae

Microcebus

Phylogeny

phylogeny

genome

2011

13 Citations (Scopus)

Evolutionary dynamics of influenza A nucleoprotein (NP) lineages revealed by large-scale sequence analyses

Xu, J., Christman, M. C., Donis, R. O. & Lu, G., Dec 1 2011, In : Infection, Genetics and Evolution. 11, 8, p. 2125-2132 8 p.

Research output: Contribution to journal › Article

nucleoproteins

influenza

Nucleoproteins

Human Influenza

Sequence Analysis

2 Citations (Scopus)

Evolution of influenza viral neuraminidase (NA) revealed by large-scale sequence analysis.

Xu, J. & Lu, G., May 1 2011, In : Influenza and other respiratory viruses. 5 Suppl 1, p. 405-408 4 p.

Research output: Contribution to journal › Article

Influenza B virus

Molecular Evolution

Influenza A virus

Neuraminidase

Phylogeny

Large-scale sequence analysis of influenza A hemagglutinin (HA): insights into a unified system for lineage assignment.

Rickert, J., Xu, J., Christman, M. & Lu, G., May 1 2011, In : Influenza and other respiratory viruses. 5 Suppl 1, p. 410-413 4 p.

Research output: Contribution to journal › Article

43 Citations (Scopus)

Pandemic (H1N1) 2009 virus revisited: An evolutionary retrospective

Christman, M. C., Kedwaii, A., Xu, J., Donis, R. O. & Lu, G., Jul 1 2011, In : Infection, Genetics and Evolution. 11, 5, p. 803-811 9 p.

Research output: Contribution to journal › Review article

H1N1 Subtype Influenza A Virus

Pandemics

pandemic

Influenza A virus

virus

6 Citations (Scopus)

Population genetic structure and evolutionary history of grass carp Ctenopharyngodon idella in the Yangtze River, China

Zhao, J., Cao, Y., Li, S., Li, J., Deng, Y. & Lu, G., Jan 1 2011, In : Environmental Biology of Fishes. 90, 1, p. 85-93 9 p.

Research output: Contribution to journal › Article

Ctenopharyngodon idella

Yangtze River

genetic structure

population genetics

grass

4 Citations (Scopus)

Significant genetic differentiation between native and introduced silver carp (Hypophthalmichthys molitrix) inferred from mtDNA analysis

Li, S. F., Xu, J. W., Yang, Q. L., Wang, C. H., Chapman, D. C. & Lu, G., Dec 1 2011, In : Environmental Biology of Fishes. 92, 4, p. 503-511 9 p.

Research output: Contribution to journal › Article

Hypophthalmichthys molitrix

genetic differentiation

silver

mitochondrial DNA

genetic variation

2010

7 Citations (Scopus)

Applying neural networks to classify influenza virus antigenic types and hosts

Attaluri, P. K., Chen, Z. & Lu, G., Aug 20 2010, 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010. p. 279-284 6 p. 5510726. (2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2010).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Viruses

Neural networks

Genes

Nucleotides

Decision trees

4 Citations (Scopus)

Cloning, characterization and expression of the pepsinogen C from the golden mandarin fish Siniperca scherzeri (Teleostei: Perciformes)

Deng, Y., Zhao, J., Lu, G., Wu, X. & Tao, Y., Aug 3 2010, In : Fisheries Science. 76, 5, p. 819-826 8 p.

Research output: Contribution to journal › Article

pepsinogen

Perciformes

mandarins

molecular cloning

fish

7 Citations (Scopus)

Genetic diversity and variation of mitochondrial DNA in native and introduced bighead carp

Li, S. F., Yang, Q. L., Xu, JIA. WEI., Wang, C. H., Chapman, D. C. & Lu, G., Dec 1 2010, In : Transactions of the American Fisheries Society. 139, 4, p. 937-946 10 p.

Research output: Contribution to journal › Article

Hypophthalmichthys nobilis

mitochondrial DNA

genetic variation

river system

river

163 Citations (Scopus)

On the origin of species: Insights from the ecological genomics of lake whitefish

Bernatchez, L., Renaut, S., Whiteley, A. R., Derome, N., Jeukens, J., Landry, L., Lu, G., Nolte, A. W., Østbye, K., Rogers, S. M. & St-Cyr, J., Jun 12 2010, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 365, 1547, p. 1783-1800 18 p.

Research output: Contribution to journal › Article

Salmonidae

Coregonus clupeaformis

Lakes

Genomics

genomics

Sequence comparison using multi-order Markov chains

Fang, X., Lu, G. & Zhang, S., Sep 6 2010, 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010. 5515258. (2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Markov Chains

DNA sequences

Markov processes

Phylogeny

Experiments

2009

12 Citations (Scopus)

7TMRmine: A Web server for hierarchical mining of 7TMR proteins

Lu, G., Wang, Z., Jones, A. M. & Moriyama, E., Jun 19 2009, In : BMC genomics. 10, 275.

Research output: Contribution to journal › Article

Genome

Proteins

Pharmacogenetics

Protein Sequence Analysis

Computational Biology

17 Citations (Scopus)

A comparison of complete mitochondrial genomes of silver carp hypophthalmichthys molitrix and bighead carp hypophthalmichthys nobilis: Implications for their taxonomic relationship and phylogeny

Li, S. F., Xu, J. W., Yang, Q. L., Wang, C. H., Chen, Q., Chapman, D. C. & Lu, G., May 1 2009, In : Journal of Fish Biology. 74, 8, p. 1787-1803 17 p.

Research output: Contribution to journal › Article

Hypophthalmichthys nobilis

Hypophthalmichthys molitrix

silver

phylogeny

genome

16 Citations (Scopus)

Analysis of genetic variation in grass carp (Ctenopharyngodon idellus) from native and colonized regions using ISSR markers

Chen, Q., Wang, C. H., Lu, G., Song, X., Xu, J. W., Yang, Q. L. & Li, S. F., Nov 1 2009, In : Biochemical Systematics and Ecology. 37, 5, p. 549-555 7 p.

Research output: Contribution to journal › Article

Ctenopharyngodon idella

Carps

Microsatellite Repeats

genetic variation

Rivers

45 Citations (Scopus)

Gene expression profiling of tolerant barley in response to diuraphis noxia (Hemiptera: Aphididae) feeding

Gutsche, A., Heng-Moss, T., Sarath, G., Twigg, P., Xia, Y., Lu, G. & Mornhinweg, D., Apr 1 2009, In : Bulletin of Entomological Research. 99, 2, p. 163-173 11 p.

Research output: Contribution to journal › Article

Diuraphis noxia

Aphididae

Hemiptera

barley

gene expression

5 Citations (Scopus)

Integrating decision tree and hidden markov model (hmm) for subtype prediction of human influenza a virus

Attaluri, P. K., Chen, Z., Weerakoon, A. M. & Lu, G., Aug 17 2009, Cutting-Edge Research Topics on Multiple Criteria Decision Making: 20th International Conference, MCDM 2009, Chengdu/Jiuzhaigou, Proceedings. p. 52-58 7 p. (Communications in Computer and Information Science; vol. 35).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Hidden Markov models

Decision trees

Viruses

Public health

Bioinformatics

Guoqing Lu, PhD