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2020

Changes in the community structure of the symbiotic microbes of wild amphibians from the eastern edge of the Tibetan Plateau

Xu, L. L., Chen, H., Zhang, M., Zhu, W., Chang, Q., Lu, G., Chen, Y., Jiang, J. & Zhu, L., Apr 1 2020, In : MicrobiologyOpen. 9, 4, e1004.

Research output: Contribution to journalArticle

Open Access

Lessons from bamboo-eating pandas and their gut microbiome: Gut microbiome flow and applications

Zhang, Z., Hu, T., Lu, G. & Zhu, L., Apr 1 2020, In : Evolutionary Applications. 13, 4, p. 615-619 5 p.

Research output: Contribution to journalArticle

Open Access

Presence and structure-activity relationship of intrinsically disordered regions across mucins

Carmicheal, J., Atri, P., Sharma, S., Kumar, S., Chirravuri Venkata, R., Kulkarni, P., Salgia, R., Ghersi, D., Kaur, S. & Batra, S. K., Feb 1 2020, In : FASEB Journal. 34, 2, p. 1939-1957 19 p.

Research output: Contribution to journalArticle

Open Access

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., Feb 1 2020, In : Evolutionary Applications. 13, 2, p. 263-277 15 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
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 journalArticle

Open Access
1 Scopus citations

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 journalArticle

Open Access
2 Scopus citations

Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction

Williams, J. J., Drew, J. C., Galindo-Gonzalez, S., Robic, S., Dinsdale, E., Morgan, W. R., Triplett, E. W., Burnette, J. M., Donovan, S. S., Fowlks, E. R., Goodman, A. L., Grandgenett, N. F., Goller, C. C., Hauser, C., Jungck, J. R., Newman, J. D., Pearson, W. R., Ryder, E. F., Sierk, M. E., Smith, T. M. & 10 others, Tosado-Acevedo, R., Tapprich, W., Tobin, T. C., Toro-Martinez, A., Welch, L. R., Wilson, M. A., Ebenbach, D., McWilliams, M., Rosenwald, A. G. & Pauley, M. A., Jan 1 2019, In : PloS one. 14, 11, e0224288.

Research output: Contribution to journalArticle

Open Access

CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection

Kamga, L., Gil, A., Song, I., Brody, R., Ghersi, D., Aslan, N., Stern, L. J., Selin, L. K. & Luzuriaga, K., Jan 1 2019, In : PLoS pathogens. 15, 11, e1008122.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

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 journalArticle

1 Scopus citations

Computer modeling of clonal dominance: Memory-anti-naïve and its curbing by attrition

Castiglione, F., Ghersi, D. & Celada, F., Jan 1 2019, In : Frontiers in immunology. 10, JUL, 1513.

Research output: Contribution to journalArticle

Open Access

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 journalArticle

Open Access
Open Access
4 Scopus citations

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 journalArticle

Uncovering and characterizing splice variants associated with survival in lung cancer patients

West, S., Kumar, S., Batra, S. K., Ali, H. & Ghersi, D., Jan 1 2019, In : PLoS computational biology. 15, 10, e1007469.

Research output: Contribution to journalArticle

Open Access
2018

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 journalArticle

6 Scopus citations

Bioinformatics core competencies for undergraduate life sciences education

Wilson Sayres, M. A., Hauser, C., Sierk, M., Robic, S., Rosenwald, A. G., Smith, T. M., Triplett, E. W., Williams, J. J., Dinsdale, E., Morgan, W. R., Burnette, J. M., Donovan, S. S., Drew, J. C., Elgin, S. C. R., Fowlks, E. R., Galindo-Gonzalez, S., Goodman, A. L., Grandgenett, N. F., Goller, C. C., Jungck, J. R. & 14 others, Newman, J. D., Pearson, W., Ryder, E. F., Tosado-Acevedo, R., Tapprich, W., Tobin, T. C., Toro-Martínez, A., Welch, L. R., Wright, R., Barone, L., Ebenbach, D., McWilliams, M., Olney, K. C. & Pauley, M. A., Jun 2018, In : PloS one. 13, 6, e0196878.

Research output: Contribution to journalArticle

7 Scopus citations

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 journalArticle

4 Scopus citations

Motifome comparison between modern human, Neanderthal and Denisovan

Cserhati, M. F., Mooter, M. E., Peterson, L., Wicks, B., Xiao, P., Pauley, M. A. & Guda, C., Jun 18 2018, In : BMC genomics. 19, 1, 472.

Research output: Contribution to journalArticle

2 Scopus citations

The development and application of bioinformatics core competencies to improve bioinformatics training and education

Mulder, N., Schwartz, R., Brazas, M. D., Brooksbank, C., Gaeta, B., Morgan, S. L., Pauley, M. A., Rosenwald, A., Rustici, G., Sierk, M., Warnow, T. & Welch, L., Feb 2018, In : PLoS computational biology. 14, 2, e1005772.

Research output: Contribution to journalArticle

9 Scopus citations

Two critical positions in zinc finger domains are heavily mutated in three human cancer types

Munro, D., Ghersi, D. & Singh, M., Jun 2018, In : PLoS computational biology. 14, 6, e1006290.

Research output: Contribution to journalArticle

2 Scopus citations
2017

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 journalArticle

2 Scopus citations

Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope

Song, I. Y., Gil, A., Mishra, R., Ghersi, D., Selin, L. K. & Stern, L. J., Apr 1 2017, In : Nature Structural and Molecular Biology. 24, 4, p. 395-406 12 p.

Research output: Contribution to journalArticle

19 Scopus citations
4 Scopus citations

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

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

Research output: Contribution to journalArticle

4 Scopus citations

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 journalArticle

Open Access
1 Scopus citations

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 journalArticle

7 Scopus citations

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 journalArticle

6 Scopus citations

Severity of acute infectious mononucleosis correlates with cross-reactive influenza CD8 T-cell receptor repertoires

Aslan, N., Watkin, L. B., Gil, A., Mishra, R., Clark, F. G., Welsh, R. M., Ghersi, D., Luzuriaga, K. & Selina, L. K., Nov 1 2017, In : mBio. 8, 6, e01841-17.

Research output: Contribution to journalArticle

12 Scopus citations

Unique influenza A cross-reactive memory CD8 T-cell receptor repertoire has a potential to protect against EBV seroconversion

Watkin, L. B., Mishra, R., Gil, A., Aslan, N., Ghersi, D., Luzuriaga, K. & Selin, L. K., Oct 2017, In : Journal of Allergy and Clinical Immunology. 140, 4, p. 1206-1210 5 p.

Research output: Contribution to journalArticle

6 Scopus citations
2016

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

Welch, L., Brooksbank, C., Schwartz, R., Morgan, S. L., Gaeta, B., Kilpatrick, A. M., Mietchen, D., Moore, B. L., Mulder, N., Pauley, M., Pearson, W., Radivojac, P., Rosenberg, N., Rosenwald, A., Rustici, G. & Warnow, T., May 2016, In : PLoS computational biology. 12, 5, e1004943.

Research output: Contribution to journalArticle

11 Scopus citations

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 journalArticle

9 Scopus citations

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 journalArticle

8 Scopus citations
2 Scopus citations

Identifying enriched drug fragments as possible candidates for metabolic engineering

Sharma, S., Karri, K., Thapa, I., Bastola, D. & Ghersi, D., Oct 8 2016, In : BMC Medical Genomics. 9, 46.

Research output: Contribution to journalArticle

5 Scopus citations

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 journalArticle

1 Scopus citations

Summit of the research coordination networks for undergraduate biology education

Eaton, C. D., Allen, D., Anderson, L. J., Bowser, G., Pauley, M. A., Williams, K. S. & Uno, G. E., Dec 1 2016, In : CBE Life Sciences Education. 15, 4, mr1.

Research output: Contribution to journalArticle

2 Scopus citations

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 journalArticle

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 journalArticle

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 journalArticle

4 Scopus citations
2015

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 journalArticle

33 Scopus citations

Genome-Wide Detection and Analysis of Multifunctional Genes

Pritykin, Y., Ghersi, D. & Singh, M., Jan 1 2015, In : PLoS computational biology. 11, 10, e1004467.

Research output: Contribution to journalArticle

21 Scopus citations

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 journalArticle

40 Scopus citations
2014

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 journalArticle

24 Scopus citations

Identifying aging-related genes in mouse hippocampus using gateway nodes

Dempsey, K. M. & Ali, H. H., May 27 2014, In : BMC systems biology. 8, 1, 62.

Research output: Contribution to journalArticle

10 Scopus citations

Interaction-based discovery of functionally important genes in cancers

Ghersi, D. & Singh, M., Feb 1 2014, In : Nucleic acids research. 42, 3, p. e18

Research output: Contribution to journalArticle

15 Scopus citations

MolBLOCKS: Decomposing small molecule sets and uncovering enriched fragments

Ghersi, D. & Singh, M., Jul 15 2014, In : Bioinformatics. 30, 14, p. 2081-2083 3 p.

Research output: Contribution to journalArticle

17 Scopus citations

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 journalArticle

9 Scopus citations