Research Output

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

Epstein-barr virus epitope-major histocompatibility complex interaction combined with convergent recombination drives selection of diverse T cell receptor α and β repertoires

Gil, A., Kamga, L., Chirravuri-Venkata, R., Aslan, N., Clark, F., Ghersi, D., Luzuriaga, K. & Selin, L. K., Mar 1 2020, In : mBio. 11, 2, e00250-20.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Evolution and genetics of bighead and silver carps: Native population conservation versus invasive species control

Lu, G., Wang, C., Zhao, J., Liao, X., Wang, J., Luo, M., Zhu, L., Bernatzhez, L. & Li, S., Jul 1 2020, In : Evolutionary Applications. 13, 6, p. 1351-1362 12 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective

Lu, G. & Luo, M., Jul 2020, In : Aquaculture and Fisheries. 5, 4, p. 163-173 11 p.

Research output: Contribution to journalReview article

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

MUCIN-4 (MUC4) is a novel tumor antigen in pancreatic cancer immunotherapy

Gautam, S. K., Kumar, S., Dam, V., Ghersi, D., Jain, M. & Batra, S. K., Feb 2020, In : Seminars in Immunology. 47, 101391.

Research output: Contribution to journalReview article

On the planarity of validated complexes of model organisms in protein-protein interaction networks

Cooper, K., Cornelius, N., Gasper, W., Bhowmick, S. & Ali, H., 2020, Computational Science – ICCS 2020 - 20th International Conference, Proceedings. Krzhizhanovskaya, V. V., Závodszky, G., Lees, M. H., Sloot, P. M. A., Sloot, P. M. A., Sloot, P. M. A., Dongarra, J. J., Brissos, S. & Teixeira, J. (eds.). Springer, p. 652-666 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12137 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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
2 Scopus citations

The Changes in the Frog Gut Microbiome and Its Putative Oxygen-Related Phenotypes Accompanying the Development of Gastrointestinal Complexity and Dietary Shift

Zhang, M., Chen, H., Liu, L., Xu, L., Wang, X., Chang, L., Chang, Q., Lu, G., Jiang, J. & Zhu, L., Mar 3 2020, In : Frontiers in Microbiology. 11, 162.

Research output: Contribution to journalArticle

Open Access
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., 2019, In : PloS one. 14, 11, e0224288.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

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., 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., 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
1 Scopus citations
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

Identifying Structural Changes in Correlation Networks Models of Cancer Gene Expression by Stage

Li, Q., Ghersi, D., Thapa, I., Zhang, L., Ali, H. & Cooper, K., Nov 2019, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Yoo, I., Bi, J. & Hu, X. T. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2075-2082 8 p. 8983069. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Network Analysis of Antibiotic Resistance Identifies Compelling Mutations across Pathways

Ameri, K. & Cooper, K., Nov 2019, Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019. Yoo, I., Bi, J. & Hu, X. T. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 188-192 5 p. 8983099. (Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

8 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

8 Scopus citations

Biological pathway analysis

Venkata, R. C. & Ghersi, D., Jan 1 2018, Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics. Elsevier, Vol. 1-3. p. 1067-1070 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biological pathway data formats and standards

Venkata, R. C. & Ghersi, D., Jan 1 2018, Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics. Elsevier, Vol. 1-3. p. 1063-1066 4 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Cluster analysis of biological networks

Sharma, A., Ali, H. & Ghersi, D., Jan 1 2018, Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics. Elsevier, Vol. 1-3. p. 1036-1046 11 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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

5 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

12 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

4 Scopus citations
2017

A compartmental network model for the spread of whooping cough

Ameri, H. & Cooper, K., 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. 2224-2225 2 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Analysis of structural measurements in correlation networks built from gene expression data across different tissue types in Mus musculus

Li, Q. & Cooper, K., 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. 1716-1722 7 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Analyzing T cell receptor alpha/beta usage in binding to the pMHC

Ehrlich, R. & Ghersi, D., 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. 83-87 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans

Cooper, K., Hassan, W. & Ali, 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. 2151-2156 6 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

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 proceedingConference contribution

2 Scopus citations

Bioinformatics for middle school aged children: Activities for exposure to an interdisciplinary field

Cooper, K., McGraw, A. & Khazanchi, D., Apr 24 2017, ISEC 2017 - Proceedings of the 7th IEEE Integrated STEM Education Conference. Institute of Electrical and Electronics Engineers Inc., p. 1-9 9 p. 7910217. (ISEC 2017 - Proceedings of the 7th IEEE Integrated STEM Education Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 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

22 Scopus citations
5 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., 2017, In : Genome Announcements. 5, 12, e01501-16.

Research output: Contribution to journalArticle

4 Scopus citations

Correlation networks: Biologically driven relationships from gene expression data

Huff, G. W. & Cooper, K., 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. 1712-1715 4 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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
2 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

8 Scopus citations

In-silico analysis of the 'memory anti-Naïve' effect in anti-viral cross-reactive responses

Castiglione, F., Ghersi, D. & Celada, F., 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. 1433-1437 5 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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., 2017, In : Crustaceana. 90, 3, p. 275-296 22 p.

Research output: Contribution to journalArticle

8 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

13 Scopus citations