Highly Cited Papers

Over the years, IGBB scientists have gained a reputation for publishing papers that are widely cited. Information regarding the 100 most highly cited papers authored/co-authored by IGBB employees, faculty fellows, and affiliates is presented below. Citation values are from Scopus. For a particular IGBB fellow/affiliate/staff member, only those papers published while at MS State are included.

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FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar

IGBB Authors:
Chuan-Yu Hsu, Joshua P. Adams, Dawn S. Luthe, Cetin Yuceer

PUBLICATION YEAR: 2011
IMPACT FACTOR: 10.425
CITATION COUNT: 376

Hsu C-Y, Adams JP, Kim H, No K, Ma C, Strauss SH, Drnevich J, Vandervelde L, Ellis JD, Rice BM, Wickett N, Gunter LE, Tuskan GA, Brunner AM, Page GP, Barakat A, Carlson JE, DePamphilis CW, Luthe DS, Yuceer C (2011) FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar. Proceedings of the National Academy of Sciences of the United States of America 108(26): 10756-10761.

DOI: 10.1016/10.1073/pnas.1104713108
EID: 2-s2.0-79960615345
PMID: 21653885

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ABSTRACT
Annual plants grow vegetatively at early developmental stages and then transition to the reproductive stage, followed by senescence in the same year. In contrast, after successive years of vegetative growth at early ages, woody perennial shoot meristems begin repeated transitions between vegetative and reproductive growth at sexual maturity. However, it is unknown how these repeated transitions occur without a developmental conflict between vegetative and reproductive growth. We report that functionally diverged paralogs FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2), products of whole-genome duplication and homologs of Arabidopsis thaliana gene FLOWERING LOCUS T (FT), coordinate the repeated cycles of vegetative and reproductive growth in woody perennial poplar (Populus spp.). Our manipulative physiological and genetic experiments coupled with field studies, expression profiling, and network analysis reveal that reproductive onset is determined by FT1 in response to winter temperatures, whereas vegetative growth and inhibition of bud set are promoted by FT2 in response to warm temperatures and long days in the growing season. The basis for functional differentiation between FT1 and FT2 appears to be expression pattern shifts, changes in proteins, and divergence in gene regulatory networks. Thus, temporal separation of reproductive onset and vegetative growth into different seasons via FT1 and FT2 provides seasonality and demonstrates the evolution of a complex perennial adaptive trait after genome duplication.

Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017)

IGBB Authors:
Sead Sabanadzovic

PUBLICATION YEAR: 2017
IMPACT FACTOR: 2.188
CITATION COUNT: 555

Optix drives the repeated convergent evolution of butterfly wing pattern mimicry

IGBB Authors:
Brian A. Counterman

PUBLICATION YEAR: 2011
IMPACT FACTOR: 20.263
CITATION COUNT: 342

Poplar FT2 shortens the juvenile phase and promotes seasonal flowering

IGBB Authors:
Chuan-Yu Hsu, Dawn S. Luthe, Cetin Yuceer

PUBLICATION YEAR: 2006
IMPACT FACTOR: 11.304
CITATION COUNT: 282

AgBase: a functional genomics resource for agriculture

IGBB Authors:
Fiona M. McCarthy, Nan Wang, G. Bryce Magee, Bindu Nanduri, Mark L. Lawrence, Dawn S. Luthe, Susan M. Bridges, Shane C. Burgess

PUBLICATION YEAR: 2006
IMPACT FACTOR: 4.188
CITATION COUNT: 246

McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP, Luthe DS, Bridges SM, Burgess SC (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics 7: 229.

DOI: 10.1186/1471-2164-7-229
EID: 2-s2.0-33750483615
PMID: 16961921

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ABSTRACT
BACKGROUND: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. DESCRIPTION: To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource http://www.agbase.msstate.edu for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. CONCLUSION: The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms.

Consensus statement: Virus taxonomy in the age of metagenomics

IGBB Authors:
Sead Sabanadzovic

PUBLICATION YEAR: 2017
IMPACT FACTOR: 25.707
CITATION COUNT: 569

The Gene Ontology: Enhancements for 2011

IGBB Authors:
Teresia J. Buza, Shane C. Burgess, Catherine R. Gresham, Fiona M. McCarthy

PUBLICATION YEAR: 2012
IMPACT FACTOR: 8.646
CITATION COUNT: 193

Blake JA, Dolan M, Drabkin H, Hill DP, Ni L, Sitnikov D, Burgess S, Buza T, Gresham C, McCarthy F, Pillai L, Wang H, Carbon S, Lewis SE, Mungall CJ, Gaudet P, Chisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, am-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Argoud-Puy G, Bely B, Blatter MC, Bougueleret L, Boutet E, Branconi-Quintaje S, Breuza L, Bridge A, Browne P, Chan WM, Coudert E, Cusin I, Dimmer E, Duek-Roggli P, Eberhardt R, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gardner M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Huntley R, James J, Jimenez S, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Moinat M, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Porras Millan P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Sehra H, Stanley E, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulger R, Lomax J, Roncaglia P, Camon E, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Gwinn Giglio M, Dolinski K, Heinicke S, Livstone MS, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall MD, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang SJ, Petri V, Lowry T, D'Eustachio P, Matthews L, Amundsen CD, Balakrishnan R, Binkley G, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Slonim D, Wick H, Thomas P, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M (2012) The Gene Ontology: Enhancements for 2011. Nucleic Acids Research 40(D1): D559-D564.

DOI: 10.1093/nar/gkr1028
EID: 2-s2.0-84859699831
PMID: 22102568

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ABSTRACT
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.

Maternal antibody transfer from dams to their egg yolks, egg whites, and chicks in meat lines of chickens

IGBB Authors:
Shane C. Burgess

PUBLICATION YEAR: 2006
IMPACT FACTOR: 1.82
CITATION COUNT: 268

Hamal KR, Burgess SC, Pevzner IY, Erf GF (2006) Maternal antibody transfer from dams to their egg yolks, egg whites, and chicks in meat lines of chickens. Poultry Science 85(8): 1364-1372.

DOI: 10.1093/ps/85.8.1364
EID: 2-s2.0-33748341473
PMID: 16903465

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ABSTRACT
Maternal antibodies are transferred from hens to the chicks via the egg. To gain insight into maternal antibody transfer and endogenous production of antibodies in broiler chicks, total IgY, IgA, IgM, as well as anti-Newcastle disease virus (NDV) and anti-infectious bronchitis (IBV) antibody levels were examined in the dams' plasma, egg yolks, egg whites, and chicks' plasma on d 3, 7, 14, and 21. Blood was collected from 39-wk-old breeder hens (line 1, n = 17; line 2, n = 21). Fertile eggs were used for antibody extraction from the egg yolks and egg whites (4 to 5 eggs/dam) and for hatching. Unvaccinated chicks (4 to 5 chicks/dam) were reared in a HEPA-filtered room and were bled on d 3, 7, 14 and 21. Based on ELISA methods, plasma levels of IgY and IgM were higher (P < 0.0001), and those of IgA were similar (P = 0.31), in line 2 compared with line 1. Egg yolk IgY and IgA, as well as egg white IgY, IgA, and IgM levels were higher in line 2 compared with line 1 (P < 0.0001). Independent of line of chicken, the percentage dam-to-chick (3 d) plasma transfer of IgY was estimated to be approximately 30%, with that for IgM and IgA less than 1%. Chicks synthesized IgM first, followed by IgA and IgY. Anti-NDV and anti-IBV antibodies were detected in the dams' plasma, egg yolks, and in the chicks' plasma on d 3 and 7, with line 2 having higher anti-IBV and lower anti-NDV levels than line 1 in all samples (P < 0.0001). In summary, IgY levels, total or antigen-specific, in the dams' plasma or eggs were found to be a direct indicator of maternal antibody transfer to the chicks' circulation, with an expected percentage transfer of approximately 30%. This knowledge, together with the observed time course of endogenous antibody production in broiler chicks, may find direct application in formulating strategies for protecting chicks, especially during the first few weeks of age when their immune system is not yet fully functional.

Applying Adverse Outcome Pathways (AOPs) to support Integrated Approaches to Testing and Assessment (IATA)

IGBB Authors:
Natàlia Garcia-Reyero

PUBLICATION YEAR: 2014
IMPACT FACTOR: 2.624
CITATION COUNT: 314

Insect feeding mobilizes a unique plant defense protease that disrupts the peritrophic matrix of caterpillars

IGBB Authors:
Tibor Pechan

PUBLICATION YEAR: 2002
IMPACT FACTOR: 10.962
CITATION COUNT: 215

Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility

IGBB Authors:
Bindu Nanduri, Jean-Magloire Nguekam Feugang, Shane C. Burgess, Erdogan Memili

PUBLICATION YEAR: 2008
IMPACT FACTOR: 3.105
CITATION COUNT: 239

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

IGBB Authors:
Michael W. Vandewege, David A. Ray, Federico G. Hoffmann

PUBLICATION YEAR: 2013
IMPACT FACTOR: 10.634
CITATION COUNT: 229

Castoe TA, de Koning APJ, Hall KT, Card DC, Shield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BSW, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowsi AM, Yandell M, Warren WC, Secor SM, Pollock DD (2013) The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences of the United States of America 110(51): 20645-20650.

DOI: 10.1073/pnas.1314475110
EID: 2-s2.0-84890812848
PMID: 24297902

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ABSTRACT
Snakes possess many extreme morphological and physiological adaptations. Identification of the molecular basis of these traits can provide novel understanding for vertebrate biology and medicine. Here, we study snake biology using the genome sequence of the Burmese python (Python molurus bivittatus), a model of extreme physiological and metabolic adaptation. We compare the python and king cobra genomes along with genomic samples from other snakes and perform transcriptome analysis to gain insights into the extreme phenotypes of the python. We discovered rapid and massive transcriptional responses in multiple organ systems that occur on feeding and coordinate major changes in organ size and function. Intriguingly, the homologs of these genes in humans are associated with metabolism, development, and pathology. We also found that many snake metabolic genes have undergone positive selection, which together with the rapid evolution of mitochondrial proteins, provides evidence for extensive adaptive redesign of snake metabolic pathways. Additional evidence for molecular adaptation and gene family expansions and contractions is associated with major physiological and phenotypic adaptations in snakes; genes involved are related to cell cycle, development, lungs, eyes, heart, intestine, and skeletal structure, including GRB2-associated binding protein 1, SSH, WNT16, and bone morphogenetic protein 7. Finally, changes in repetitive DNA content, guanine-cytosine isochore structure, and nucleotide substitution rates indicate major shifts in the structure and evolution of snake genomes compared with other amniotes. Phenotypic and physiological novelty in snakes seems to be driven by system-wide coordination of protein adaptation, gene expression, and changes in the structure of the genome.

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