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Showing 1 to 12 of 12 entries
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Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems.

Global change biology. Bioenergy

Morris GP, Hu Z, Grabowski PP, Borevitz JO, de Graaff MA, Miller RM, Jastrow JD.
PMID: 27668013
Glob Change Biol Bioenergy. 2016 Sep;8(5):1000-1014. doi: 10.1111/gcbb.12309. Epub 2016 Jan 10.

The perennial grass species that are being developed as biomass feedstock crops harbor extensive genotypic diversity, but the effects of this diversity on biomass production are not well understood. We investigated the effects of genotypic diversity in switchgrass (

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Morris GP, Hu Z, Grabowski PP, et al. Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems. Glob Change Biol Bioenergy. 2016;8(5):1000-1014doi: 10.1111/gcbb.12309.
Morris, G. P., Hu, Z., Grabowski, P. P., Borevitz, J. O., de Graaff, M. A., Miller, R. M., & Jastrow, J. D. (2016). Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems. Global change biology. Bioenergy, 8(5), 1000-1014. https://doi.org/10.1111/gcbb.12309
Morris, Geoffrey P, et al. "Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems." Global change biology. Bioenergy vol. 8,5 (2016): 1000-1014. doi: https://doi.org/10.1111/gcbb.12309
Morris GP, Hu Z, Grabowski PP, Borevitz JO, de Graaff MA, Miller RM, Jastrow JD. Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems. Glob Change Biol Bioenergy. 2016 Sep;8(5):1000-1014. doi: 10.1111/gcbb.12309. Epub 2016 Jan 10. PMID: 27668013; PMCID: PMC5019262.
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A novel dataset for identifying sex-biased genes in Drosophila.

Journal of genomics

VanKuren NW, Vibranovski MD.
PMID: 25031657
J Genomics. 2014 Mar 10;2:64-7. doi: 10.7150/jgen.7955. eCollection 2014.

Phenotypic differences between males and females of sexually dimorphic species are caused in large part by differences in gene expression between the sexes, most of which occurs in the gonads. To accurately identify genes differentially expressed between males and...

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VanKuren NW, Vibranovski MD. A novel dataset for identifying sex-biased genes in Drosophila. J Genomics. 2014;2:64-7doi: 10.7150/jgen.7955.
VanKuren, N. W., & Vibranovski, M. D. (2014). A novel dataset for identifying sex-biased genes in Drosophila. Journal of genomics, 264-7. https://doi.org/10.7150/jgen.7955
VanKuren, Nicholas W, and Vibranovski, Maria D. "A novel dataset for identifying sex-biased genes in Drosophila." Journal of genomics vol. 2 (2014): 64-7. doi: https://doi.org/10.7150/jgen.7955
VanKuren NW, Vibranovski MD. A novel dataset for identifying sex-biased genes in Drosophila. J Genomics. 2014 Mar 10;2:64-7. doi: 10.7150/jgen.7955. eCollection 2014. PMID: 25031657; PMCID: PMC4091448.
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A Rab-based view of membrane traffic in the ciliate Tetrahymena thermophila.

Small GTPases

Turkewitz AP, Bright LJ.
PMID: 22145095
Small GTPases. 2011 Jul;2(4):222-226. doi: 10.4161/sgtp.2.4.16706. Epub 2011 Jul 01.

Biologists have long recognized that some single-celled organisms show striking morphological and behavioral complexity, and details of the genetic underpinnings can be mined from the trove of newly-sequenced genomes. Ciliates, among which Tetrahymena thermophila and Paramecium tetraurelia have received...

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Turkewitz AP, Bright LJ. A Rab-based view of membrane traffic in the ciliate Tetrahymena thermophila. Small GTPases. 2011;2(4):222-226doi: 10.4161/sgtp.2.4.16706.
Turkewitz, A. P., & Bright, L. J. (2011). A Rab-based view of membrane traffic in the ciliate Tetrahymena thermophila. Small GTPases, 2(4), 222-226. https://doi.org/10.4161/sgtp.2.4.16706
Turkewitz, Aaron P, and Bright, Lydia J. "A Rab-based view of membrane traffic in the ciliate Tetrahymena thermophila." Small GTPases vol. 2,4 (2011): 222-226. doi: https://doi.org/10.4161/sgtp.2.4.16706
Turkewitz AP, Bright LJ. A Rab-based view of membrane traffic in the ciliate Tetrahymena thermophila. Small GTPases. 2011 Jul;2(4):222-226. doi: 10.4161/sgtp.2.4.16706. Epub 2011 Jul 01. PMID: 22145095; PMCID: PMC3225912.
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Detecting the Genetic Signature of Natural Selection in Human Populations: Models, Methods, and Data.

Annual review of anthropology

Hancock AM, Rienzo AD.
PMID: 20622977
Annu Rev Anthropol. 2008;37:197-217. doi: 10.1146/annurev.anthro.37.081407.085141.

Patterns of DNA sequence variation in the genome contain a record of past selective events. The ability to collect increasingly large data sets of polymorphisms has allowed investigators to perform hypothesis-driven studies of candidate genes as well as genome-wide...

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Hancock AM, Rienzo AD. Detecting the Genetic Signature of Natural Selection in Human Populations: Models, Methods, and Data. Annu Rev Anthropol. 2008;37:197-217doi: 10.1146/annurev.anthro.37.081407.085141.
Hancock, A. M., & Rienzo, A. D. (2008). Detecting the Genetic Signature of Natural Selection in Human Populations: Models, Methods, and Data. Annual review of anthropology, 37197-217. https://doi.org/10.1146/annurev.anthro.37.081407.085141
Hancock, Angela M, and Rienzo, Anna Di. "Detecting the Genetic Signature of Natural Selection in Human Populations: Models, Methods, and Data." Annual review of anthropology vol. 37 (2008): 197-217. doi: https://doi.org/10.1146/annurev.anthro.37.081407.085141
Hancock AM, Rienzo AD. Detecting the Genetic Signature of Natural Selection in Human Populations: Models, Methods, and Data. Annu Rev Anthropol. 2008;37:197-217. doi: 10.1146/annurev.anthro.37.081407.085141. PMID: 20622977; PMCID: PMC2901121.
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Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish.

Developmental biology

Boyle-Anderson EAT, Mao Q, Ho RK.
PMID: 34756968
Dev Biol. 2022 Jan;481:201-214. doi: 10.1016/j.ydbio.2021.10.008. Epub 2021 Oct 28.

The T-box containing family member, TBX5, has been shown to play important functional roles in the pectoral appendages of a variety of vertebrate species. While a single TBX5 gene exists in all tetrapods studied to date, the zebrafish genome...

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Boyle-Anderson EAT, Mao Q, Ho RK. Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish. Dev Biol. 2021;481:201-214doi: 10.1016/j.ydbio.2021.10.008.
Boyle-Anderson, E. A. T., Mao, Q., & Ho, R. K. (2022). Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish. Developmental biology, 481201-214. https://doi.org/10.1016/j.ydbio.2021.10.008
Boyle-Anderson, Erin A T, et al. "Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish." Developmental biology vol. 481 (2022): 201-214. doi: https://doi.org/10.1016/j.ydbio.2021.10.008
Boyle-Anderson EAT, Mao Q, Ho RK. Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish. Dev Biol. 2022 Jan;481:201-214. doi: 10.1016/j.ydbio.2021.10.008. Epub 2021 Oct 28. PMID: 34756968; PMCID: PMC8665139.
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De novo mutation rate estimation in wolves of known pedigree.

Molecular biology and evolution

Koch E, Schweizer RM, Schweizer TM, Stahler DR, Smith DW, Wayne RK, Novembre J.
PMID: 31297530
Mol Biol Evol. 2019 Jul 12; doi: 10.1093/molbev/msz159. Epub 2019 Jul 12.

Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation...

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Koch E, Schweizer RM, Schweizer TM, et al. De novo mutation rate estimation in wolves of known pedigree. Mol Biol Evol. 2019;doi: 10.1093/molbev/msz159.
Koch, E., Schweizer, R. M., Schweizer, T. M., Stahler, D. R., Smith, D. W., Wayne, R. K., & Novembre, J. (2019). De novo mutation rate estimation in wolves of known pedigree. Molecular biology and evolution, . https://doi.org/10.1093/molbev/msz159
Koch, Evan, et al. "De novo mutation rate estimation in wolves of known pedigree." Molecular biology and evolution vol. (2019). doi: https://doi.org/10.1093/molbev/msz159
Koch E, Schweizer RM, Schweizer TM, Stahler DR, Smith DW, Wayne RK, Novembre J. De novo mutation rate estimation in wolves of known pedigree. Mol Biol Evol. 2019 Jul 12; doi: 10.1093/molbev/msz159. Epub 2019 Jul 12. PMID: 31297530; PMCID: PMC6805234.
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Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation.

Genome biology

Shah A, Mittleman BE, Gilad Y, Li YI.
PMID: 34649612
Genome Biol. 2021 Oct 14;22(1):291. doi: 10.1186/s13059-021-02502-z.

BACKGROUND: Alternative cleavage and polyadenylation (APA), an RNA processing event, occurs in over 70% of human protein-coding genes. APA results in mRNA transcripts with distinct 3' ends. Most APA occurs within 3' UTRs, which harbor regulatory elements that can...

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Shah A, Mittleman BE, Gilad Y, et al. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biol. 2021;22(1):291doi: 10.1186/s13059-021-02502-z.
Shah, A., Mittleman, B. E., Gilad, Y., & Li, Y. I. (2021). Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome biology, 22(1), 291. https://doi.org/10.1186/s13059-021-02502-z
Shah, Ankeeta, et al. "Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation." Genome biology vol. 22,1 (2021): 291. doi: https://doi.org/10.1186/s13059-021-02502-z
Shah A, Mittleman BE, Gilad Y, Li YI. Benchmarking sequencing methods and tools that facilitate the study of alternative polyadenylation. Genome Biol. 2021 Oct 14;22(1):291. doi: 10.1186/s13059-021-02502-z. PMID: 34649612; PMCID: PMC8518154.
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Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus.

Genome medicine

Soliai MM, Kato A, Helling BA, Stanhope CT, Norton JE, Naughton KA, Klinger AI, Thompson EE, Clay SM, Kim S, Celedón JC, Gern JE, Jackson DJ, Altman MC, Kern RC, Tan BK, Schleimer RP, Nicolae DL, Pinto JM, Ober C.
PMID: 34629083
Genome Med. 2021 Oct 10;13(1):157. doi: 10.1186/s13073-021-00967-y.

BACKGROUND: Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover, GWASs do not provide context-specific information on cell types or...

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Soliai MM, Kato A, Helling BA, et al. Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus. Genome Med. 2021;13(1):157doi: 10.1186/s13073-021-00967-y.
Soliai, M. M., Kato, A., Helling, B. A., Stanhope, C. T., Norton, J. E., Naughton, K. A., Klinger, A. I., Thompson, E. E., Clay, S. M., Kim, S., Celedón, J. C., Gern, J. E., Jackson, D. J., Altman, M. C., Kern, R. C., Tan, B. K., Schleimer, R. P., Nicolae, D. L., Pinto, J. M., & Ober, C. (2021). Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus. Genome medicine, 13(1), 157. https://doi.org/10.1186/s13073-021-00967-y
Soliai, Marcus M, et al. "Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus." Genome medicine vol. 13,1 (2021): 157. doi: https://doi.org/10.1186/s13073-021-00967-y
Soliai MM, Kato A, Helling BA, Stanhope CT, Norton JE, Naughton KA, Klinger AI, Thompson EE, Clay SM, Kim S, Celedón JC, Gern JE, Jackson DJ, Altman MC, Kern RC, Tan BK, Schleimer RP, Nicolae DL, Pinto JM, Ober C. Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus. Genome Med. 2021 Oct 10;13(1):157. doi: 10.1186/s13073-021-00967-y. PMID: 34629083; PMCID: PMC8504130.
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Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster.

Nature ecology & evolution

Siddiq MA, Loehlin DW, Montooth KL, Thornton JW.
PMID: 28812605
Nat Ecol Evol. 2017 Jan 13;1(2):25. doi: 10.1038/s41559-016-0025.

Identifying the genetic basis for adaptive differences between species requires explicit tests of historical hypotheses concerning the effects of past changes in gene sequence on molecular function, organismal phenotype and fitness. We address this challenge by combining ancestral protein...

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Siddiq MA, Loehlin DW, Montooth KL, et al. Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nat Ecol Evol. 2017;1(2):25doi: 10.1038/s41559-016-0025.
Siddiq, M. A., Loehlin, D. W., Montooth, K. L., & Thornton, J. W. (2017). Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nature ecology & evolution, 1(2), 25. https://doi.org/10.1038/s41559-016-0025
Siddiq, Mohammad A, et al. "Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster." Nature ecology & evolution vol. 1,2 (2017): 25. doi: https://doi.org/10.1038/s41559-016-0025
Siddiq MA, Loehlin DW, Montooth KL, Thornton JW. Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster. Nat Ecol Evol. 2017 Jan 13;1(2):25. doi: 10.1038/s41559-016-0025. PMID: 28812605; PMCID: PMC5703048.
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Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation.

The Journal of clinical investigation

Simonett SP, Shin S, Herring JA, Bacher R, Smith LA, Dong C, Rabaglia ME, Stapleton DS, Schueler KL, Choi J, Bernstein MN, Turkewitz DR, Perez-Cervantes C, Spaeth J, Stein R, Tessem JS, Kendziorski C, Keleş S, Moskowitz IP, Keller MP, Attie AD.
PMID: 34491912
J Clin Invest. 2021 Nov 01;131(21). doi: 10.1172/JCI144833.

The transcription factor NFATC2 induces β cell proliferation in mouse and human islets. However, the genomic targets that mediate these effects have not been identified. We expressed active forms of Nfatc2 and Nfatc1 in human islets. By integrating changes...

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Simonett SP, Shin S, Herring JA, et al. Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation. J Clin Invest. 2021;131(21)doi: 10.1172/JCI144833.
Simonett, S. P., Shin, S., Herring, J. A., Bacher, R., Smith, L. A., Dong, C., Rabaglia, M. E., Stapleton, D. S., Schueler, K. L., Choi, J., Bernstein, M. N., Turkewitz, D. R., Perez-Cervantes, C., Spaeth, J., Stein, R., Tessem, J. S., Kendziorski, C., Keleş, S., Moskowitz, I. P., Keller, M. P., & Attie, A. D. (2021). Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation. The Journal of clinical investigation, 131(21), . https://doi.org/10.1172/JCI144833
Simonett, Shane P, et al. "Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation." The Journal of clinical investigation vol. 131,21 (2021). doi: https://doi.org/10.1172/JCI144833
Simonett SP, Shin S, Herring JA, Bacher R, Smith LA, Dong C, Rabaglia ME, Stapleton DS, Schueler KL, Choi J, Bernstein MN, Turkewitz DR, Perez-Cervantes C, Spaeth J, Stein R, Tessem JS, Kendziorski C, Keleş S, Moskowitz IP, Keller MP, Attie AD. Identification of direct transcriptional targets of NFATC2 that promote β cell proliferation. J Clin Invest. 2021 Nov 01;131(21). doi: 10.1172/JCI144833. PMID: 34491912; PMCID: PMC8553569.
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Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.

Scientific data

Fellows Yates JA, Andrades Valtueña A, Vågene ÅJ, Cribdon B, Velsko IM, Borry M, Bravo-Lopez MJ, Fernandez-Guerra A, Green EJ, Ramachandran SL, Heintzman PD, Spyrou MA, Hübner A, Gancz AS, Hider J, Allshouse AF, Zaro V, Warinner C.
PMID: 33500403
Sci Data. 2021 Jan 26;8(1):31. doi: 10.1038/s41597-021-00816-y.

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is...

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Fellows Yates JA, Andrades Valtueña A, Vågene ÅJ, et al. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci Data. 2021;8(1):31doi: 10.1038/s41597-021-00816-y.
Fellows Yates, J. A., Andrades Valtueña, A., Vågene, �. �. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-Lopez, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., Zaro, V., & Warinner, C. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific data, 8(1), 31. https://doi.org/10.1038/s41597-021-00816-y
Fellows Yates, James A, et al. "Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir." Scientific data vol. 8,1 (2021): 31. doi: https://doi.org/10.1038/s41597-021-00816-y
Fellows Yates JA, Andrades Valtueña A, Vågene ÅJ, Cribdon B, Velsko IM, Borry M, Bravo-Lopez MJ, Fernandez-Guerra A, Green EJ, Ramachandran SL, Heintzman PD, Spyrou MA, Hübner A, Gancz AS, Hider J, Allshouse AF, Zaro V, Warinner C. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci Data. 2021 Jan 26;8(1):31. doi: 10.1038/s41597-021-00816-y. PMID: 33500403; PMCID: PMC7838265.
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Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish.

Developmental biology

Boyle-Anderson EAT, Mao Q, Ho RK.
PMID: 34756968
Dev Biol. 2022 Jan;481:201-214. doi: 10.1016/j.ydbio.2021.10.008. Epub 2021 Oct 28.

The T-box containing family member, TBX5, has been shown to play important functional roles in the pectoral appendages of a variety of vertebrate species. While a single TBX5 gene exists in all tetrapods studied to date, the zebrafish genome...

Cite
Boyle-Anderson EAT, Mao Q, Ho RK. Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish. Dev Biol. 2021;481:201-214doi: 10.1016/j.ydbio.2021.10.008.
Boyle-Anderson, E. A. T., Mao, Q., & Ho, R. K. (2022). Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish. Developmental biology, 481201-214. https://doi.org/10.1016/j.ydbio.2021.10.008
Boyle-Anderson, Erin A T, et al. "Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish." Developmental biology vol. 481 (2022): 201-214. doi: https://doi.org/10.1016/j.ydbio.2021.10.008
Boyle-Anderson EAT, Mao Q, Ho RK. Tbx5a and Tbx5b paralogues act in combination to control separate vectors of migration in the fin field of zebrafish. Dev Biol. 2022 Jan;481:201-214. doi: 10.1016/j.ydbio.2021.10.008. Epub 2021 Oct 28. PMID: 34756968; PMCID: PMC8665139.
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Showing 1 to 12 of 12 entries