Cheng-Ting "Eddy" Yeh
(葉政廷)

Bioinformatics Analyst/Systems Analyst III

EDUCATION:

  • B.S., Computer Science, Iowa State University, 2002
  • M.S., Computer Science, Oklahoma State University, 2005

EXPERIENCE:

  • Lab Assistant, Schnable Lab, Jun 2002-Dec 2002
  • Bioinformatics Analyst/Systems Support Specialist II, Schnable Lab, Sep 2005-Aug 2011
  • Bioinformatics Analyst/Systems Analyst III, Schnable Lab, Sep 2011-Present

E-mail:

ORCID ID: 0000-0002-1392-2018

PUBLICATIONS (31):

* Authors contributed equally to the article
  • McFarland BA*, N Alkhalifah*, M Bohn, J Bubert, ES Buckler, I Ciampitti, J Edwards, D Ertl, JL Gage, CM Falcon, S Flint-Garcia, MA Gore, C Graham, CN Hirsch, JB Holland, E Hood, DC Hooker, D Jarquín, SM Kaeppler, J Knoll, G Kruger, N Lauter, EC Lee, DC Lima, AJ Lorenz, JP Lynch, J McKay, ND Miller, SP Moose, SC Murray, R Nelson, C Poudyal, T Rocheford, O Rodriguez, MC Romay, JC Schnable, PS Schnable, B Scully, R Sekhon, K Silverstein, M Singh, M Smith, EP Spalding, NM Springer, K Thelen, P Thomison, MR Tuinstra, J Wallace, R Walls, D Wills, RJ Wisser, W Xu, CT Yeh, N de Leon « view remaining 4 author(s) » (2020) Maize genomes to fields (G2F): 2014-2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets. BMC Res Notes, 13(1): 71.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1186/s13104-020-4922-8 | PMID: 32051026 | Impact Factor: 1.1 ]
  • Zheng J*, C He*, Y Qin, G Lin, WD Park, M Sun, J Li, X Lu, C Zhang, CT Yeh, CJ Gunasekara, E Zeng, H Wei, PS Schnable, G Wang, S Liu (2019) Co-expression analysis aids in the identification of genes in the cuticular wax pathway in maize. Plant J, 97: 530-542.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1111/tpj.14140 | PMID: 30375131 | Impact Factor: 5.7 ]
  • Yang J, CT Yeh, RK Ramamurthy, X Qi, RL Fernando, JC Dekkers, DJ Garrick, D Nettleton, PS Schnable (2018) Empirical comparisons of different statistical models to identify and validate kernel row number-associated variants from structured multi-parent mapping populations of maize. G3 (Bethesda), 8(11): 3567-3575.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1534/g3.118.200636 | PMID: 30213868 | Impact Factor: 2.6 ]
  • Liu S*, JC Schnable*, A Ott*, CT Yeh, NM Springer, J Yu, GJ Muehlbauer, MC Timmermans, MJ Scanlon, PS Schnable (2018) Intragenic meiotic crossovers generate novel alleles with transgressive expression levels. Mol Biol Evol, 35(11): 2762-2772.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1093/molbev/msy174 | PMID: 30184112 | Impact Factor: 14.8 ]
  • Ott A, JC Schnable, CT Yeh, L Wu, C Liu, HC Hu, CL Dalgard, S Sarkar, PS Schnable (2018) Linked read technology for assembling large complex and polyploid genomes. BMC Genomics, 19(1): 651.
    [ Abstract | Full Text PDF | doi:10.1186/s12864-018-5040-z | PMID: 30180802 | Impact Factor: 3.5 ]
  • Alkhalifah N*, DA Campbell*, CM Falcon*, J Gardiner*, ND Miller*, MC Romay*, R Walls*, R Walton*, CT Yeh*, M Bohn, J Bubert, ES Buckler, I Ciampitti, S Flint-Garcia, MA Gore, C Graham, CN Hirsch, JB Holland, DC Hooker, SM Kaeppler, J Knoll, N Lauter, EC Lee, AJ Lorenz, JP Lynch, SP Moose, SC Murray, R Nelson, T Rocheford, O Rodriguez, JC Schnable, B Scully, M Smith, NM Springer, P Thomison, MR Tuinstra, RJ Wisser, W Xu, D Ertl, PS Schnable, N de Leon, EP Spalding, J Edwards, CJ Lawrence-Dill (2018) Maize genomes to fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. BMC Res Notes, 11(1): 452.
    [ Abstract | Full Text PDF | doi:10.1186/s13104-018-3508-1 | PMID: 29986751 | Impact Factor: 1.1 ]
  • Liang Z, SK Gupta, CT Yeh, Y Zhang, DW Ngu, R Kumar, HT Patil, KD Mungra, D Yadav, A Rathore, RK Srivastava, R Gupta, J Yang, RK Varshney, PS Schnable, JC Schnable (2018) Phenotypic data from inbred parents can improve genomic prediction in pearl millet hybrids. G3 (Bethesda), 8(7): 2513-2522.(Selected as the outstanding scientific article of 2018 by ICRISAT's research program in Asia)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1534/g3.118.200242 | PMID: 29794163 | Impact Factor: 2.6 ]
  • Ott A*, S Liu*, JC Schnable, CT Yeh, KS Wang, PS Schnable (2017) tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci. Nucleic Acids Res, 45(21): e178.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1093/nar/gkx853 | PMID: 29036322 | Impact Factor: 11.1 ]
  • Mei W, S Liu, JC Schnable, CT Yeh, NM Springer, PS Schnable, WB Barbazuk (2017) A comprehensive analysis of alternative splicing in paleopolyploid maize. Front Plant Sci, 8: 694.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.3389/fpls.2017.00694 | PMID: 28539927 | Impact Factor: 4.1 ]
  • Yang J*, H Jiang*, CT Yeh, J Yu, JA Jeddeloh, D Nettleton, PS Schnable (2015) Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel. Plant J, 84(3): 587-596.(Selected as an Editors' Choice by MaizeGDB, 11/2015)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1111/tpj.13029 | PMID: 26386250 | Impact Factor: 5.7 | Cited 53 times ]
  • Li L*, S Hill-Skinner*, S Liu, D Beuchle, HM Tang, CT Yeh, D Nettleton, PS Schnable (2015) The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase. Plant J, 81(3): 493-504.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1111/tpj.12745 | PMID: 25495051 | Impact Factor: 5.7 ]
  • Paschold A, NB Larson, C Marcon, JC Schnable, CT Yeh, C Lanz, D Nettleton, HP Piepho, PS Schnable, F Hochholdinger (2014) Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids. The Plant Cell, 26(10): 3939-3948.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1105/tpc.114.130948 | PMID: 25315323 | Impact Factor: 8.6 ]
  • Zhang Y, A Paschold, C Marcon, S Liu, H Tai, J Nestler, CT Yeh, N Opitz, C Lanz, PS Schnable, F Hochholdinger (2014) The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots. J Exp Bot, 65(17): 4919-4930.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1093/jxb/eru249 | PMID: 24928984 | Impact Factor: 5.4 ]
  • Li L, SR Eichten, R Shimizu, KA Petsch, CT Yeh, W Wu, AM Chettoor, SA Givan, RA Cole, JE Fowler, MM Evans, MJ Scanlon, J Yu, PS Schnable, MC Timmermans, NM Springer, GJ Muehlbauer (2014) Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol, 15(2): R40.(Selected as an Editors' Choice by MaizeGDB, 07/2014)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1186/gb-2014-15-2-r40 | PMID: 24576388 | Impact Factor: 14.0 | Cited 274 times ]
  • Tang HM*, S Liu*, S Hill-Skinner, W Wu, D Reed, CT Yeh, D Nettleton, PS Schnable (2014) The maize brown midrib2 (bm2) gene encodes a methylenetetrahydrofolate reductase that contributes to lignin accumulation. Plant J, 77(3): 380-392.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1111/tpj.12394 | PMID: 24286468 | Impact Factor: 5.7 ]
  • Eichten SR, NA Ellis, I Makarevitch, CT Yeh, JI Gent, L Guo, KM McGinnis, X Zhang, PS Schnable, MW Vaughn, RK Dawe, NM Springer (2012) Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genet, 8(12): e1003127.("Recommended" by the Faculty of 1000 Biology)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1371/journal.pgen.1003127 | PMID: 23271981 | Impact Factor: 5.2 | Cited 127 times ] Faculty1000 Recommeded Article
  • Paschold A*, Y Jia*, C Marcon, S Lund, NB Larson, CT Yeh, S Ossowski, C Lanz, D Nettleton, PS Schnable, F Hochholdinger (2012) Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents. Genome Res, 22(12): 2445-2454.
    [ Abstract | Full Text PDF | Supplemental Materials | Press Release | doi:10.1101/gr.138461.112 | PMID: 23086286 | Impact Factor: 9.9 | Cited 101 times ]
  • Liu S, K Ying, CT Yeh, J Yang, RA Swanson-Wagner, W Wu, T Richmond, DJ Gerhardt, J Lai, NM Springer, D Nettleton, JA Jeddeloh, PS Schnable (2012) Changes in genome content generated via segregation of non-allelic homologs. Plant J, 72(3): 390-399.("Recommended" by the Faculty of 1000 Biology)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1111/j.1365-313X.2012.05087.x | PMID: 22731681 | Impact Factor: 5.7 ] Faculty1000 Recommeded Article
  • Li X, C Zhu, CT Yeh, W Wu, EM Takacs, KA Petsch, F Tian, G Bai, ES Buckler, GJ Muehlbauer, MC Timmermans, MJ Scanlon, PS Schnable, J Yu (2012) Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res, 22(12): 2436-2444.(Selected as an Editors' Choice by MaizeGDB, 08/2012)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1101/gr.140277.112 | PMID: 22701078 | Impact Factor: 9.9 ]
  • Lin Z, X Li, LM Shannon, CT Yeh, M Wang, G Bai, Z Peng, J Li, HN Trick, TE Clemente, J Doebley, PS Schnable, MR Tuinstra, TT Tesso, F White, J Yu (2012) Parallel domestication of the Shattering1 genes in cereals. Nat Genet, 44(6): 720-724.(Epub: 13 May 2012; Selected as an Editors' Choice by MaizeGDB, 07/2012; "Recommended" by the Faculty of 1000 Biology)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1038/ng.2281 | PMID: 22581231 | Impact Factor: 25.5 | Cited 256 times ] Faculty1000 Recommeded Article
  • Liu S, CT Yeh, HM Tang, D Nettleton, PS Schnable (2012) Gene mapping via Bulked Segregant RNA-Seq (BSR-Seq). PLOS ONE, 7(5): e36406.(Selected as an Editors' Choice by MaizeGDB, 06/2012; Among the top 10% most cited PLOS ONE articles)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1371/journal.pone.0036406 | PMID: 22586469 | Impact Factor: 2.8 | Cited 205 times ]
  • Waters AJ*, I Makarevitch*, SR Eichten*, RA Swanson-Wagner, CT Yeh, WW Xu, PS Schnable, MW Vaughn, M Gehring, NM Springer (2011) Parent-of-origin effects on gene expression and DNA methylation in the Maize endosperm. The Plant Cell, 23(12): 4221-4233.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1105/tpc.111.092668 | PMID: 22198147 | Impact Factor: 8.6 | Cited 173 times ]
  • Eichten SR*, RA Swanson-Wagner*, JC Schnable, AJ Waters, PJ Hermanson, S Liu, CT Yeh, Y Jia, K Gendler, M Freeling, PS Schnable, MW Vaughn, NM Springer (2011) Heritable epigenetic variation among maize inbreds. PLoS Genet, 7(11): e1002372.(Selected as an Editors' Choice by MaizeGDB, 01/2012; "Recommended" by the Faculty of 1000 Biology)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1371/journal.pgen.1002372 | PMID: 22125494 | Impact Factor: 5.2 | Cited 141 times ] Faculty1000 Recommeded Article
  • Eichten SR, JM Foerster, N de Leon, K Ying, CT Yeh, S Liu, JA Jeddeloh, PS Schnable, SM Kaeppler, NM Springer (2011) B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize. Plant Physiol, 156(4): 1679-1690.(Selected as an Editors' Choice by MaizeGDB, 09/2011)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1104/pp.111.174748 | PMID: 21705654 | Impact Factor: 6.3 | Cited 77 times ]
  • Koesterke L, D Stanzione, MW Vaughn, SM Welch, W Kusnierczyk, J Yang, CT Yeh, D Nettleton, PS Schnable (2011) An efficient and scalable implementation of SNP-pair interaction testing for genetic association studies. IEEE International Workshop on High Performance Computational Biology: 523-530.(2011 IEEE International Symposium)
    [ Abstract | Full Text PDF | doi:10.1109/IPDPS.2011.190 ]
  • Fu Y*, NM Springer*, K Ying*, CT Yeh, AL Iniguez, T Richmond, W Wu, WB Barbazuk, D Nettleton, JA Jeddeloh, PS Schnable (2010) High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes. PLOS ONE, 5(12): e14178.
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1371/journal.pone.0014178 | PMID: 21152036 | Impact Factor: 2.8 ]
  • Fu Y, NM Springer, DJ Gerhardt, K Ying, CT Yeh, W Wu, RA Swanson-Wagner, M D'Ascenzo, T Millard, L Freeberg, N Aoyama, J Kitzman, D Burgess, T Richmond, TJ Albert, WB Barbazuk, JA Jeddeloh, PS Schnable (2010) Repeat subtraction-mediated sequence capture from a complex genome. Plant J, 62(5): 898-909.(Epub: 4 Mar 2010; Cover image; Selected by journal editors as a "Featured Article"; Selected as an Editors' Choice by MaizeGDB, 09/2010)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1111/j.1365-313X.2010.04196.x | PMID: 20230488 | Impact Factor: 5.7 | Cited 92 times ]
  • Schnable PS*, D Ware*, RS Fulton, JC Stein, F Wei, S Pasternak, C Liang, J Zhang, LA Fulton, TA Graves, P Minx, AD Reily, L Courtney, SS Kruchowski, C Tomlinson, C Strong, K Delehaunty, C Fronick, W Courtney, SM Rock, E Belter, F Du, K Kim, RM Abbott, M Cotton, A Levy, P Marchetto, K Ochoa, SM Jackson, B Gillam, W Chen, L Yan, J Higginbotham, M Cardenas, J Waligorski, E Applebaum, L Phelps, J Falcone, K Kanchi, T Thane, A Scimone, N Thane, J Henke, T Wang, J Ruppert, N Shah, K Rotter, J Hodges, E Ingenthron, M Cordes, S Kohlberg, J Sgro, B Delgado, K Mead, A Chinwalla, S Leonard, K Crouse, K Collura, D Kudrna, J Currie, R He, A Angelova, S Rajasekar, T Mueller, R Lomeli, G Scara, A Ko, K Delaney, M Wissotski, G Lopez, D Campos, M Braidotti, E Ashley, W Golser, H Kim, S Lee, J Lin, Z Dujmic, W Kim, J Talag, A Zuccolo, C Fan, A Sebastian, M Kramer, L Spiegel, L Nascimento, T Zutavern, B Miller, C Ambroise, S Muller, W Spooner, A Narechania, L Ren, S Wei, S Kumari, BP Faga, MJ Levy, L McMahan, P Van Buren, MW Vaughn, K Ying, CT Yeh, SJ Emrich, Y Jia, A Kalyanaraman, AP Hsia, WB Barbazuk, RS Baucom, TP Brutnell, NC Carpita, C Chaparro, JM Chia, JM Deragon, JC Estill, Y Fu, JA Jeddeloh, Y Han, H Lee, P Li, DR Lisch, S Liu, Z Liu, DH Nagel, MC McCann, P San Miguel, AM Myers, D Nettleton, J Nguyen, BW Penning, L Ponnala, KL Schneider, DC Schwartz, A Sharma, C Soderlund, NM Springer, Q Sun, H Wang, M Waterman, R Westerman, TK Wolfgruber, L Yang, Y Yu, L Zhang, S Zhou, Q Zhu, JL Bennetzen, RK Dawe, J Jiang, N Jiang, GG Presting, SR Wessler, S Aluru, RA Martienssen, SW Clifton, WR McCombie, RA Wing, RK Wilson « view remaining 107 author(s) » (2009) The B73 maize genome: complexity, diversity, and dynamics. Science, 326(5956): 1112-1115.(Cover image; a commentary on this manuscript solicited by journal editors and written by C. Feuillet and K. Eversole was provided in 326: 1071-1072; cited in Wikipedia: http://en.wikipedia.org/wiki/Maize; Selected as an Editors' Choice by MaizeGDB, 12/2009; selected as a "must read" by the Faculty of 1000 Biology)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1126/science.1178534 | PMID: 19965430 | Impact Factor: 41.0 | Cited 3,398 times ] Faculty1000 Recommeded Article
  • Wei F, JC Stein, C Liang, J Zhang, RS Fulton, RS Baucom, E De Paoli, S Zhou, L Yang, Y Han, S Pasternak, A Narechania, L Zhang, CT Yeh, K Ying, DH Nagel, K Collura, D Kudrna, J Currie, J Lin, H Kim, A Angelova, G Scara, M Wissotski, W Golser, L Courtney, SS Kruchowski, TA Graves, SM Rock, S Adams, LA Fulton, C Fronick, W Courtney, M Kramer, L Spiegel, L Nascimento, A Kalyanaraman, C Chaparro, JM Deragon, P San Miguel, N Jiang, SR Wessler, PJ Green, Y Yu, DC Schwartz, BC Meyers, JL Bennetzen, RA Martienssen, WR McCombie, S Aluru, SW Clifton, PS Schnable, D Ware, RK Wilson, RA Wing « view remaining 5 author(s) » (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genet, 5(11): e1000728.(Selected as an Editors' Choice by MaizeGDB, 12/2009)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1371/journal.pgen.1000728 | PMID: 19936048 | Impact Factor: 5.2 ]
  • Springer NM*, K Ying*, Y Fu, T Ji, CT Yeh, Y Jia, W Wu, T Richmond, J Kitzman, H Rosenbaum, AL Iniguez, WB Barbazuk, JA Jeddeloh, D Nettleton, PS Schnable (2009) Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet, 5(11): e1000734.(Selected as an Editors' Choice by MaizeGDB, 12/2009)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1371/journal.pgen.1000734 | PMID: 19956538 | Impact Factor: 5.2 | Cited 466 times ]
  • Liu S, CT Yeh, T Ji, K Ying, H Wu, HM Tang, Y Fu, D Nettleton, PS Schnable (2009) Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet, 5(11): e1000733.(Selected as an Editors' Choice by MaizeGDB, 12/2009)
    [ Abstract | Full Text PDF | Supplemental Materials | doi:10.1371/journal.pgen.1000733 | PMID: 19936291 | Impact Factor: 5.2 | Cited 187 times ]