Publications

  1. Jones DL, Meridew JA, Link PA, Ducharme MT, Lydon KL, Choi KM, Caporarello N, Tan Q, Diaz Espinosa AM, Xiong Y, Lee JH, Ye Z, Yan H, Ordog T, Ligresti G, Varelas X, Tschumperlin DJ. ZNF416 is a pivotal transcriptional regulator of fibroblast mechanoactivation. J Cell Biol. 2021 May 3; 220 (5)
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  2. Tian S, Zhang H, Zhang P, Kalmbach M, Lee JH, Ordog T, Hampel PJ, Call TG, Witzig TE, Kay NE, Klee EW, Slager SL, Yan H, Ding W. Epigenetic alteration contributes to the transcriptional reprogramming in T-cell prolymphocytic leukemia. Sci Rep. 2021 Apr 15; 11 (1):8318
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  3. Hayashi Y, Asuzu DT, Bardsley MR, Gajdos GB, Kvasha SM, Linden DR, Nagy RA, Saravanaperumal SA, Syed SA, Toyomasu Y, Yan H, Chini EN, Gibbons SJ, Kellogg TA, Khazaie K, Kuro-O M, Machado Espindola Netto J, Singh MP, Tidball JG, Wehling-Henricks M, Farrugia G, Ordog T. Wnt-induced, TRP53-mediated Cell Cycle Arrest of Precursors Underlies Interstitial Cell of Cajal Depletion During Aging. Cell Mol Gastroenterol Hepatol. 2021; 11 (1):117-145 Epub 2020 Aug 07
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  4. Eckel-Passow JE, Yan H, Kosel ML, Serie D, Decker PA, Jenkins RB, Costello B, Leibovich B, Ho TH, Parker A. 8q24 clear cell renal cell carcinoma germline variant is associated with VHL mutation status and clinical aggressiveness. BMC Urol. 2020 Oct 29; 20 (1):173
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  5. Lenkiewicz E, Malasi S, Hogenson TL, Flores LF, Barham W, Phillips WJ, Roesler AS, Chambers KR, Rajbhandari N, Hayashi A, Antal CE, Downes M, Grandgenett PM, Hollingsworth MA, Cridebring D, Xiong Y, Lee JH, Ye Z, Yan H, Hernandez MC, Leiting JL, Evans RM, Ordog T, Truty MJ, Borad MJ, Reya T, Von Hoff DD, Fernandez-Zapico ME, Barrett MT. Genomic and Epigenomic Landscaping Defines New Therapeutic Targets for Adenosquamous Carcinoma of the Pancreas. Cancer Res. 2020 Oct 15; 80 (20):4324-4334 Epub 2020 Sept 14
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  6. Yan H, Tian S, Kleinstern G, Wang Z, Lee JH, Boddicker NJ, Cerhan JR, Kay NE, Braggio E, Slager SL. Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci. Hum Mol Genet. 2020 Sep 29; 29 (16):2761-2774
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  7. Kleinstern G, O'Brien DR, Li X, Tian S, Kabat BF, Rabe KG, Norman AD, Yan H, Vachon CM, Boddicker NJ, Call TG, Parikh SA, Bruins L, Bonolo de Campos C, Leis JF, Shanafelt TD, Ding W, Cerhan JR, Kay NE, Slager SL, Braggio E. Tumor mutational load predicts time to first treatment in chronic lymphocytic leukemia (CLL) and monoclonal B-cell lymphocytosis beyond the CLL international prognostic index. Am J Hematol. 2020 Aug; 95 (8):906-917 Epub 2020 May 07
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  8. Vaubel RA, Tian S, Remonde D, Schroeder MA, Mladek AC, Kitange GJ, Caron A, Kollmeyer TM, Grove R, Peng S, Carlson BL, Ma DJ, Sarkar G, Evers L, Decker PA, Yan H, Dhruv HD, Berens ME, Wang Q, Marin BM, Klee EW, Califano A, LaChance DH, Eckel-Passow JE, Verhaak RG, Sulman EP, Burns TC, Meyer FB, O'Neill BP, Tran NL, Giannini C, Jenkins RB, Parney IF, Sarkaria JN. Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma. Clin Cancer Res. 2020 Mar 1; 26 (5):1094-1104 Epub 2019 Dec 18
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  9. Puthanmadhom Narayanan S, Lee JH, Bhagwate A, Kuwelker S, Yan H, Ordog T, Bharucha AE. Epigenetic Alterations Are Associated With Gastric Emptying Disturbances in Diabetes Mellitus. Clin Transl Gastroenterol. 2020 Mar; 11 (3):e00136
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  10. Kleinstern G, Yan H, Hildebrandt MAT, Vijai J, Berndt SI, Ghesquieres H, McKay J, Wang SS, Nieters A, Ye Y, Monnereau A, Brooks-Wilson AR, Lan Q, Melbye M, Jackson RD, Teras LR, Purdue MP, Vajdic CM, Vermeulen RCH, Giles GG, Cocco PL, Birmann BM, Kraft P, Albanes D, Zeleniuch-Jacquotte A, Crouch S, Zhang Y, Sarangi V, Asmann Y, Offit K, Salles G, Wu X, Smedby KE, Skibola CF, Slager SL, Rothman N, Chanock SJ, Cerhan JR. Inherited variants at 3q13.33 and 3p24.1 are associated with risk of diffuse large B-cell lymphoma and implicate immune pathways. Hum Mol Genet. 2020 Jan 1; 29 (1):70-79
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  11. Jones DL, Haak AJ, Caporarello N, Choi KM, Ye Z, Yan H, Varelas X, Ordog T, Ligresti G, Tschumperlin DJ. TGFbeta-induced fibroblast activation requires persistent and targeted HDAC-mediated gene repression. J Cell Sci. 2019 Oct 18; 132 (20)
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  12. Luchtel RA, Zimmermann MT, Hu G, Dasari S, Jiang M, Oishi N, Jacobs HK, Zeng Y, Hundal T, Rech KL, Ketterling RP, Lee JH, Eckloff BW, Yan H, Gaonkar KS, Tian S, Ye Z, Kadin ME, Sidhu J, Jiang L, Voss J, Link BK, Syrbu SI, Facchetti F, Bennani NN, Slager SL, Ordog T, Kocher JP, Cerhan JR, Ansell SM, Feldman AL. Recurrent MSC (E116K) mutations in ALK-negative anaplastic large cell lymphoma. Blood. 2019 Jun 27; 133 (26):2776-2789 Epub 2019 May 17
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  13. Zhong J, Ye Z, Clark CR, Lenz SW, Nguyen JH, Yan H, Robertson KD, Farrugia G, Zhang Z, Ordog T, Lee JH. Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq. BMC Genomics. 2019 Mar 29; 20 (1):249
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  14. Tian S, Peng S, Kalmbach M, Gaonkar KS, Bhagwate A, Ding W, Eckel-Passow J, Yan H, Slager SL. Identification of factors associated with duplicate rate in ChIP-seq data. PLoS One. 2019; 14 (4):e0214723 Epub 2019 Apr 03
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  15. McMaster ML, Berndt SI, Zhang J, Slager SL, Li SA, Vajdic CM, Smedby KE, Yan H, Birmann BM, Brown EE, Smith A, Kleinstern G, Fansler MM, Mayr C, Zhu B, Chung CC, Park JH, Burdette L, Hicks BD, Hutchinson A, Teras LR, Adami HO, Bracci PM, McKay J, Monnereau A, Link BK, Vermeulen RCH, Ansell SM, Maria A, Diver WR, Melbye M, Ojesina AI, Kraft P, Boffetta P, Clavel J, Giovannucci E, Besson CM, Canzian F, Travis RC, Vineis P, Weiderpass E, Montalvan R, Wang Z, Yeager M, Becker N, Benavente Y, Brennan P, Foretova L, Maynadie M, Nieters A, de Sanjose S, Staines A, Conde L, Riby J, Glimelius B, Hjalgrim H, Pradhan N, Feldman AL, Novak AJ, Lawrence C, Bassig BA, Lan Q, Zheng T, North KE, Tinker LF, Cozen W, Severson RK, Hofmann JN, Zhang Y, Jackson RD, Morton LM, Purdue MP, Chatterjee N, Offit K, Cerhan JR, Chanock SJ, Rothman N, Vijai J, Goldin LR, Skibola CF, Caporaso NE. Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenstrom macroglobulinemia. Nat Commun. 2018 Oct 10; 9 (1):4182
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  16. Tian S, Yan H, Klee EW, Kalmbach M, Slager SL. Comparative analysis of de novo assemblers for variation discovery in personal genomes. Brief Bioinform. 2018 Sep 28; 19 (5):893-904
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  17. Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, Armenoult L, Ayadi M, Ordog T, Lee JH, Oliver G, Klee E, Moutardier V, Gayet O, Bian B, Duconseil P, Gilabert M, Bigonnet M, Garcia S, Turrini O, Delpero JR, Giovannini M, Grandval P, Gasmi M, Secq V, De Reynies A, Dusetti N, Iovanna J, Urrutia R. Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nat Commun. 2018 May 17; 9 (1):1978
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  18. Karakashev S, Zhu H, Wu S, Yokoyama Y, Bitler BG, Park PH, Lee JH, Kossenkov AV, Gaonkar KS, Yan H, Drapkin R, Conejo-Garcia JR, Speicher DW, Ordog T, Zhang R. CARM1-expressing ovarian cancer depends on the histone methyltransferase EZH2 activity. Nat Commun. 2018 Feb 12; 9 (1):631
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  19. Ding W, LaPlant BR, Call TG, Parikh SA, Leis JF, He R, Shanafelt TD, Sinha S, Le-Rademacher J, Feldman AL, Habermann TM, Witzig TE, Wiseman GA, Lin Y, Asmus E, Nowakowski GS, Conte MJ, Bowen DA, Aitken CN, Van Dyke DL, Greipp PT, Liu X, Wu X, Zhang H, Secreto CR, Tian S, Braggio E, Wellik LE, Micallef I, Viswanatha DS, Yan H, Chanan-Khan AA, Kay NE, Dong H, Ansell SM. Pembrolizumab in patients with CLL and Richter transformation or with relapsed CLL. Blood. 2017 Jun 29; 129 (26):3419-3427 Epub 2017 Apr 19
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  20. Heim JB, Squirewell EJ, Neu A, Zocher G, Sominidi-Damodaran S, Wyles SP, Nikolova E, Behrendt N, Saunte DM, Lock-Andersen J, Gaonkar KS, Yan H, Sarkaria JN, Krendel M, van Deursen J, Sprangers R, Stehle T, Bottcher RT, Lee JH, Ordog T, Meves A. Myosin-1E interacts with FAK proline-rich region 1 to induce fibronectin-type matrix. Proc Natl Acad Sci U S A. 2017 Apr 11; 114 (15):3933-3938 Epub 2017 Mar 27
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  21. Dudakovic A, Camilleri ET, Riester SM, Paradise CR, Gluscevic M, O'Toole TM, Thaler R, Evans JM, Yan H, Subramaniam M, Hawse JR, Stein GS, Montecino MA, McGee-Lawrence ME, Westendorf JJ, van Wijnen AJ. Enhancer of Zeste Homolog 2 Inhibition Stimulates Bone Formation and Mitigates Bone Loss Caused by Ovariectomy in Skeletally Mature Mice. J Biol Chem. 2016 Nov 18; 291 (47):24594-24606 Epub 2016 Oct 10
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  22. Tian S, Yan H, Kalmbach M, Slager SL. Impact of post-alignment processing in variant discovery from whole exome data. BMC Bioinformatics. 2016 Oct 3; 17 (1):403 Epub 2016 Oct 03
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  23. Tian S, Yan H, Neuhauser C, Slager SL. An analytical workflow for accurate variant discovery in highly divergent regions. BMC Genomics. 2016 Sep 2; 17:703 Epub 2016 Sept 02
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  24. Yan H, Tian S, Slager SL, Sun Z. ChIP-seq in studying epigenetic mechanisms of disease and promoting precision medicine: progresses and future directions. Epigenomics. 2016 Sep; 8 (9):1239-58 Epub 2016 June 20
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  25. Ho TH, Park IY, Zhao H, Tong P, Champion MD, Yan H, Monzon FA, Hoang A, Tamboli P, Parker AS, Joseph RW, Qiao W, Dykema K, Tannir NM, Castle EP, Nunez-Nateras R, Teh BT, Wang J, Walker CL, Hung MC, Jonasch E. High-resolution profiling of histone h3 lysine 36 trimethylation in metastatic renal cell carcinoma. Oncogene. 2016 Mar 24; 35 (12):1565-74 Epub 2015 June 15
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  26. Kitange GJ, Mladek AC, Schroeder MA, Pokorny JC, Carlson BL, Zhang Y, Nair AA, Lee JH, Yan H, Decker PA, Zhang Z, Sarkaria JN. Retinoblastoma Binding Protein 4 Modulates Temozolomide Sensitivity in Glioblastoma by Regulating DNA Repair Proteins. Cell Rep. 2016 Mar 22; 14 (11):2587-98 Epub 2016 Mar 10
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  27. Yan H, Tian S, Slager SL, Sun Z, Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016 Jan 15; 183: (2)96-109.
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  28. Champion MD, Hlady RA, Yan H, Evans J, Nie J, Lee JH, Bogenberger J, Nandakumar K, Davila J, Moore R, Nair A, O'Brien D, Zhu YX, Kortum KM, Ordog T, Zhang Z, Joseph RW, Stewart AK, Kocher JP, Jonasch E, Robertson KD, Tibes R, Ho TH. Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing. BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015. 2015:163-70.
  29. Ho TH, Nateras RN, Yan H, Park JG, Jensen S, Borges C, Lee JH, Champion MD, Tibes R, Bryce AH, Carballido EM, Todd MA, Joseph RW, Wong WW, Parker AS, Stanton ML, Castle EP. A Multidisciplinary Biospecimen Bank of Renal Cell Carcinomas Compatible with Discovery Platforms at Mayo Clinic, Scottsdale, Arizona. PLoS One. 2015; 10 (7):e0132831 Epub 2015 July 16
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  30. Wang L, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Nov 10; 42 (20):e156 Epub 2014 Sept 23
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  31. Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. BMC Bioinformatics. 2014 Aug 15; 15:280
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  32. Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics. 2014 Jun 3; 15:423 Epub 2014 June 03
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  33. Myers KS, Yan H, Ong IM, Chung D, Liang K, Tran F, Keles S, Landick R, Kiley PJ. Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet. 2013 Jun; 9(6):e1003565. Epub 2013 Jun 20.
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  34. Wu Y, Kikuchi S, Yan H, Zhang W, Rosenbaum H, Iniguez AL, Jiang J. Euchromatic subdomains in rice centromeres are associated with genes and transcription. Plant Cell. 2011 Nov; 23(11):4054-64. Epub 2011 Nov 11.
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  35. Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, Chen F, Jiang J. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J. 2010 May 06. [Epub ahead of print]
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  36. Hirsch CD, Wu Y, Yan H, Jiang J. Lineage-specific adaptive evolution of the centromeric protein CENH3 in diploid and allotetraploid Oryza species. Mol Biol Evol. 2009 Dec; 26(12):2877-85. Epub 2009 Sep 09.
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  37. Yan H, Talbert PB, Lee HR, Jett J, Henikoff S, Chen F, Jiang J. Intergenic locations of rice centromeric chromatin. PLoS Biol. 2008 Nov 25; 6(11):e286.
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  38. Neumann P, Yan H, Jiang J. The centromeric retrotransposons of rice are transcribed and differentially processed by RNA interference. Genetics. 2007 Jun; 176(2):749-61. Epub 2007 Apr 03.
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  39. Yan H, Jiang J. Rice as a model for centromere and heterochromatin research. Chromosome Res. 2007; 15(1):77-84.
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  40. Yan H, Ito H, Nobuta K, Ouyang S, Jin W, Tian S, Lu C, Venu RC, Wang GL, Green PJ, Wing RA, Buell CR, Meyers BC, Jiang J. Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell. 2006 Sep; 18(9):2123-33. Epub 2006 Jul 28.
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  41. Yan H, Jin W, Nagaki K, Tian S, Ouyang S, Buell CR, Talbert PB, Henikoff S, Jiang J. Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell. 2005 Dec; 17(12):3227-38. Epub 2005 Nov 04.
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  42. Lee HR, Zhang W, Langdon T, Jin W, Yan H, Cheng Z, Jiang J. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci U S A. 2005 Aug 16; 102(33):11793-8. Epub 2005 Jul 22.
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  43. Mudge J, Huihuang Y, Denny RL, Howe DK, Danesh D, Marek LF, Retzel E, Shoemaker RC, Young ND. Soybean bacterial artificial chromosome contigs anchored with RFLPs: insights into genome duplication and gene clustering. Genome. 2004 Apr; 47(2):361-72.
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  44. Yan HH, Mudge J, Kim DJ, Shoemaker RC, Cook DR, Young ND. Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome. 2004 Feb; 47(1):141-55.
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  45. Yan HH, Mudge J, Kim DJ, Larsen D, Shoemaker RC, Cook DR, Young ND. Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana. Theor Appl Genet. 2003 May; 106(7):1256-65. Epub 2003 Jan 25.
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  46. Foster-Hartnett D, Mudge J, Larsen D, Danesh D, Yan H, Denny R, Penuela S, Young ND. Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G. Genome. 2002 Aug; 45(4):634-45.
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  47. Yan HH, Liu GQ, Cheng ZK, Li XB, Liu GZ, Min SK, Zhu LH. A genome-specific repetitive DNA sequence from Oryza eichingeri: characterization, localization, and introgression to O. sativa. Theor Appl Genet. 2002 Feb; 104(2-3):177-83.
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  48. Marek LF, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow JA, Retzel E, Young ND, Shoemaker RC. Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome. 2001 Aug; 44(4):572-81.
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  49. Yan HH, Liu GQ, Cheng ZK, Min SK, Zhu LH. Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by using RFLP analysis and genomic in situ hybridization. Genome. 2001; 44:86-95.
  50. Cheng Z, Yan H, Yu H, Tang S, Jiang J, Gu M, Zhu L. Development and applications of a complete set of rice telotrisomics. Genetics. 2001 Jan; 157(1):361-8.
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  51. Chen C, Yan H, Zhai W, Zhu L, Sun J. Identification and chromosomal location of a new tandemly repeated DNA in maize. Genome. 2000 Feb; 43(1):181-4.
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  52. Cheng ZK, Yu HX, Yan HH, Gu MH, Zhu LH. B chromosome in a rice aneuploid variation. Theor Appl Genet. 2000; 101:564-8.
  53. Liu GQ, Yan HH, Fu Q, Qian Q, Zhang ZT, Zhai WX, Zhu LH. Mapping of a new gene for brown planthopper resistance transferred from Oryza eichingeri. Chinese Science Bulletin. 2000; 46:1459-61.
  54. Cheng ZK, Yan HH, Yu HX, Qian Q, Yi CD, Gu MH, Zhu LH. Fast assignment of DNA sequences to individual chromosome arms based on dosage effects from a set of rice telotrisomics. Acta Bot Sin. 2000; 42:708-11.
  55. Zhai W, Chen H, Yan H, Yan C, Wang G, Zhu L. Analysis and location of a rice BAC clone containing telomeric DNA sequences. Sci China C Life Sci. 1999 Feb; 42(1):68-73.
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  56. Yan HH, Min SK, Zhu LH. Visualization of Oryza eichingeri chromosomes in intergenomic hybrid plants from O. sativa x O. eichingeri via fluorescent in situ hybridization. Genome. 1999; 42:48-51.
  57. Liu GQ, Yan HH, Luo YW, Min SK, Zhu LH. RFLP analysis of euploid plants from cross between Oryza sativa and Oryza eichingeri [Chinese]. Chinese J Rice Sci. 1999; 13:129-33.
  58. Yan HH, Cheng ZK, Liu GQ, Chen CX, Min SK, Zhu LH. Identification of Oryza sativa x Oryza officinalis F1 and backcross progenies using genomic in-situ hybridization [Chinese]. Chinese J of Genet. 1999; 26:53-58.
  59. Cheng ZK, Yan HH, Gu MH. The descending order of chromosomal length and the numbering system of rice chromosome. Hereditas (Beijing) [Chinese]. 1999; 21:46-9.
  60. Cheng ZK, Yan HH, Dang BY, Hu ZM, Gu MH, Zhu LH. Microdissection and amplification of the chromosome arm 5S in a rice telotetrasomic. Chinese Science Bulletin. 1998; 43:590-4.
  61. Yan HH, Hu HY, Zhang XQ, Zhang ZT, Tian SL, Xiong ZM, Min SK. Cytogenetical studies on the pollen-derived plants from interspecific hybrid in genus Oryza [Chinese]. Acta Agronomica Sinica. 1997; 23:689-92.
  62. Yan HH, Xiong ZM, Min SK, Hu HY, Zhang ZT, Tian SL, Fu Q. The production and cytogenetical studies of Oryza sativa-Oryza eichingeri amphiploid. Chinese Journal of Genetics. 1997; 24:23-9.
  63. Yan HH, Xiong ZM, Min SK, Hu HY, Zhang ZT, Tian SL, Tang S. The transfer of planthopper resistance from Oryza eichingeri to Oryza sativa. Chinese Journal of Genetics. 1997; 24:277-84.
  64. Yan HH, Hu HY, Fu Q, Yu HY, Tang S, Xiong ZM, Min SK. Morphological and cytological studies of the hybrid between Oryza sativa and Oryza officinalis [Chinese]. Chinese J Rice Sci. 1996; 10:138-42.