Jiaqian Wu, PhD

Biography

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1. Omrani, M., Beyrampour-Basmenj, H., Jahanban-Esfahlan, R., Talebi, M., Raeisi, M., Serej, Z. A., Akbar-Gharalari, N., Khodakarimi, S., Wu, J., & Ebrahimi-Kalan, A. Global trend in exosome isolation and application: an update concept in management of diseases. 2023. Molecular and cellular biochemistry, 10.1007/s11010-023-04756-6. DOI: 10.1007/s11010-023-04756-6. PMID: 37166542.
2. Wei, H*., Wu, X*., Withrow, J*., Cuevas-Diaz Duran, R., Singh, S., Chaboub, L. S., Rakshit, J., Mejia, J., Rolfe, A., Herrera, J. J., Horner, P. J., & Wu, J. Q. Glial progenitor heterogeneity and key regulators revealed by single-cell RNA sequencing provide insight to regeneration in spinal cord injury. 2023. Cell reports, 42(5), 112486. DOI: 10.1016/j.celrep.2023.112486. PMID: 37149868
3. Kobayashi, M., Wei, H., Yamanashi, T., Azevedo Portilho, N., Cornelius, S., Valiente, N., Nishida, C., Cheng, H., Latorre, A., Zheng, W. J., Kang, J., Seita, J., Shih, D. J., Wu, J. Q., and Yoshimoto, M. HSC-independent definitive hematopoiesis persists into adult life. 2023. Cell reports, 42(3), 112239. DOI: 10.1016/j.celrep.2023.112239. PMID: 36906851
4. Cuevas-Diaz Duran R., González-Orozco JC., Velasco I and Wu, J. Q., Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases. 2022. Front. Cell Dev. doi: 10.3389/fcell.2022.884748. PMID: 36353512
5. Cuevas-Diaz Duran R., Li Y., Garza Carbajal A., You Y., Dessauer CW*., Wu, J. Q*., Walters ET*. Major differences in transcriptional alterations in dorsal root ganglia between spinal cord injury and peripheral neuropathic pain models. J Neurotrauma. 2022 Sep 30. doi: 10.1089/neu.2022.0238. PMID: 36178348.
6. Wu, X., Wei, H., Wu, J. Q. Coding and long non-coding gene expression changes in the CNS traumatic injuries. Cell Mol Life Sci. 2022 Feb 7;79(2):123. doi: 10.1007/s00018-021-04092-2. PMID: 35129669.
7. Emily, F. Mendez., Wei, H., Hu, R., Stertz, L., Fries, GR., Wu, X., Najera, KE., Monterey, MD., Lincoln, CM., Kim, JW., Moriel, K., Meyer, TD., Selvaraj, S., Teixeira, AL., MD, Zhao, Z., Xu, J., Wu, J. Q., Walss-Bass, C. Angiogenic Gene Networks are Dysregulated in Opioid Use Disorder: Evidence from Multi-Omics and Imaging of Postmortem Human Brain. Mol Psychiatry. 2021 Aug 12. doi:10.1038/s41380-021-01259-y. PMID: 34385598.
8. Monterey, MD., Wei, H., Wu, X., Wu, J. Q. The Many Faces of Astrocytes in Alzheimer’s Disease. Front Neurol. 2021 Aug 31;12:619626. doi: 10.3389/fneur.2021.619626. PMID: 34531807.
9. Yuan, Z., Fan, X., Zhu, JJ., Fu, TM., Wu, J. Q., Xu H., Zhang, N., An, Z., Zheng, W. Presence of complete murine viral genome sequences in patient-derived xenografts. Nat Commun. 2021 Apr 1;12(1):2031. doi: 10.1038/s41467-021-22200-5. PMID: 33795676.
10. Kondiles, B*., Wei, H*., Chaboub, LS., Horner, PJ., Wu, J. Q*., Perlmutter, SI*. Transcriptome of rat subcortical white matter and spinal cord after spinal injury and cortical stimulation. Sci Data. 2021 Jul 15;8(1):175. https://doi.org/10.1038/s41597-021-00953-4. PMID: 34267212.
11. Wei, H*., Dong, X*., You, Y., Hai, B., Cuevas-Diaz Duran, RC., Wu, X., Kharas, N., Wu, J. Q. OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation. BMC Biol. 2021 Jun 25;19(1):132. https://doi.org/10.1186/s12915-021-01057-6. PMID: 34172044.
12. Wei, H*., Wu, X*., You, Y*., Cuevas-Diaz Duran, R., Zheng, Y., Narayanan, L.K., Hai, B., Li X., Tallapragada, N., Prajapati, T.J, Kim, D.H., Deneen, B., Cao, Q., Wu, J. Q. Systematic analysis of purified astrocytes after SCI unveils Zeb2os function during astrogliosis. Cell Reports. 2021 Feb 2;34(5):108721. doi: 10.1016/j.celrep.2021.108721. PMID: 33535036.
13. Escartin, C*., Galea, E*., Lakatos, A., O’Callaghan, JP., Petzold, GC., …, Wu, J. Q., …., Zheng, B., Zimmer, ER., Zorec, R., Sofroniew, MV., Verkhratsky, A. Reactive astrocyte nomenclature, definitions, and future directions. Nature Neuroscience. 2021. doi: 10.1038/s41593-020-00783-4. PMID: 33589835.
14. Narayanan, L.K.*, Wu, X.*, Wei, H. and Wu, J. Q. Evolving Roles of Long Noncoding RNAs. The Chemical Biology of Long Noncoding RNAs. 2020 (Chapter 10). Springer Publishing. Netherlands.
15. Bhoi, J.D., Zhang, Z., Janz, R., You, Y., Wei, H., Wu, J. Q, Ribelayga, C.P. The SNARE Regulator Complexin3 is a Target of the Cone Circadian Clock. J Comp Neurol. 2020 Aug 12. doi:10.1002/cne.25004. PMID:32783205
16. Jin, N., Zhang, Z., Keung, J., Youn, S.B., Ishibashi, M., Tian, L-M., Marshak, D. W., Solessio, E., Umino, Y., Fahrenfort, I., Kiyama, T., Mao, C-A., You, Y., Wei, H., Wu, J. Q., Postma, F., Paul, D. L., Massey, S. C., Ribelayga, C. P. Molecular and functional architecture of the mouse photoreceptor network. Science Advances. 2020 Jul; (6) : 28, eaba7232. doi: 10.1126/sciadv.aba7232. PMID: 32832605
17. Kobayashi M, Tarnawsky SP, Wei H, Mishra A, Azevedo Portilho N, Wenzel P, Davis B, Wu J, Hadland B, Yoshimoto M.Hemogenic Endothelial Cells Can Transition to Hematopoietic Stem Cells through a B-1 Lymphocyte-Biased State during Maturation in the Mouse Embryo. Stem Cell Reports. 2019 Jul 9;13(1):21-30. doi: 10.1016/j.stemcr.2019.05.025. Epub 2019 Jun 20. PubMed PMID: 31231025; PubMed Central PMCID: PMC6626887.
18. He L, Zhou J, Chen M, Lin CS, Kim SG, Zhou Y, Xiang L, Xie M, Bai H, Yao H, Shi C, Coelho PG, Bromage TG, Hu B, Tovar N, Witek L, Wu J, Chen K, Gu W, Zheng J, Sheu TJ, Zhong J, Wen J, Niu Y, Cheng B, Gong Q, Owens DM, Stanislauskas M, Pei J, Chotkowski G, Wang S, Yang G, Zegarelli DJ, Shi X, Finkel M, Zhang W, Li J, Cheng J, Tarnow DP, Zhou X, Wang Z, Jiang X, Romanov A, Rowe DW, Wang S, Ye L, Ling J, Mao J. Parenchymal and stromal tissue regeneration of tooth organ by pivotal signals reinstated in decellularized matrix. Nat Mater. 2019 Jun;18(6):627-637. doi: 10.1038/s41563-019-0368-6. Epub 2019 May 21. PubMed PMID: 31114073.
19. Cuevas-Diaz Duran R, Wang CY, Zheng H, Deneen B, Wu JQ. Brain Region-Specific Gene Signatures Revealed by Distinct Astrocyte Subpopulations Unveil Links to Glioma and Neurodegenerative Diseases. 2019 Mar-Apr;6(2). doi: 10.1523/ENEURO.0288-18.2019. eCollection 2019 Mar-Apr. PubMed PMID: 30957015; PubMed Central PMCID: PMC6449165.
20. Cuevas-Diaz Duran R, Wei H, Kim DH, Wu JQ. Review: Long non-coding RNAs: important regulators in the development, function and disorders of the central nervous system. Neuropathol Appl Neurobiol. 2019 Jan 13;. doi: 10.1111/nan.12541. [Epub ahead of print] Review. PubMed PMID: 30636336; PubMed Central PMCID: PMC6626588.
21. You Y, Cuevas-Diaz Duran R, Jiang L, Dong X, Zong S, Snyder M, Wu JQ. An integrated global regulatory network of hematopoietic precursor cell self-renewal and differentiation. Integr Biol (Camb). 2018 Jul 16;10(7):390-405. doi: 10.1039/c8ib00059j. PubMed PMID: 29892750; PubMed Central PMCID: PMC6047913.
22. Dong X, Cuevas-Diaz Duran R, You Y, Wu JQ. Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis. J Vis Exp. 2018 Apr 16;(134). doi: 10.3791/57547. PubMed PMID: 29708547; PubMed Central PMCID: PMC5933511.
23. Cuevas-Diaz Duran R, Wei H, Wu JQ. Single-cell RNA-sequencing of the brain. Clin Transl Med. 2017 Dec;6(1):20. doi: 10.1186/s40169-017-0150-9. Epub 2017 Jun 8. Review. PubMed PMID: 28597408; PubMed Central PMCID: PMC5465230.
24. Jiang N, Xiang L, He L, Yang G, Zheng J, Wang C, Zhang Y, Wang S, Zhou Y, Sheu TJ, Wu J, Chen K, Coelho PG, Tovar NM, Kim SH, Chen M, Zhou YH, Mao JJ. Exosomes Mediate Epithelium-Mesenchyme Crosstalk in Organ Development. ACS Nano. 2017 Aug 22;11(8):7736-7746. doi: 10.1021/acsnano.7b01087. Epub 2017 Jul 27. PubMed PMID: 28727410; PubMed Central PMCID: PMC5634743.
25. Liu Y, Zheng Y, Li S, Xue H, Schmitt K, Hergenroeder GW, Wu J, Zhang Y, Kim DH, Cao Q. Human neural progenitors derived from integration-free iPSCs for SCI therapy. Stem Cell Res. 2017 Mar;19:55-64. doi: 10.1016/j.scr.2017.01.004. Epub 2017 Jan 5. PubMed PMID: 28073086; PubMed Central PMCID: PMC5629634.
26. Duran RC, Yan H, Zheng Y, Huang X, Grill R, Kim DH, Cao Q, Wu JQ. The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury. Sci Rep. 2017 Jan 20;7:41008. doi: 10.1038/srep41008. PubMed PMID: 28106101; PubMed Central PMCID: PMC5247719.
27. Dong X, You Y, Wu JQ. Building an RNA Sequencing Transcriptome of the Central Nervous System. 2016 Dec;22(6):579-592. doi: 10.1177/1073858415610541. Epub 2015 Oct 13. Review. PubMed PMID: 26463470; PubMed Central PMCID: PMC4833695.
28. Dong X, Muppani N, Wu J. Long Non-coding RNAs: Critical Regulators for Cell Lineage Commitment in the Central Nervous System . In: Transcriptomics and Gene Regulation. Wu J, editor. Dordrecht: Springer; 2016. Chapter 4; p.73-98.
29. Cuevas-Diaz Duran R, Menon S, Wu J. The Analyses of Global Gene Expression and Transcription Factor Regulation . In:Transcriptomics and Gene Regulation. Wu J, editor. Dordrecht: Springer; 2016. Chapter 1; p.1-35.
30. Transcriptomics and Gene Regulation. Wu J, editor. Dordrecht: Springer; 2016.
31. Dong X, Chen K, Cuevas-Diaz Duran R, You Y, Sloan SA, Zhang Y, Zong S, Cao Q, Barres BA, Wu JQ. Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. PLoS Genet. 2015 Dec;11(12):e1005669. doi: 10.1371/journal.pgen.1005669. eCollection 2015 Dec. PubMed PMID: 26683846; PubMed Central PMCID: PMC4980008.
32. Yan Q, Weyn-Vanhentenryck SM, Wu J, Sloan SA, Zhang Y, Chen K, Wu JQ, Barres BA, Zhang C. Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3445-50. doi: 10.1073/pnas.1502849112. Epub 2015 Mar 3. PubMed PMID: 25737549; PubMed Central PMCID: PMC4371929.
33. Chen K, Dai X, Wu J. Alternative splicing: An important mechanism in stem cell biology. World J Stem Cells. 2015 Jan 26;7(1):1-10. doi: 10.4252/wjsc.v7.i1.1. Review. PubMed PMID: 25621101; PubMed Central PMCID: PMC4300919.
34. Chen K, Dong X, Wu J. The Application of Single-Cell Sequencing in Dynamic Transcriptomes . In: Single Cell Sequencing and Systems Immunology: Translational Bioinformatics 5. Wang X, editor. Dordrecht: Springer; 2015. p.41-63.
35. Zong S, Deng S, Chen K, Wu JQ. Identification of key factors regulating self-renewal and differentiation in EML hematopoietic precursor cells by RNA-sequencing analysis. J Vis Exp. 2014 Nov 11;(93):e52104. doi: 10.3791/52104. PubMed PMID: 25407807; PubMed Central PMCID: PMC4353975.
36. Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O’Keeffe S, Phatnani HP, Guarnieri P, Caneda C, Ruderisch N, Deng S, Liddelow SA, Zhang C, Daneman R, Maniatis T, Barres BA, Wu JQ. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci. 2014 Sep 3;34(36):11929-47. doi: 10.1523/JNEUROSCI.1860-14.2014. PubMed PMID: 25186741; PubMed Central PMCID: PMC4152602.
37. Chen K, Wu J. A database of spinal cord Injury RNA-Seq displayed using an interactive web browser. In: Acute and subacute spinal cord injury RNA-Seq database [Internet]. Houston, TX: Jiaqian Wu Lab; 2014 September. Available from: http://jiaqianwulab.org/resource.htm . .
38. Chen K, Wu J. A RNA-Seq database of purified brain cell types. In: A RNA-Seq database of purified brain cell types displayed using an interactive web browser [Internet]. Houston, TX: Jiaqian Wu Lab; 2014 September. Available from: http://jiaqianwulab.org/resource.htm . .
39. Chen K, Deng S, Lu H, Zheng Y, Yang G, Kim D, Cao Q, Wu JQ. RNA-seq characterization of spinal cord injury transcriptome in acute/subacute phases: a resource for understanding the pathology at the systems level. PLoS One.2013;8(8):e72567. doi: 10.1371/journal.pone.0072567. eCollection 2013. PubMed PMID: 23951329; PubMed Central PMCID: PMC3739761.
40. Wu JQ, Seay M, Schulz VP, Hariharan M, Tuck D, Lian J, Du J, Shi M, Ye Z, Gerstein M, Snyder MP, Weissman S. Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line. PLoS Genet. 2012;8(3):e1002565. doi: 10.1371/journal.pgen.1002565. Epub 2012 Mar 8. PubMed PMID: 22412390; PubMed Central PMCID: PMC3297581.
41. Wu J. Characterize mammalian transcriptome complexity. Deutschland: LAP LAMBERT Academic Publishing; 2011.
42. Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5254-9. doi: 10.1073/pnas.0914114107. Epub 2010 Mar 1. PubMed PMID: 20194744; PubMed Central PMCID: PMC2841935.
43. Temple G, Gerhard DS, Rasooly R, Feingold EA, Good PJ, Robinson C, Mandich A, Derge JG, Lewis J, Shoaf D, Collins FS, Jang W, Wagner L, Shenmen CM, Misquitta L, Schaefer CF, Buetow KH, Bonner TI, Yankie L, Ward M, Phan L, Astashyn A, Brown G, Farrell C, Hart J, Landrum M, Maidak BL, Murphy M, Murphy T, Rajput B, Riddick L, Webb D, Weber J, Wu W, Pruitt KD, Maglott D, Siepel A, Brejova B, Diekhans M, Harte R, Baertsch R, Kent J, Haussler D, Brent M, Langton L, Comstock CL, Stevens M, Wei C, van Baren MJ, Salehi-Ashtiani K, Murray RR, Ghamsari L, Mello E, Lin C, Pennacchio C, Schreiber K, Shapiro N, Marsh A, Pardes E, Moore T, Lebeau A, Muratet M, Simmons B, Kloske D, Sieja S, Hudson J, Sethupathy P, Brownstein M, Bhat N, Lazar J, Jacob H, Gruber CE, Smith MR, McPherson J, Garcia AM, Gunaratne PH, Wu J, Muzny D, Gibbs RA, Young AC, Bouffard GG, Blakesley RW, Mullikin J, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Hirst M, Zeng T, Tse K, Moksa M, Deng M, Ma K, Mah D, Pang J, Taylor G, Chuah E, Deng A, Fichter K, Go A, Lee S, Wang J, Griffith M, Morin R, Moore RA, Mayo M, Munro S, Wagner S, Jones SJ, Holt RA, Marra MA, Lu S, Yang S, Hartigan J, Graf M, Wagner R, Letovksy S, Pulido JC, Robison K, Esposito D, Hartley J, Wall VE, Hopkins RF, Ohara O, Wiemann S. The completion of the Mammalian Gene Collection (MGC). Genome Res. 2009 Dec;19(12):2324-33. doi: 10.1101/gr.095976.109. Epub 2009 Sep 18. PubMed PMID: 19767417; PubMed Central PMCID: PMC2792178.
44. Wu JQ, Snyder M. RNA polymerase II stalling: loading at the start prepares genes for a sprint. Genome Biol.2008;9(5):220. doi: 10.1186/gb-2008-9-5-220. Epub 2008 May 2. Review. PubMed PMID: 18466645; PubMed Central PMCID: PMC2441479.
45. Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.Genome Biol. 2008 Jan 3;9(1):R3. doi: 10.1186/gb-2008-9-1-r3. PubMed PMID: 18173853; PubMed Central PMCID: PMC2395237.
46. Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. 2007 Jun 14;447(7146):799-816. doi: 10.1038/nature05874. PubMed PMID: 17571346; PubMed Central PMCID: PMC2212820.
47. Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome.Genome Res. 2007 Jun;17(6):720-31. doi: 10.1101/gr.5716607. PubMed PMID: 17567992; PubMed Central PMCID: PMC1891333.
48. Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res. 2007 Jun;17(6):732-45. doi: 10.1101/gr.5696007. PubMed PMID: 17567993; PubMed Central PMCID: PMC1891334.
49. Tenney AE, Wu JQ, Langton L, Klueh P, Quatrano R, Brent MR. A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices. Genome Res. 2007 Feb;17(2):212-8. doi: 10.1101/gr.5661407. Epub 2007 Jan 8. PubMed PMID: 17210930; PubMed Central PMCID: PMC1781353.
50. Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M. Novel transcribed regions in the human genome. Cold Spring Harb Symp Quant Biol.2006;71:111-6. doi: 10.1101/sqb.2006.71.054. PubMed PMID: 17381286.
51. Finishing the euchromatic sequence of the human genome. 2004 Oct 21;431(7011):931-45. doi: 10.1038/nature03001. PubMed PMID: 15496913.
52. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. doi: 10.1101/gr.2596504. PubMed PMID: 15489334; PubMed Central PMCID: PMC528928.
53. Dewey C, Wu JQ, Cawley S, Alexandersson M, Gibbs R, Pachter L. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res. 2004 Apr;14(4):661-4. doi: 10.1101/gr.1939804. PubMed PMID: 15060007; PubMed Central PMCID: PMC383310.
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