Steven Jones Publications

1. Lian EY, Maritan SM, Cockburn JG, Kasaian K, Crupi MJ, Hurlbut D, Jones SJ, Wiseman SM, Mulligan LM. Differential roles of RET isoforms in medullary and papillary thyroid carcinomas. Endocr Relat Cancer. 2017 Jan;24(1):53-69. PMID: 27872141
2. Cancer Genome Atlas Research Network (346 collaborators) including Jones SJ, Integrated genomic characterization of oesophageal carcinoma.  Nature. 2017 Jan 12; 541(7636):169-175. doi: 10.1038/nature20805. PMID: 28052061
3. Sheffield BS, Tessier-Cloutier B, Li-Chang H, Shen Y, Pleasance E, Kasaian K, Li Y, Jones SJ, Lim HJ, Renouf DJ, Huntsman DG, Yip S, Laskin J, Marra M, Schaeffer DF. Personalized oncogenomics in the management of gastrointestinal carcinomas-early experiences from a pilot study. Curr Oncol. 2016 Dec; 23(6):e571-e575. doi: 10.3747/co.23.3165. PMID: 28050146
4. Chan CK, Pan Y, Nyberg K, Marra MA, Lim EL, Jones SJ, Maar D, Gibb EA, Gunaratne PH, Robertson AG, Rowat AC. Tumour-suppressor microRNAs regulate ovarian cancer cell physical properties and invasive behaviour. Open Biol. 2016 Nov;6(11). pii: 160275. PMID: 27906134
5. International Human Epigenome Consortium (228 Collaborators) including Jones SJ. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell. 2016 Nov 17;167(5):1145-1149. doi: 10.1016/j.cell.2016.11.007.PMID:27863232
6. Pellacani D, Bilenky M, Kannan N, Heravi-Moussavi A, Knapp DJ, Gakkhar S, Moksa M, Carles A, Moore R, Mungall AJ, Marra MA, Jones SJ, Aparicio S, Hirst M, Eaves CJ. Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks. Cell Rep. 2016 Nov 15;17(8):2060-2074. doi: 10.1016/j.celrep.2016.10.058. PMID: 27851968
7. Feau N, Taylor G, Dale AL, Dhillon B, Bilodeau GJ, Birol I, Jones SJ, Hamelin RC. Genome sequences of six Phytophthora species threatening forest ecosystems. Genom Data. 2016 Oct 3;10:85-88. PMID: 27752469
8. Lever, Jake, and Steven JM Jones. "VERSE: Event and Relation Extraction in the BioNLP 2016 Shared Task." ACL 2016 Aug 13, (2016): 42.
9. Coombe L, Warren RL, Jackman SD, Yang C, Vandervalk BP, Moore RA, Pleasance S, Coope RJ, Bohlmann J, Holt RA, Jones SJ, Birol I. Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data. PLoS One. 2016 Sep 15;11(9):e0163059. doi: 10.1371/journal.pone.0163059. eCollection 2016. PMID: 27632164
10. Sheffield BS, Fulton R, Kalloger SE, Milne K, Geller G, Jones M, Jacquemont C, Zachara S, Zhao E, Pleasance E, Laskin J, Jones SJ, Marra MA, Yip S, Nelson BH, Gown AM, Ho C, Ionescu DN. Investigation of PD-L1 Biomarker Testing Methods for PD-1 Axis Inhibition in Non-squamous Non-small Cell Lung Cancer. J Histochem Cytochem. 2016 Sep 2. pii: 0022155416665338. [Epub ahead of print] PMID: 27591097
11. Grinshtein N, Rioseco CC, Marcellus R, Uehling D, Aman A, Lun X, Muto O, Podmore L, Lever J, Shen Y, Blough MD, Cairncross GJ, Robbins SM, Jones SJ, Marra MA, Al-Awar R, Senger DL, Kaplan DR. Small molecule epigenetic screen identifies novel EZH2 and HDAC inhibitors that target glioblastoma brain tumor-initiating cells.Oncotarget. 2016 Jul 18. doi: 10.18632/oncotarget.10661. [Epub ahead of print] PMID: 27449082
12. Younesy H, Nielsen CB, Lorincz MC, Jones SJ, Karimi MM, Möller T. ChAsE: chromatin analysis and exploration tool. Bioinformatics. 2016 Jul 4. pii: btw382. [Epub ahead of print]  PMID: 27378294
13. Jones MR, Schrader KA, Shen Y, Pleasance E, Ch'ng C, Dar N, Yip S, Renouf DJ, Schein JE, Mungall AJ, Zhao Y, Moore R, Ma Y, Sheffield BS, Ng T, Jones SJ, Marra MA, Laskin J, Lim HJ. Response to angiotensin blockade with irbesartan in a patient with metastatic colorectal cancer. Ann Oncol. 2016 May;27(5):801-6. doi: 10.1093/annonc/mdw060. Epub 2016 Feb 18. PMID: 27022066
14. Miller RR, Langille MG, Montoya V, Crisan A, Stefanovic A, Martin I, Hoang L, Patrick DM, Romney M, Tyrrell G, Jones SJ, Brinkman FS, Tang P. Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005-2009. Can J Infect Dis Med Microbiol. 2016;2016:5381871. doi: 10.1155/2016/5381871. Epub 2016 Apr 14. PMID: 27366170
15. de Leeuw CN, Korecki AJ, Berry GE, Hickmott JW, Lam SL, Lengyell TC, Bonaguro RJ, Borretta LJ, Chopra V, Chou AY, D'Souza CA, Kaspieva O, Laprise S, McInerny SC, Portales-Casamar E, Swanson-Newman MI, Wong K, Yang GS, Zhou M,Jones SJ, Holt RA, Asokan A, Goldowitz D, Wasserman WW, Simpson EM. rAAV-compatible MiniPromoters for restricted expression in the brain and eye. Mol Brain. 2016 May 10;9(1):52. doi: 10.1186/s13041-016-0232-4. PMID: 27164903
16. Kasaian K, Wiseman SM, Walker BA, Schein JE, Hirst M, Moore RA, Mungall AJ, Marra MA, Jones SJ. Putative BRAF activating fusion in a medullary thyroid cancer. Cold Spring Harb Mol Case Stud. 2016 Mar;2(2):a000729. doi: 10.1101/mcs.a000729.PMID: 27148585
17. Craig DW, Nasser S, Corbett R, Chan SK, Murray L, Legendre C, Tembe W, Adkins J, Kim N, Wong S, Baker A, Enriquez D, Pond S, Pleasance E, Mungall AJ, Moore RA, McDaniel T, Ma Y, Jones SJ, Marra MA, Carpten JD, Liang WS.  A somatic reference standard for cancer genome sequencing.  Sci Rep. 2016 Apr 20;6:24607. doi: 10.1038/srep24607. PMID: 27094764
18.  Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Inge Våge D, de Jong P, Moen T, Baranski M, Palti Y, Smith DR, Yorke JA, Nederbragt AJ, Tooming-Klunderud A, Jakobsen KS, Jiang X, Fan D, Hu Y, Liberles DA, Vidal R, Iturra P, Jones SJ, Jonassen I, Maass A, Omholt SW, Davidson WS. The Atlantic salmon genome provides insights into rediploidization.  Nature. 2016 Apr 18. doi: 10.1038/nature17164. [Epub ahead of print]  PMID: 27088604
19. Pan Y, Robertson AG, Pedersen L, Lim E, Hernandez-Herrera A, Rowat A, Chan C, Wen Y, Zhang X, Patil S, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Ma Y, Moore R, Schein J, Mungall A, Pecot C, Sood A, Jones S, Marra M, Gunaratne P.  miR-509-3p is clinically significant and  strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget. 2016 Mar 27. doi: 10.18632/oncotarget.8412. PMID:27036018
20.  Chun H-Y, Lim EL, Heravi Moussavi A, Saberi S, Mungall KL, Bilenky M, Carles A, Tse K, Shlafman I, Zhu K, Qian JQ, Harvey D, He A, Long W, Goya R, Ng M, LeBlanc VG, Pleasance E, Thiessen N, Wong T, Chuah E, Zhao YJ, Schein JE, Gerhard DS, Taylor MD, Mungall AJ, Moore RA, Ma Y, Jones SJM, Perlman EJ, Hirst M, Marra MA. Genome-wide profiles of extra-cranial malignant rhabdoid tumors reveal heterogeneity and dysregulated developmental pathways. Cancer Cell. 2016 Mar 14;29(3):394-406. PMID: 26977886
21. Cancer Genome Atlas Research Network. (228 collaborators including) Jones SJ, Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2016 Jan 14;374(2):135-45. doi: 10.1056/NEJMoa1505917. PMID: 26536169
22. Ceccarelli M, Barthel FP, Malta TM, TCGA Research Network (162 Collaborators) including, Jones SJ. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell. 2016 Jan 28;164(3):550-63. doi: 10.1016/j.cell.2015.12.028. PMID: 26824661
23. Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, MacDonald TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD. Divergent clonal selection dominates medulloblastoma at recurrence.  Nature. 2016 Jan 13. doi: 10.1038/nature16478. [Epub ahead of print] PMID: 26760213
24. Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJ, Bohlmann J, Birol I. Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation. Genome Biol Evol. 2015 Dec 8;8(1):29-41. doi: 10.1093/gbe/evv244. PMID: 26645680
25. Kasaian K, Wiseman SM, Walker BA, Schein JE, Zhao Y, Hirst M, Moore RA, Mungall AJ, Marra MA, Jones SJ. The genomic and transcriptomic landscape of anaplastic thyroid cancer: implications for therapy. BMC Cancer. 2015 Dec 18;15(1):984. doi: 10.1186/s12885-015-1955-9. PMID: 26680454
26. Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL; Open Regulatory Annotation Consortium. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 2015 Nov 17. pii: gkv1203. [Epub ahead of print]  PMID:26578589
27. Cancer Genome Atlas Research Network. (312 Collaborators including) Jones SJ. The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015 Nov 5;163(4):1011-25. doi: 10.1016/j.cell.2015.10.025. PMID: 26544944
28. Garside VC, Cullum R, Alder O, Lu DY, Vander Werff R, Bilenky M, Zhao Y, Jones SJ, Marra MA, Underhill TM, Hoodless PA. SOX9 modulates the expression of key transcription factors required for heart valve development. Development. 2015 Nov 2. pii: dev.125252. [Epub ahead of print] PMID: 26525672
29. Liu L, Li H, Dargahi D, Shynlova O, Slater D, Jones SJ, Lye SJ, Dong X. HoxA13 Regulates Phenotype Regionalization of Human Pregnant Myometrium. J Clin Endocrinol Metab. 2015 Oct 20:jc20152815. [Epub ahead of print] PMID: 26485220
30. TCGA Research Network, (126 collaborators including) Jones SJ. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 8;163(2):506-19. doi: 10.1016/j.cell.2015.09.033. PMID: 26451490
31. Janessa Laskin, Steven Jones, Samuel Aparicio, Stephen Chia, Carolyn Ch’ng, Rebecca Deyell, Peter Eirew, Alexandra Fok, Karen Gelmon, Cheryl Ho, David Huntsman,, Martin Jones, Katayoon Kasaian, Aly Karsan,, Sreeja Leelakumari, Yvonne Li, Howard Lim, Yussanne Ma, Colin Mar, Monty Martin, Richard Moore, Andrew Mungall, Karen Mungall, Erin Pleasance, S. Rod Rassekh, Daniel Renouf, Yaoqing Shen, Jacqueline Schein, Kasmintan Schrader, Sophie Sun, Anna Tinker, Eric Zhao, Stephen Yip, and Marco A. Marra. Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers. molecularcasestudies.cshlp.org. On October 9, 2015 - Published by Cold Spring Harbor Laboratory Press
32. Younesy H, Möller T, Lorincz MC, Karimi MM, Jones SJ. VisRseq: R-based visual framework for analysis of sequencing data.BMC Bioinformatics. 2015 Aug 13;16 Suppl 11:S2. doi: 10.1186/1471-2105-16-S11-S2. Epub 2015 Aug 13.  PMID: 26328469
33. Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, Ma Y, Jones S, Marra MA. Nucleic Acids Res. Large-scale profiling of microRNAs for The Cancer Genome Atlas. 2015 Aug 13. pii: gkv808. [Epub ahead of print] PMID: 26271990.
34. Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A, Jones SJ, Birol I. LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience. 2015 Aug 4;4:35. doi: 10.1186/s13742-015-0076-3. eCollection 2015. PMID: 26244089
35. Schmouth JF, Arenillas D, Corso-Díaz X, Xie YY, Bohacec S, Banks KG, Bonaguro RJ, Wong SH, Jones SJ, Marra MA, Simpson EM, Wasserman WW. Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development. BMC Genomics. 2015 Jul 24;16:545. doi: 10.1186/s12864-015-1770-3. PMID: 26204903
36. Lebovitz CB, Robertson AG, Goya R, Jones SJ, Morin RD, Marra MA, Gorski SM. Autophagy. 2015 Jul 24:0. [Epub ahead of print] Cross-cancer profiling of molecular alterations within the human autophagy interaction network. PMID: 26208877
37. Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B, Mitra S, Mohammed A, James AR, Hoberg E, Moustakas A, Gyllensten U, Jones SJ, Gustafsson CM, Sims AH, Westerlund F, Gorab E, Kanduri C. MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures. Nat Commun. 2015 Jul 24;6:7743. doi: 10.1038/ncomms8743. PMID: 26205790
38. Bose P, Pleasance ED, Jones M, Shen Y, Ch'ng C, Reisle C, Schein JE, Mungall AJ, Moore R, Ma Y, Sheffield BS, Thomson T, Rasmussen S, Ng T, Yip S, Lee CW, Ho C, Laskin J, Marra MA, Jones SJ. Integrative genomic analysis of ghost cell odontogenic carcinoma. Oral Oncol. 2015 Jul 11. pii: S1368-8375(15)00262-6. doi: 10.1016/j.oraloncology.2015.06.013. [Epub ahead of print] PMID:26173781
39. Cusulin C, Chesnelong C, Bose P, Bilenky M, Kopciuk K, Chan JA, Cairncross JG, Jones SJ, Marra MA, Luchman HA, Weiss S. Precursor States of Brain Tumor Initiating Cell Lines Are Predictive of Survival in Xenografts and Associated with Glioblastoma Subtypes. Stem Cell Reports. 2015 Jun 16. pii: S2213-6711(15)00153-8. doi: 10.1016/j.stemcr.2015.05.010. [Epub ahead of print] PMID: 26095605
40. Cancer Genome Atlas Network. (352 collaborators including) Jones, SJ. Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-96. PMID:26091043
41. Warren RL, Keeling CI, Yuen MM, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJ, MacKay J, Birol I, Bohlmann J. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. Plant J. 2015 May 28. doi: 10.1111/tpj.12886. [Epub ahead of print] PMID: 26017574
42. Kasaian K, Chindris AM, Wiseman SM, Mungall KL, Zeng T, Tse K, Schein JE, Rivera M, Necela BM, Kachergus JM, Casler JD, Mungall AJ, Moore RA, Marra MA, Copland JA, Thompson EA, Smallridge RC, Jones SJ. MEN1 Mutations in Hürthle Cell (Oncocytic) Thyroid Carcinoma. J Clin Endocrinol Metab. 2015 Apr;100(4):E611-5.  PMID: 25625803
43. Halwani Y, Kojic LD, Chan SK, Phang TP, Masoudi H, Jones SJ, Nabi IR, Wiseman SM. Prognostic significance of autocrine motility factor receptor expression by colorectal cancer and lymph node metastases. Am J Surg. 2015 May;209(5):884-9. doi: 10.1016/j.amjsurg.2015.01.010. Epub 2015 Mar 14. PMID: 25852009
44. Choi H, Kasaian K, Melck A, Ong K, Jones SJ, White A, Wiseman SM. Papillary thyroid carcinoma: prognostic significance of cancer presentation. Am J Surg. 2015 Aug;210(2):298-301. PMID: 25997714
45. Sheffield BS, Tinker AV, Shen Y, Hwang H, Li-Chang HH, Pleasance E, Ch'ng C, Lum A, Lorette J, McConnell YJ, Sun S, Jones SJ, Gown AM, Huntsman DG, Schaeffer DF, Churg A, Yip S, Laskin J, Marra MA. Personalized oncogenomics: clinical experience with malignant peritoneal mesothelioma using whole genome sequencing. PLoS One. 2015 Mar 23;10(3):e0119689. doi: 10.1371/journal.pone.0119689. eCollection 2015. PMID: 25798586
46. Cohen AS, Tuysuz B, Shen Y, Bhalla SK, Jones SJ, Gibson WT. A novel mutation in EED associated with overgrowth. J Hum Genet. 2015 Mar 19. doi: 10.1038/jhg.2015.26. [Epub ahead of print] PMID: 25787343
47. Shoshan E, Mobley AK, Braeuer RR, Kamiya T, Huang L, Vasquez ME, Salameh A, Lee HJ, Kim SJ, Ivan C, Velazquez-Torres G, Nip KM, Zhu K, Brooks D, Jones SJ, Birol I, Mosqueda M, Wen YY, Eterovic AK, Sood AK, Hwu P, Gershenwald JE, Gordon Robertson A, Calin GA, Markel G, Fidler IJ, Bar-Eli M. Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis. Nat Cell Biol. 2015 Mar;17(3):311-21. PMID: 25686251
48. Roadmap Epigenomics Consortium (258 Collaborators including) Jones SJ. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248. PMID: 25693563
49. Gascard P, Bilenky M, Sigaroudinia M, Zhao J, Li L, Carles A, Delaney A, Tam A, Kamoh B, Cho S, Griffith M, Chu A, Robertson G, Cheung D, Li I, Heravi-Moussavi A, Moksa M, Mingay M, Hussainkhel A, Davis B, Nagarajan RP, Hong C, Echipare L, O'Geen H, Hangauer MJ, Cheng JB, Neel D, Hu D, McManus MT, Moore R, Mungall A, Ma Y, Plettner P, Ziv E, Wang T, Farnham PJ, Jones SJ, Marra MA, Tlsty TD, Costello JF, Hirst M. Epigenetic and transcriptional determinants of the human  breast. Nat Commun. 2015 Feb 18;6:6351. doi: 10.1038/ncomms7351. PMID: 25690954
50. Li-Chang HH, Kasaian K, Ng Y, Lum A, Kong E, Lim H, Jones S, Huntsman DG, Schaeffer DF, Yip S. Retrospective review using targeted deep sequencing reveals mutational differences between gastroesophageal junction and gastric carcinomas. BMC Cancer. 2015 Feb 6;15(1):32. [Epub ahead of print] PMID: 25656989
51. Cancer Genome Atlas Network. (348 Collaborators including) , Ally A, Balasundaram M,Birol I, Bowlby R, Brooks D, Butterfield YS, Carlsen R, Cheng D, Chu A, Dhalla N, Guin R, Holt RA, Jones SJ, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall AJ, Robertson AG, Schein JE, Sipahimalani P, Tam A, Thiessen N, Wong T. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 Jan 29;517(7536):576-82. doi: 10.1038/nature14129. PMID: 25631445
52. Kulic I, Robertson G, Chang L, Baker JH, Lockwood WW, Mok W, Fuller M, Fournier M, Wong N, Chou V, Robinson MD, Chun HJ, Gilks B, Kempkes B, Thomson TA, Hirst M, Minchinton AI, Lam WL, Jones S, Marra M, Karsan A. Loss of the Notch effector RBPJ promotes tumorigenesis. J Exp Med. 2015 Jan 12;212(1):37-52. doi: 10.1084/jem.20121192. Epub 2014 Dec 15. PMID: 25512468
53. Dargahi D, Swayze RD, Yee L, Bergqvist PJ, Hedberg BJ, Heravi-Moussavi A, Dullaghan EM, Dercho R, An J, Babcook JS, Jones SJ. A pan-cancer analysis of alternative splicing events reveals novel tumor-associated splice variants of matriptase. Cancer Inform. 2014 Dec 4;13:167-77. doi: 10.4137/CIN.S19435.  eCollection 2014. PMID: 25506199
54. Chetaille P, Preuss C, Burkhard S, Côté JM, Houde C, Castilloux J, Piché J, Gosset N, Leclerc S, Wünnemann F, Thibeault M, Gagnon C, Galli A, Tuck E, Hickson GR, Amine NE, Boufaied I, Lemyre E, de Santa Barbara P, Faure S, Jonzon A, Cameron M, Dietz HC, Gallo-McFarlane E, Benson DW, Moreau C, Labuda D; FORGE Canada Consortium, Zhan SH, Shen Y, Jomphe M, Jones SJ, Bakkers J, Andelfinger G. Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm. Nat Genet. 2014 Nov;46(11):1245-9. doi: 10.1038/ng.3113. Epub 2014 Oct 5. PubMed PMID: 25282101. Related citations
55. Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network; Cancer Genome Atlas Network.Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. doi: 10.1073/pnas.1416074111. Epub 2014 Oct 13. PubMed PMID: 25313082; PubMed Central PMCID: PMC4217452. Related citations
56. Dubuc AM, Remke M, Korshunov A, Northcott PA, Zhan SH, Mendez-Lago M, Kool M, Jones DT, Unterberger A, Morrissy AS, Shih D, Peacock J, Ramaswamy V, Rolider A, Wang X, Witt H, Hielscher T, Hawkins C, Vibhakar R, Croul S, Rutka JT, Weiss WA, Jones SJ, Eberhart CG, Marra MA, Pfister SM, Taylor MD.Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma. Acta Neuropathol. 2013 Mar;125(3):373-84.
57. Tennant BR, Robertson AG, Kramer M, Li L, Zhang X, Beach M, Thiessen N, Chiu R, Mungall K, Whiting CJ, Sabatini PV, Kim A, Gottardo R, Marra MA, Lynn FC, Jones SJ, Hoodless PA, Hoffman BG.  Identification and analysis of murine pancreatic islet enhancers. Diabetologia. 2013 Mar;56(3):542-52. doi: 10.1007/s00125-012-2797-5.
58. Clemons AM, Brockway HM, Yin Y, Kasinathan B, Butterfield YS, Jones SJ, Colaiácovo MP, Smolikove S. Akirin is required for diakinesis bivalent structure and synaptonemal complex disassembly at meiotic prophase I. Mol Biol Cell. 2013 Apr;24(7):1053-67.
59. Pugh TJ, Morozova O, Attiyeh EF, Asgharzadeh S, Wei JS, Auclair D, Carter SL, Cibulskis K, Hanna M, Kiezun A, Kim J, Lawrence MS, Lichenstein L, McKenna A, Pedamallu CS, Ramos AH, Shefler E, Sivachenko A, Sougnez C, Stewart C, Ally A, Birol I, Chiu R, Corbett RD, Hirst M, Jackman SD, Kamoh B, Khodabakshi AH, Krzywinski M, Lo A, Moore RA, Mungall KL, Qian J, Tam A, Thiessen N, Zhao Y, Cole KA, Diamond M, Diskin SJ, Mosse YP, Wood AC, Ji L, Sposto R, Badgett T, London WB, Moyer Y, Gastier-Foster JM, Smith MA, Auvil JM, Gerhard DS, Hogarty MD, Jones SJ, Lander ES, Gabriel SB, Getz G, Seeger RC, Khan J, Marra MA, Meyerson M, Maris JM. The genetic landscape of high-risk neuroblastoma. Nat Genet. 2013 Mar;45(3):279-84.
60. Wei W, Hou J, Alder O, Ye X, Lee S, Cullum R, Chu A, Zhao Y, Warner SM, Knight DA, Yang D, Jones SJ, Marra MA, Hoodless PA. Genome-wide microRNA and mRNA profiling in mouse liver development implicates mir302b and mir20a in repressing TGFβ signaling. Hepatology. 2013 Jan 12.
61. Qin Z, Bilenky M, Su G, Jones S. MotifOrganizer: a scalable model-based motif clustering tool for mammalian genomes. Front Biosci (Elite Ed). 2013 Jan 1;5:785-97.
62. Wu C, Wyatt AW, McPherson A, Lin D, McConeghy BJ, Mo F, Shukin R, Lapuk AV, Jones SJ, Zhao Y, Marra MA, Gleave ME, Volik SV, Wang Y, Sahinalp SC, Collins CC. Poly-gene fusion transcripts and chromothripsis in prostate cancer. Genes Chromosomes Cancer. 2012 Dec;51(12):1144-53.
63. Khodabakhshi AH, Morin RD, Fejes AP, Mungall AJ, Mungall KL, Bolger-Munro M, Johnson NA, Connors JM, Gascoyne RD, Marra MA, Birol I, Jones SJ. Recurrent targets of aberrant somatic hypermutation in lymphoma. Oncotarget. 2012 Nov;3(11):1308-19.
64. Nielsen CB, Younesy H, O'Geen H, Xu X, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ. Spark: A Navigational Paradigm for Genetic Data Exploration. Genome Res. 2012 Sep 7.[Epub ahead of print]
65. Zhang W, Prakash C, Sum C, Gong Y, Li Y, Kwok JJ, Thiessen N, Pettersson S, Jones SJ, Knapp S, Yang H, Chin KC. Bromodomain-containing protein 4 (BRD4) regulates RNA polymerase II serine 2 phosphorylation in human CD4+ T cells. J Biol Chem. 2012 Dec 14;287(51):43137-55.
66. Cancer Genome Atlas Network (357 authors). Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, Fulton LL, Dooling DJ, Ding L, Mardis ER, Wilson RK, Ally A, Balasundaram M, Butterfield YS, Carlsen R, Carter C, Chu A, Chuah E, Chun HJ, Coope RJ, Dhalla N, Guin R, Hirst C, Hirst M, Holt RA, Lee D, Li HI, Mayo M, Moore RA, Mungall AJ, Pleasance E, Robertson A, Schein JE, Shafiei A, Sipahimalani P, Slobodan JR, Stoll D, Tam A, Thiessen N, Varhol RJ, Wye N, Zeng T, Zhao Y, Birol I, Jones SJ, Marra MA, et al. Comprehensive molecular portraits of human breast tumours. Nature. 2012 Oct 4;490(7418):61-70.
67. Cancer Genome Atlas Research Network (412 authors). Hammerman PS, Lawrence MS, Voet D, Jing R, Cibulskis K, Sivachenko A, Stojanov P, McKenna A, Lander ES, Gabriel S, Getz G, Sougnez C, Imielinski M, Helman E, Hernandez B, Pho NH, Meyerson M, Chu A, Chun HJ, Mungall AJ, Pleasance E, Robertson A, Sipahimalani P, Stoll D, Balasundaram M, Birol I, Butterfield YS, Chuah E, Coope RJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Lee D, Li HI, Mayo M, Moore RA, Mungall K, Nip KM, Olshen A, Schein JE, Slobodan JR, Tam A, Thiessen N, Varhol R, Zeng T, Zhao Y, Jones SJ, Marra MA, et al. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27;489(7417):519-25.
68. Roberts KG, Morin RD, Zhang J, Hirst M, Zhao Y, Su X, Chen SC, Payne-Turner D, Churchman ML, Harvey RC, Chen X, Kasap C, Yan C, Becksfort J, Finney RP, Teachey DT, Maude SL, Tse K, Moore R, Jones S, Mungall K, Birol I, Edmonson MN, Hu Y, Buetow KE, Chen IM, Carroll WL, Wei L, Ma J, Kleppe M, Levine RL, Garcia-Manero G, Larsen E, Shah NP, Devidas M, Reaman G, Smith M, Paugh SW, Evans WE, Grupp SA, Jeha S, Pui CH, Gerhard DS, Downing JR, Willman CL, Loh M, Hunger SP, Marra MA, Mullighan CG. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell. 2012 Aug 14;22(2):153-66.
69. Northcott PA, Shih DJ, Peacock J, Garzia L, Sorana Morrissy A, Zichner T, Stutz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Ming Nip K, Qian JQ, Raymond AG, Thiessen N., Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Weschler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CG, Febre-Montagne M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Yancey Gillespie G, Di Rocco C, Massimi L, MIchiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognar L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Shin Ra Y, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD. Sugroup-specific structural variations across 1,000 medulloblastoma genomes. Nature. 2012 Jul 25.doi:10.1038/nature11327.[Epub ahead of print]
70. Chu A, Chun HJ, Mungall AJ, Pleasance E, Robertson A, Stoll D, Balasundaram M, Birol I, Butterfield YS, Chuah E, Coope RJ, Dhalla N, Guin R, Hirst C, Hirst M, Holt RA, Lee D, Li HL, Mayo M, Moore RA, Schein JE, Slobodan JR, Tam A, Thiessen N, Varhol R, Zeng T, Zhao Y, Jones SJ, Marra MA and the Cancer Genome Atlas Network. (297 collaborators). Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 487(7407)doi: 10.1038/nature11252.
71. Vrljicak P, CUllum R, Xu E, Chang ACY, Wederell ED, Bilenky M, Jones SJM, Marra MA, Karsan A, Hoodless PA. Twist1 Trascriptional Targets in the Developing Atrioventricular Canal of the Mouse. PLos One. 2012;7(7):e40815. Epub 2012 Jul 16.
72. Chiu CG, Yao R, Chan SK, Strugnell SS, Bugis S, Irvine R, Anderson D, Walker B, Jones SJ, Wiseman SM. Hemithyroidectomy is the preferred initial operative approach for an indeterminate fine needle aspiration biopsy diagnosis. Can J. Surg. 2012 Jun; 55(3):191-8.
73. Wu C, Wyatt AW, Lapuk AV, McPherson A, McConeghy BJ, Bell RH, Anderson S, Haegert A, Brahmbhatt S, Shukin R, Mo F, Li E, Fazli L, Hurtado-Coll A, Jones EC, Butterfield YS, Hach F, Hormozdiari F, Hajirasouliha I, Boutros PC, Bristow RG, Jones SJ, Hirst M, Marra MA, Maher CA, Chinnaiyan AM, Sahinalp SC, Gleave ME, Volik SV, Collins CC. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. J Pathol. 2012 May; 227(1):53-61.doi:10.1002/path.3987.Epub 2012 Mar 21.
74. Doherty D, Chudley AE, Coghlan G, Ishak GE, Innes AM, Lemire EG, Rogers RC, Mhanni AA, Phelps IG, Jones SJ, Zhan SH, Fejes AP, Shahin H, Kanaan M, Akay H, Tekin M; FORGE Canada Consortium, Triggs Raine B, Zelinski T. GPSM2 Mutations Cause the Brain Malformations and Hearing Loss in Chudley-McCullough Syndrome. Am J Hum Genet. 2012 Jul 13;91(1):209[PubMed - indexed for MEDLINE]
75. Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, Jones SJ, Marra MA, Ley TJ, Mardis ER, Wilson RK, Weistein JN, Ding L, BreakFusion: Targeted Assembly-based Identification of Gene Fusions in Whole Transcriptome Paired-end Sequencing Data. Bioinformatics. 2012 Jul 15;28(14): 1923-4. Epub 2012 May 4.
76. Chiu CG, Chan SK, Fang ZA, Masoudi H, Wood-Baker R, Jones SJ, Gilks B, Laskin J, Wiseman SM, Beta-catenin expression is prognostic of improved non-small cell lung cancer survival. Am J Surg. 2012 may; 203(5): 654-9. Epub 2012 Mar 7.
77. Simonis M, Atanur SS, Linsen SE, Guryev V, Ruzius FP, Game L, Lansu N, de Bruijn E, van Heesch S, Jones SJ, Pravenec M, Aitman TJ, Cuppen E. Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel. Genome Biol. 2012 Apr 27;13(4):R31.[Epub ahead of print]
78. Shankar J, Wiseman SM, Meng F, Kasaian K, Strugnell S, Mofid A, Gown A, Jones SJ, Nabi IR, Coordinate Expression of Galetctin-3 and Cavolin-1 in Thyroid Cancer. J Pathol. 2012 Apr 19. doi: 10.1002/path.4041. [Epub ahead of print]
79. Chu JS, Johnsen RC, Chua SY, Tu D, Dennison M, Marra M, Jones SJ, Baiillie DL, Rose AM. Allelic ratios and the mutational landscape reveal biologically significant heterozygous SNVs. Genetics. 2012 Apr; 190 (4): 1225-33. Epub 2012 Jan 20.
80. Keeling CI, Henderson H, Li M, Yuen M, Clark EL, Fraser JD, Huber DPW, Liao NY, Docking TR, Birol I, Chan SK, Taylor GA, Palmquist D, Jones SJM and Bohlmann J. Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests. Insect Biochemistry and Molecular Biology. 2012 Apr 7. [Epub ahead of print]
81. Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012 Apr 4. [Epub ahead of print]
82. Lee CH, Ou WB, Mariño-Enriquez A, Zhu M, Mayeda M, Wang Y, Guo X, Brunner AL, Amant F, French CA, West RB, McAlpine JN, Gilks CB, Yaffe MB, Prentice LM, McPherson A, Jones SJ, Marra MA, Shah SP, van de Rijn M, Huntsman DG, Dal Cin P, Debiec-Rychter M, Nucci MR, Fletcher JA. 14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma. Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):929-34. Epub 2012 Jan 5.
83. Yip S, Butterfield YS, Morozova O, Chittaranjan S, Blough MD, An J, Birol I, Chesnelong C, Chiu R, Chuah E, Corbett R, Docking R, Firme M, Hirst M, Jackman S, Karsan A, Li H, Louis DN, Maslova A, Moore R, Moradian A, Mungall KL, Perizzolo M, Qian J, Roldan G, Smith EE, Tamura-Wells J, Thiessen N, Varhol R, Weiss S, Wu w, Young S, Zhao YJ, Mungall AJ, Jones SJM, Morin GB, Chan JA, Cairncross JG, Marra MA. Concurrent CIC mutations, IDH mutations and 1p/19q loss distinguish oligodendrogliomas from other cancers. J Pathol. 2012 Jan;226(1):7-16. Epub 2011 Nov 10
84. Heravi-Moussavi A, Anglesio MS, Cheng S-WG, Senz J, Yang W, Prentice L, Fejes A, Chow C, Tone A, Kalloger SE, Hamel N, Roth A, Ha G, Wan ANC, Maines-Bandiera S, Salamanca C, Pasini B, Clarke BA, Lee AF, Lee C-H, Zhou C, Young RH, Aparicio AS, Sorensen PHB, Woo MMM, Boyd N,  Jones SJM, Hirst M, Marra MA, Gilks B, Shah SP, Foulkes WD, Morin GB, Huntsman DG. Recurrent Somatic DICER1 Mutations in Non-Epithelial Ovarian Tumors.  N Engl J Med. 2011 Dec 21. [Epub ahead of print]
85. Gibson WT, Hood RL, Zhan SH, Bulman DE, Fejes AP, Moore R, Mungall AJ,  Eydoux P, Babul-Hirji R, Chitayat D, An J, Marra MA, FORGE Canada Consortium, Boycott KM, Weaver DD, Jones SJ. Mutations in EZH2 cause Weaver syndrome. Am J Hum Genet. 2011 Dec 14. [Epub ahead of print]
86. Krzywinski M, Birol I, Jones S, Marra M. Hive Plots – Rational Approach to Visualizing Networks. Brief Bioinform. 2011 Dec 9. [Epub ahead of print].
87. Chan QW, Cornman RS, Birol I, Liao NY, Chan SK, Docking TR, Jackman SD, Taylor GA, Jones SJ, de Graaf DC, Evans JD, Foster LJ. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. BMC Genomics. 2011 Sep 16;12:450.
88. Rebollo R, Karimi MM, Bilenky M, Gagnier L, Miceli-Royer K, Zhang Y, Goyal P, Keane TM, Jones S, Hirst M, Lorincz MC, Mager DL. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genet. 2011 Sep;7(9):e1002301. Epub 2011 Sep 29.
89. Schrader KA, Heravi-Moussavi A, Water PJ, Senz J, Whelan J, Ha G, Eydoux P, Nielsen T, Gallagher B, Oloumi A, Boyd N, Fernandez BA, Young T-L, Jones SJM, Hirst M, Shah SP, Marra MA, Green J, Huntsman DG. Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities. The Journal of Pathology. 2011 Sep;225(1):12-8.
90. Johner A, Griffith OL, Walker B, Wood L, Piper H, Wilkins G, Baliski C, Jones SJ, Wiseman SM. Detection and management of hypothyroidism following thyroid lobectomy: evaluation of a clinical algorithm. Ann Surg Oncol. 2011 Sep;18(9):2548-54. Epub 2011 Mar 10.
91. Li YY, An J, Jones SJM. A Computational Approach to Finding Novel Targets for Existing Drugs. PLoS Comput Biol. 2011 Sep;7(9):e1002139. Epub 2011 Sep 1.
92. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303.
93. Olexandr Yakovenko, Yvonne Y. Li, Alexander A. Oliferenko, Volodymyr G. Bdzhola, Ganna M. Vashchenko, and Steven J.M. Jones. Ab initio parameterization of YFF1, a universal force field for drug-design applications. J Mol Model. 2011 May 12. [Epub ahead of print] PMID: 21562826 [PubMed - as supplied by publisher]
94. Wiseman SM, Griffith OL, Gown A, Walker B, Jones SJM. Immunophenotyping of thyroid tumors identifies molecular markers altered during transformation of differentiated into anaplastic carcinoma. Am J Surg. 2011 May 1;201(5):578-84.
95. Steidl C, Shah SP, Woolcock BW, Rui L, Kawahara M, Farinha P, Johnson NA, Zhao Y, Telenius A, Neriah SB, McPherson A, Meissner B, Okoye UC, Diepstra A, van den Berg A, Sun M, Leung G, Jones SJ, Connors JM, Huntsman DG, Savage KJ, Rimsza LM, Horsman DE, Staudt LM, Steidl U, Marra MA, Gascoyne RD. MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature. 2011 Mar 2.
96. Shin H, Lee H, Fejes AP, Baillie DL, Koo H-S, Jones SJ. Gene expression profiling of oxidative stress response of C. elegans aging defective AMPK mutants using massively parallel transcriptome sequencing. BMC Res Notes. 2011 Jan 1;4:34.
97. Schrader KA, Heravi-Moussavi A, Waters PJ, Senz J, Whelan J, Ha G, Eydoux P, Nielsen T, Gallagher B, Oloumi A, Boyd Niki, Fernandez BA, Young T, Jones SJM, Hirst M, Shah SP, Marra MA, Green J, Huntsman DG. Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities. J Pathol. 2011 Sep 1;225(1):12-8.
98. Rebollo R, Karimi MM, Bilenky M, Gagnier L, Miceli-Royer K, Zhang Y, Goyal P, Keane TM, Jones S, HIrst M, Lorincz MC, Mager DL.. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genet. 2011 Sep 1;7(9):e1002301.
99. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, HIrst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Aug 18;476(7360):298-303.
100. Li YY, An J, Jones SJM. A computational approach to finding novel targets for existing drugs. PLoS Comput Biol. 2011 Sep 1;7(9):e1002139.
101. Kasaian K, Jones SJ. A new frontier in personalized cancer therapy: mapping molecular changes. Future Oncol. 2011 Jul 1;7(7):873-94.
102. Karimi MM, Goyal P, Maksakova IA, Bilenky M, Leung D, Tang JX, Shinkai Y, Mager DL, Jones S, Hirst M, Lorincz MC. DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs. Cell Stem Cell. 2011 Jun 3;8(6):676-87.
103. Johner A, Griffith OL, Walker B, Wood L, Piper H, Wilkins G, Baliski C, Jones SJM, Wiseman SM. Detection and Management of Hypothyroidism Following Thyroid Lobectomy: Evaluation of a Clinical Algorithm. Ann Surg Oncol. 2011 Mar 10.
104. Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJM, Cronk QCB, Douglas CJ. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour. 2011 Mar 1;11 Suppl 1:81-92.
105. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Empel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJM, Brinkman FSL, Brunham RC, Tang P. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011 Feb 24;364(8):730-9.
106. Fejes AP, Hadj Khodabakhshi A, Birol I, Jones SJM. Human Variation Database: An open source database template for genomic discovery. Bioinformatics. 2011 Mar 2.
107. D'Souza CA, Kronstad JW, Taylor G, Warren R, Yuen M, Hu G, Jung WH, Sham A, Kidd SE, Tangen K, Lee N, Zeilmaker T, Sawkins J, McVicker G, Shah S, Gnerre S, Griggs A, Zeng Q, Bartlett K, Li W, Wang X, Heitman J, Stajich JE, Fraser JA, Meyer W, Carter D, Schein J, Krzywinski M, Kwon-Chung KJ, Varma A, Wang J, Brunham R, Fyfe M, Ouellette BFF, Siddiqui A, Marra M, Jones S, Holt R, Birren BW, Galagan JE, Cuomo CA. Genome Variation in Cryptococcus gattii, an Emerging Pathogen of Immunocompetent Hosts. MBio. 2011 Jan 1;2(1).
108. DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Alamouti SM, Tsui CKM, Docking RT, Levasseur A, Haridas S, Robertson G, Birol I, Holt RA, Marra MA, Hamelin RC, HIrst M, Jones SJM, Bohlmann J, Breuil C. Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci USA. 2011 Feb 8;108(6):2504-9.
109. Chan QW, Cornman RS, Birol I, Liao NY, Chan SK, Docking TR, Jackman SD, Taylor GA, Jones SJM de Graaf DC, Evans JD, Foster LJ. Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees. BMC Genomics. 2011 Jan 1;12:450.
110. Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S, Gottardo R. PICS: Probabilistic Inference for ChIP-seq. Biometrics. 2010 Jun 1.
111. Wong R, Flibotte S, Corbett R, Saeedi P, Jones S, Marra M, Schein J, Birol I. LaneRuler: Automated Lane Tracking for DNA Electrophoresis Gel Images. Automation Science and Engineering, IEEE Transactions on. 2010 Jul 20;7(3):706 - 8.
112. Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, Miller D, Jones SJM, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih L, Mes-Masson A, Bowtell DD, HIrst M, Gilks B, Marco MA, Huntsman DG. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010 Oct 14;363(16):1532-43.
113. Swanson TW, Chan SK, Jones SJ, Bugis S, Irvine R, Belzberg A, Levine D, Wiseman SM. Determinants of Tc-99m sestamibi SPECT scan sensitivity in primary hyperparathyroidism. Am J Surg. 2010 May 1;199(5):614-20.
114. Steidl C, Lee T, Shah SP, Farinha P, Han G, Nayar T, Delaney A, Jones SJ, Iqbal J, Weisenburger DD, Bast MA, Rosenwald A, Muller-Hermelink H, Rimsza LM, Campo E, Delabie J, Braziel RM, Cook JR, Tubbs RR, Jaffe ES, Lenz G, Connors JM, Staudt LM, Chan WC, Gascoyne RD. Tumor-associated macrophages and survival in classic Hodgkin's lymphoma. N Engl J Med. 2010 Mar 11;362(10):875-85.
115. Sleumer MC, Mah AK, Baillie DL, Jones SJM. Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. Nucleic Acids Res. 2010 May 1;38(9):2990-3004.
116. Rose AM, O'Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJM. Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. BMC Genomics. 2010 Jan 1;11:131.
117. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nat Methods. 2010 Nov;7(11):909-12. Epub 2010 Oct 10.
118. Law MJ, Lower KM, Voon HP, Hughes JR, Garrick D, Viprakasit V, Mitson M, De Gobbi M, Marra M, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ. ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner. Cell. 2010 Oct 29;143(3):367-78. PMID: 21029860 [PubMed - in process.
119. Hesse-Orce U, Diguistini S, Keeling CI, Wang Y, Li M, Henderson H, Docking TR, Liao NY, Robertson G, Holt RA, Jones SJ, Bohlmann J, Breuil C. Gene discovery for the bark beetle-vectored fungal tree pathogen Grosmannia clavigera.BMC Genomics. 2010 Oct 4;11:536.PMID: 20920358 [PubMed - in process]
120. Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, Tse K, Zeng T, Senz J, McConechy MK, Anglesio MS, Kalloger SE, Yang W, Heravi-Moussavi A, Giuliany R, Chow C, Fee J, Zayed A, Prentice L, Melnyk N, Turashvili G, Delaney AD, Madore J, Yip S, McPherson AW, Ha G, Bell L, Fereday S, Tam A, Galletta L, Tonin PN, Provencher D, Miller D, Jones SJ, Moore RA, Morin GB, Oloumi A, Boyd N, Aparicio SA, Shih IeM, Mes-Masson AM, Bowtell DD, Hirst M, Gilks B, Marra MA, Huntsman DG. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010 Oct 14;363(16):1532-1543.
121. Law JH, Li Y, Wang M, Astanehe A, Lambie K, Dhillon J, Jones SJ, Gleave ME, Eaves CJ, Dunn SE. Molecular decoy to the Y-box binding protein-1 suppresses the growth of breast and prostate cancer cells whilst sparing normal cell viability. PLoS One. 2010 Sept 10;5(9). pii: e12661.
122. Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW. Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol. 2010 Sep 30;11(9):403. [Epub ahead of print]
123. Portales-Casamar E, Swanson DJ, Liu L, de Leeuw CN, Banks KG, Ho Sui SJ, Fulton DL, Ali J, Amirabbasi M, Arenillas DJ, Babyak N, Black SF, Bonaguro RJ, Brauer E, Candido TR, Castellarin M, Chen J, Chen Y, Cheng JC, Chopra V, Docking TR, Dreolini L, D'Souza CA, Flynn EK, Glenn R, Hatakka K, Hearty TG, Imanian B, Jiang S, Khorasan-zadeh S, Komljenovic I, Laprise S, Liao NY, Lim JS, Lithwick S, Liu F, Liu J, Lu M, McConechy M, McLeod AJ, Milisavljevic M, Mis J, O'Connor K, Palma B, Palmquist DL, Schmouth JF, Swanson MI, Tam B, Ticoll A, Turner JL, Varhol R, Vermeulen J, Watkins RF, Wilson G, Wong BK, Wong SH, Wong TY, Yang GS, Ypsilanti AR, Jones SJ, Holt RA, Goldowitz D, Wasserman WW, Simpson EM. A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16589-94. Epub 2010 Aug 31.
124. Liang B, Luo M, Ball TB, Jones SJ, Plummer FA. QUASI analysis of host immune responses to Gag polyproteins of human immunodeficiency virus type 1 by a systematic bioinformatics approach. Biochem Cell Biol. 2010 Aug;88(4):671-81.
125. Steven J.M. Jones, Janessa Laskin, Yvonne Y. Li, Obi L. Griffith, Jianghong An, Mikhail Bilenky, Yaron S. Butterfield, Timothee Cezard, Eric Chuah, Richard Corbett, Anthony Fejes, Malachi Griffith, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D. Morin, Trevor J. Pugh, Tesa Severson, Sohrab P. Shah,, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A. Moore, David G. Huntsman, Inanc Birol, Martin Hirst, Robert A. Holt, Marco A. Marra. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology. 2010 Aug 9;11(8):R82. [Epub ahead of print]
126. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, ThiessenN, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ,Haussler D, Marra MA, Hirst M, Wang T, Costello JF. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul8;466(7303):253-7. (PubMed PMID: 20613842)
127. Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao Y, Hirst M, Verchere CB, Helgason CD, Marra MA, Jones SJ, Hoodless PA. Locus Co-occupany, Nucleosme Positioning and H3K4me1 Regulate the Functionality of Foxa2, Hnf4a, and Pdx1 Bound Loci in Islets and Liver. Genome Res. 2010 Jun 15. [Epub ahead of print]
128. Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S, and Gottardo R. PICS: Probabilistic Inference for ChIP-Seq. Biometrics. 2010 Jun 1. [Epub ahead of print]
129. Swanson TW, Chan SK, Jones SJ, Bugis S, Irvine R, Belzberg A, Levine D, Wiseman SM. Determinants of Tc-99m sestamibi SPECT scan sensitivity in primary hyperparathyroidism. Am J Surg. 2010 May;199(5):614-20.
130. Chiu CG, Strugnell SS, Griffith OL, Jones SJ, Gown AM, Walker B, Nabi IR, Wiseman SM. Diagnostic utility of galectin-3 in thyroid cancer. Am J Pathol. 2010 May;176(5):2067-81. Epub 2010 Apr 2.
131. Flibotte S, Edgley ML, Chaudhry I, Taylor J, Neil SE, Rogula A, Zapf R, Hirst M, Butterfield Y, Jones SJ, Marra MA, Barstead RJ, Moerman DG. Whole-Genome profiling of mutagenesis in Caenorhabditis elegans.Genetics 2010 May 3. [Epub ahead of print].
132. Leong JS, Jantzen SG, von Schalburg KR, Cooper GA, Messmer AM, Liao NY, Munro S, Moore R, Holt RA, Jones SJ, Davidson WS, Koop BF. Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. BMC Genomics. 2010 Apr 30;11(1):279. [Epub ahead of print].
133. Atanur SS, Birol I, Guryev V, Hirst M, Hummer O, Behmoaras J, Fernandez X, Johnson MD, McLaren W, Morrissey C, Patone G, Petretto E, Plessy C, Saar K, Zhao YJ, Carninci P*, Flicek P*, Kurtz T*, Cuppen E*, Pravenec M*, Hubner N*, Jones SJM*, Birney E*, Aitman TJ*. The genome of the spontaneously hypertensive rat: analysis and functional significance. Genome Research 2010 Apr 29. [Epub ahead of print] *These authors contributed equally to the work.
134. Malhis N, Jones SJ. High quality SNP calling using Illumina data at shallow coverage. Bioinformatics. 2010 Apr 15;26(8):1029-35. Epub 2010 Feb 26.
135. Jones SJM and 411 Collaborators (International Cancer Genome Consortium.) International network of cancer genome projects. Nature. 2010 Apr 15;464(7291):993-8.
136. Steidl C, Lee T, Shah SP, Farinha P, Han G, Nayar T, Delaney A, Jones SJ, Iqbal J, Weisenburger DD, Bast MA, Rosenwald A, Muller-Hermelink HK, Rimsza LM, Campo E, Delabie J, Braziel RM, Cook JR, Tubbs RR, Jaffe ES, Lenz G, Connors JM, Staudt LM, Chan WC, Gascoyne RD. Tumor-associated macrophages and survival in classic Hodgkin's lymphoma. N Engl J Med. 2010 Mar 11;362(10):875-85.
137. Rose AM, O’Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJM. Genomic Sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. BMC Genomics. 2010 Feb 23;11(1):131. [Epub ahead of print].
138. Sleumer Monica C, Mah Allan K, Baillie David L, Jones Steven JM. Conserved Elements Associated with Ribosomal Genes and their Trans-splice Acceptor Sites in Caenorhabditis elegans. Nucleic Acids Research. 2010 Jan 25. [Epub ahead of print] PMID: 20100800.
139. Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA.Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin Nature Genetics. 2010 Jan 17. [Epub ahead of print]
140. Nielsen CB, Jackman SD, Birol I, Jones SJ. AbySS-Explorer: Visualizing Genome Sequence Assemblies. IEEE Trans Vis Comput. Graph. 2009 Nov-Dec; 15(6):881-8.
141. The MGC Project Team including: 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 SJM, Holt RA, Marra MA. The Completion of the Mammilian Gene Collection (MGC). Genome Research. 2009 Oct. 28. [Epub ahead of print].
142. Romanuik T, Wang G, Holt RA, Jones SJM, Marra MA, Sadar MD. Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries. BMC Genomics. 2009 Oct. 15;10:476.
143. Shah SP, Morin R, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, Steidl C, Holt RA, Jones SJ, Sun M, Leung G, Moore R, Severson T, Taylor G, Teschendorff AE, Tse K, Turashvili G, Varhol R, Warren RL, Watson P, Zhao YJ, Caldas C, Huntsman D, Hirst M, Marra MA, Aparicio S. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009 Oct. 8;461(7265):809-13.
144. DiGuistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJM. De novo assembly of a genome sequence for the filamentous fungus, Grosmannia clavigera, assembled using Sanger, 454 and Illumina sequence data. Genome Biology. 2009 Sep 11;10(9):R94. [Epub ahead of print]. PMID: 19747388.
145. Deen S, Griffith OL, Masoudi H, Gown A, Jones SJ, Wiseman SM. Anaplastic thyroid carcinoma exhibits intratumoral molecular homogeneity for a therapeutic target panel. Anticancer Research. 2009 Jul;29(7):2437-44.
146. Meissner B, Warner A, Wong K, Dube N, Lorch A, McKay SJ, Khattra J, Rogalski T, Somasiri A, Chaudhry I, Fox RM, Miller DM, Baillie DL, Holt RA, Jones SJM, Marra MA, Moerman DG. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genetics. 2009 Jun;5 (6):e1000537. Epub 2009 Jun 26.
147. Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Zhao YJ, Hirst M, Jones S, Marra MA. Next generation tag sequencing for cancer gene expression profiling. Genome Research. 2009 Oct;19(10):1825-35. Epub 2009 Jun 18.
148. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra M. Circos: an Information Aesthetic for Comparative Genomics. Genome Research. 2009 Sep;19(9):1639-45. 2009 Jun 18. [Epub ahead of print].
149. Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJ. De novo Transcriptome Assembly with ABySS. Bioinformatics. 2009 Nov 1;25(21):2872-7. 2009 Jun 15. [Epub ahead of print].
150. Shah SP, Köbel M, Senz J, Morin RD, Clarke BA, Wiegand KC, Leung G, Zayed A, Mehl E, Kalloger SE, Sun M, Giuliany R, Yorida E, Jones S, Varhol R, Swenerton KD, Miller D, Clement PB, Crane C, Madore J, Provencher D, Leung P, DeFazio A, Khattra J, Turashvili G, Zhao Y, Zeng T, Glover JN, Vanderhyden B, Zhao C, Parkinson CA, Jimenez-Linan M, Bowtell DD, Mes-Masson AM, Brenton JD, Aparicio SA, Boyd N, Hirst M, Gilks CB, Marra M, Huntsman DG. Mutation of the FOXL2 Gene in Granulosa Cell Tumors of the Ovary. New England Journal of Medicine. 2009 June 10; 360(26): 2719-29. [Epub ahead of print].
151. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: A parallel assembler for short read sequence data. Genome Research. 2009 Jun;19(6):1117-23. Epub 2009 Feb 27.
152. An J, Lee DC, Law AH, Yang CL, Poon LL, Lau AS, Jones SJ. A novel small-molecule inhibitor of the avian influenza H5N1 virus determined through computational screening against the neuraminidase. Journal of Medicinal Chemistry. 2009 May 14;52(9):2667-72.
153. Wang X, Zhao YJ, Wong K, Ehlers P, Kohara Y, Jones SJ, Marra MA, Holt RA, Moerman DG, Hansen D. Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE. BMC Genomics. 2009 May 9;10(1):213. [Epub ahead of print]
154. Bovine Genome Sequencing and Analysis Consortium, et al, including Holt RA, Jones SJ, Marra MA, Moore R, Schein JE, The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 Apr 24;324 (5926):522-8.
155. Sleumer MC, Bilenky M, He A, Robertson AG, Jones SJM. C. elegans cisRED: A catalogue of conserved genomic elements. Nucleic Acids Research. 2009 Jan 16. [Epub ahead of print].
156. Malhis N, Butterfield YS, Ester M, Jones SJ. Slider--maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics 2009 Jan 1;25(1):6-13.
157. McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao YJ, Khattra J, Hirst M, Jones SJ, Marra MA, Ruzanov P, Warner A, Zapf R, Moerman DG, Kalb JM. ELT-2 Is the Predominant Transcription Factor Controlling Differentiation and Function of the C. elegans Intestine, from Embryo to Adult. Developmental Biology. 2008 Dec 9. [Epub ahead of print].
158. Robertson GA, Bilenky M, Tam A, Zhao YJ, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJM. Genome wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding. Genome Research. (18) 1906-1917 Sept. 2008.
159. Ralph SG, Chun HJ, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S, Holt RA, Jones SJ, Marra MA, Douglas CJ, Ritland K, Bohlmann J. A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics. 2008 Oct 14;9(1):484. [Epub ahead of print]
160. Joshi B, Strugnell S, Goetz JG, Kojic LD, Cox ME, Griffith OL, Jones S, Leung S, Masoudi H, Leung S, Wiseman SM, Nabi IR. Phospho-caveolin-1 regulates Rho/ROCK-dependent focal adhesion dynamics and tumor cell migration. Cancer Research. 2008 Oct 15;68(20):8210-20.
161. Morin RD, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh TJ, McDonald H, Varhol R, Jones SJM, Marra MA. (first 2 are first co-authors) Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques. 2008 Jul ;45(1):81-94.
162. D’Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao YJ, Lee LC, Bilenky M, Portales-Casamar E, he A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJM. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neuroscience. 2008 Jul 14; 9(1):66. [Epub ahead of print]
163. Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL. Jones SJ. Transcriptome analysis for Caenorhabiditis elegans based on novel expressed sequence tags. BMC Biology. 2008 Jul 8;6:30.
164. Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao YJ, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA. Global Analysis of In Vivo FoxA2 Binding Sites in Mouse Adult Liver Using Massively Parallel Sequencing. Nucleic Acids Research. 2008 Aug;36(14):4549-64. 2008 Jul 8. [Epub ahead of print]
165. Raouf A, Zhao Y, Stingl J, Delaney A, Barbara M, Iscove N, Jones S, McKinney S, Emerman J, Aparicio S, Marra M, Eaves C. Transcriptome analysis of the normal human mammary cell commitment and differentiation process. Cell Stem Cell. 2008 Jul 3; 3(1);109-18.
166. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJM. FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short read sequencing technology. Bioinformatics. 2008 Aug 1;24(15):1729-30. 2008 Jul 3. [Epub ahead of print].
167. Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones S, Marra MA, Helgason CD. Identification of Transcripts with Enriched Expression in the Developing and Adult Pancreas. Genome Biology. 2008 June 14;9(6):R99. [Epub ahead of print].
168. Liang B, Luo M, Ball TB, Yao X, van Domselaar G, Cuff WR, Cheang M, Jones SJM, Plummer FA. Systematic Analysis of host immunological pressure on the envelope gene of human immunodeficiency virus type 1 by an immunological approach. Current HIV Research. 2008 Jun;6(4):370-9.
169. Leung SP, Griffith OL, Masoudi H, Gown A, Jones SJ, Phang T, Wiseman SM. Clinical Utility of Type 1 Growth Factor Receptor Expression by Colon Cancer. The American Journal of Surgery. 2008 May;195(5):604-10.>
170. Wiseman SM, Griffith OL, Melck A, Masoudi H, Gown A, Nabi IR, Jones SJM. Evaluation of type 1 growth factor receptor family expression in benign and malignant thyroid lesions. The American Journal of Surgery. 2008 May;195(5):667-73.
171. Shivaswamy S, Bhinge A, Zhao Y, Jones SJM, Hirst M, Iyer VR. Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation. PLoS Biology. 2008 Mar 18;6(3):e65 [Epub ahead of print]
172. Chan SK, Griffith OL, Tai IT, Jones SJM. Meta-Analysis of Colorectal Cancer Gene Expression Profiling Studies Identifies Consistently Reported Candidate Biomarkers. Cancer Epidemiol Biomarkers Prev. 2008 Mar;17(3):543–52.
173. Aerts S, Haeussler M, Griffith OL, van Vooren S, Jones SJM, Montgomery SB, Bergman CM, The Open Regulatory Annotation Consortium. Text-mining assisted regulatory annotation. Genome Biology. 2008 Feb 13;9(2):R31 [Epub ahead of print].
174. Griffith M, Tang MJ, Griffith OL, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Morin RD, Hirst M, Jones SJM, Morin GB, Tai IT and Marra MA. ALEXA – A microarray design platform for alternative expression analysis. Nature Methods. 2008 Feb;5(2):118.
175. Ralph SG, Chun HJ, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJ, Marra MA, Bohlmann J. Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding. BMC Genomics. 2008 Jan 29;9(1):57 [Epub ahead of print]
176. Kneller JM, Ehlen T, Matisic JP, Miller D, van Niekerk D, Lam WL, Marra M, Richards-Kortum R, Follen M, MacAulay C, Jones SJM. Using longSAGE to detect biomarkers of cervical cancer potentially amenable to optical contrast agent labelling. Biomarker Insights. 2007 Dec 11;2:447-61.
177. Griffith OL, Montgomery SB, Bernier B, Chu B, Aerts S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Mahony S, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJM; The Open Regulatory Annotation Consortium. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Research. 2008 Jan: 36(Database Issue):D107-13. Epub 2007 Nov. 15.
178. Quayle AP, Siddiqui AS, Jones SJM. Perturbation of Interaction Networks for Application to Cancer Therapy. Cancer Informatics.(Edition: Systems Biology Special Issue) 2007: (2) 45-65.
179. Ruzanov P, Jones SJ, Riddle DL. Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data. BMC Genomics. 2007 Nov 30;8:447.
180. Peng FY, Reid KE, Liao N, Schlosser J, Lijavetzky D, Holt R, Martinez Zapater JM, Jones S, Marra M, Bohlmann J, Lund ST. Generation of EST’s in Vitis vinifera Wine Grape (Cabernet Sauvingnon) and Table Grape (Muscat Hamburg) and discovery of new candidate genes with possible roles in berry development. Gene. 2007 Nov 1 ;402 (1-2) :40-50. Epub 2007 Jul 31.
181. Krzywinski MI, Bosdet I, Mathewson C, Wye N, Brebner J, Chiu R, Corbett R, Field M, Lee D, Pugh T, Volik S, Siddiqui AS, Jones SJM, Schein JE, Collins C, Marra A. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biology. 2007 Oct 22; 8(10):R224 [Epub ahead of print]
182. Huang P, Pleasance ED, Maydan JS, Hunt-Newbury R, O’Neil NJ, Mah A, Baillie DL, Marra MA, Moerman DG, Jones SJ. Identification and analysis of internal promoters in Caenorhabditis elegans Operons. Genome Res. 2007 Oct; 17 (10): 1478-85. Epub 2007 Aug 21.
183. Melck AL, Masoudi H, Griffith OL, Rajput A, Wilkins GE, Bugis S, Jones S, Wiseman SM. Cell Cycle Regulators Show Diagnostic and Prognostic Utility for Differentiated Thyroid Cancer. Annals of Surgical Oncology. 2007 Sep 20; 14(12):3403-3411.[Epub ahead of print]
184. Hunt Newbury R, Viveiros R, Johnsen R, Mah A, Anastis D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, MacKay S, Okada M, Pan J, Shultz AK, Tu D, Wong K, Zhao Z, Aleeyenko A, Buerglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG. High throughput in vivo analysis of gene expression in C elegans. PloS Biology. 2007 Sep; 5 (9) :e237.
185. Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwaN JC, McKay S, McWilliam S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas F, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel R, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor J, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G and Zhao S. A physical map of the bovine genome. Genome Biology. 2007 Aug 14; 8(8):R165 [Epub ahead of print]
186. Wiseman SM, Griffith OL, Deen S, Rajput A, Masoudi H, Gilks B, Goldstein L, Gown A, Jones SJM. Identification of Molecular Markers Altered during Transformation Of Differentiated Into Anaplastic Thyroid Carcinoma. Archives of Surgery. 2007 Aug. 142 (8): 717-729.
187. Hou J, Charters AM, Lee SC, Zhou Y, Wu M, Jones SJM, Marra MA, Hoodless PA. A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE). BMC Developmental Biology. 2007 Aug 2;7:92.
188. Etchberger JF, Lorch A, Sleumer M, Zapf R, Jones SJ, Marra MA, Holt RA, Moerman DG, Hobert O. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron. Genes Development. 2007 Jul 1;21(13):1653-74.
189. Zhao Y, Raouf A. Kent D, Khattra J, Delaney A, Schnerch A, Asano J, MacDonald H, Chan C, Jones S, Marra M, Eaves C. A modified polymerase chain reaction-long serial analysis of gene expression protocol identifies novel novel transcripts in human CD34+ bone marrow cells. Stem Cells. 2007 Jul; 25 (7): 1681-9. [Epub ahead of print] Apr 5.
190. Hu G, Linning R, McCallum B, Banks T, Cloutier S, Butterfield Y, Liu J, Kirkpatrick R, Stott J, Yang G, Smailus D, Jones S, Marra M, Schein J, Bakkeren G. Generation of a wheat leaf rust, Puccinia triticina, EST database from stage-specific cDNA libraries. Molecular Plant Pathology. 2007 July 8 (4), 451-467.
191. Montgomery SB, Griffith OG, Scheutz JM, Brooks-Wilson A, Jones SJM. A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms. PLoS, Computational Biology. 2007 Jun 8;3 (6) :e106 Epub 2007 Apr 25.
192. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods. 2007 Jun 11; [Epub ahead of print]
193. Hirst M, Delaney A, Rogers SA, Schnerch A, Persaud DR, O’Connor MD, Zeng T, Moksa M, Fichter K, Mah D, Go A, Morin RD, Baross A, Zhao Y, Khattra J, Prabhu A-L, Pandoh P, McDonald H, Asano J, Dhalla N, Ma K, Lee S, Ally A, Chahal N, Menzies S, Siddiqui A, Holt R, Jones S, Gerhard DS, Thomson JA, Eaves CJ, Marra MA. LongSAGE profiling of nine human embryonic stem cell lines. Genome Biology. 2007 Jun 14; 8(6):R113.
194. Kelleher CT, Chiu R, Shin H, Bosdet IE, Krzywinski MI, Fjell CD, Wilkin J, Yin T, DiFazio SP, Ali J, Asano JK, Chan S, Cloutier A, Girn N, Leach S, Lee D, Mathewson CA, Olson T, O'connor K, Prabhu AL, Smailus DE, Stott JM, Tsai M, Wye NH, Yang GS, Zhuang J, Holt RA, Putnam NH, Vrebalov J, Giovannoni JJ, Grimwood J, Schmutz J, Rokhsar D, Jones SJ, Marra MA, Tuskan GA, Bohlmann J, Ellis BE, Ritland K, Douglas CJ, Schein JE. A physical map of the highly Heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation. Plant Journal. 2007 Jun;50(6):1063-78. Epub 2007 May 3.
195. Ruzanov P, Riddle DL, Marra MA, McKay SJ, Jones SJM. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Experimental Gerontol. 2007 Aug;42(8):825-39. Epub 2007 Apr 21.
196. Rhesus Macaque Genome Sequencing and Analysis Consortium (incl. Schein, J, Jones, S). Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. Science. 2007 Apr 13. 316, 222.
197. Warren RL, Sutton GG, Jones SJM and Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 2007 Feb 15;23(4):500-1. Epub 2006 Dec 8
198. McGhee JD, Sleumer M, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG, Robertson AG. The ELT-2 GATA-Factor and the Global Regulation of Transcription in the C. Elegans Intestine. Development Biology. 2007 Feb 15: 302(2): 627-45.
199. DiGuistini S, Ralph S, Lim Y, Holt R, Jones S, Bohlmann J, Breuil C. Generation and annotation of lodgepole pine and oleoresin induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain Pine Beetle associated pathogen. FEMS Microbiology Letters. 2007, 267: 151-158
200. Khattra J, Delaney AD, Zhao Y, Siddiqui A, Asano J, McDonald H, Pandoh P, Dhalla N, Prabhu AL, Ma K, Lee S, Ally A, Tam A, Sa D, Rogers S, Charest D, Stott J, Zuyderduyn S, Varhol R, Eaves C, Jones S, Holt R, Hirst M, Hoodless PA, Marra MA.Large scale production of SAGE libraries from microdissected tissues, flow-sorted cells and cell lines. Genome Research. 2007 Jan; 17(1) 108-116. Epub 2006 Nov 29.
201. Robertson N, Oveisi-Fordorei M, Zuyderduyn S, Varhol R, Fjell C, Marra MA, Jones SJM, Siddiqui AS. DiscoverySpace: an interactive data analysis application. Genome Biology. 2007 Jan 8;8(1):R6.
202. Quayle S, Hare H, Delaney A, Hwang D, Schein J, Jones S, Marco M, Sadar M. Novel expressed sequences identified in a model of androgen independent prostate cancer. BMC Genomics. 2007, 8:32.
203. Elnitski L, Jin VX, Farnham PJ, Jones SJM. Locating Mammalian Transcription Factor Binding Sites: A Survey of Computational and Experimental Techniques. Genome Research. 2006 Dec;16(12):1455-64. Epub 2006 Oct 19.
204. Lonergan K, Chari R, deLeeuw R, Shadeo A, Chi B, Tsao M-S, Jones S, Marra M, Ling V, Ng R, MacAulay C, Lam S, Lam W. Identification of novel lung genes in bronchial epithelium by serial analysis of gene expression. American Journal of Respiratory Cell and Molecular Biology. 2006, Dec, 235 (6): 651-61.
205. Wang G, Jones SJM, Marra MA, Sadar M. Identification of genes targeted by the androgen and PKA signaling pathways in prostate cancer cells. Oncogene. 2006, Nov. 25:7311-23.
206. Griffith OL, Melck A, Jones SJM, Wiseman SM. A Meta-analysis and Meta-review of Thyroid Cancer Gene Expression Profiling Studies Identifies Important Diagnostic Biomarkers. Journal of Clinical Investigation. 2006 Nov 1;24 (31):5043-51
207. Bainbridge M.N, Warren R.L, He A, Bilenky M, Robertson A.G, Jones S. THOR: Targeted High-throughput Ortholog Reconstructor. Bioinformatics. 2007 Oct 1;23(19):2622-4. 2006 Oct 11; [Epub ahead of print]
208. McLeod MP, Warren RL, Araki N, Hsiao WWL, Miyazawa D, Myhre M, Fernandes C, Morin RD, Wong W, Lillquist AL, Wang D, Petrescu A, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield Y, Siddiqui AS, Marra MA, Jones SJM, Holt R, Brinkman FSL, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. The complete genome of Rhodococcus sp. RHA1: insights into a catabolic powerhouse. Proceedings of the National Academy of Science. 2006 Oct 17;103(42):15582-7. Epub 2006 Oct 9
209. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delany A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJM. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006, Sept. 7:246.
210. Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Asano J, Bailey DK, Barber S, Birch P, Brown-John M, Cao M, Chan S, Charest DL, Farnoud N, Fernandes N, Flibotte S, Go A, Gibson WT, Holt RA, Jones SJM, Kennedy GC, Krzywinski M, Langlois S, Li HI, McGillivray BC, Nayar T, Pugh TJ, Rajcan-Separovic E, Schein JE, Schnerch A, Siddiqui A, Van Allen MI, Wilson G, Yong SL, Eydoux P, Marra MA. Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation. American Journal of Human Genetics. 2006 Sept. 79(3):500-13.
211. Quayle AP, Siddiqui AS, Jones SJM. Preferential perturbation and network topology. Physica A. 2006 Sept. 371, 823-840.
212. Tuskan G, DiFazio S, Bohlmann J, Grigoriev I, Hellsten U, Jansson S,. Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao R.R, Bhalerao R.P, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen G.-L, Cooper D, Coutinho P, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S,. Déjardin A, dePamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R,. Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé J, Locascio P, Luo Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson D.R., Nelson C, Nieminen K, Nilsson O, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A., Sterky F, Terry A, Tsai C, Uberbache E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray ex Brayshaw) Science. 2006 Sep 15; 313(5793):1596-604.
213. Bakkeren G, Jiang G, Warren RL, Butterfield Y, Shin H, Chiu R, Linning R, Schein J, Lee N, Hu G, Kupfer DM, Tang Y, Roe BA, Jones S, Marra M, Kronstad JW. Mating factor linkage and genome evolution in basidiomycetous pathogens of Cereals. Fungal Genetics & Biology. 2006 Sept 43: (9) 655-666.
214. Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YSN, Kirkpatrick R, Liu J, Jones SJM, Marra M, Douglas CJ, Ritland K, Bohlmann J. Conifer defence against insects: microarray gene expression profiling of Sitka spruce (Picea sitchensis) induced by mechanical wounding or feeding by spruce budworms (Choristoneura occidentalis) or white pine weevils (Pissodes strobi ) reveals large-scale changes of the host transcriptome. Plant, Cell and Environment . Aug (2006) 29, 1545–1570.
215. Gao BJ, Griffith OL, Ester M, Jones SJ. Discovering significant OPSM subspace clusters in massive gene expression data. Proceedings of the 12th ACM SIGKDD international Conference on Knowledge Discovery and Data Mining (Philadelphia, PA, USA, August 20 - 23, 2006). KDD '06. ACM Press, New York, NY, 922-928.
216. Siddiqui A, Delaney A, Schnerch A, Griffith O, Jones S, Marra M. Sequence biases in large scale gene expression profiling data. Nucleic Acids Research. 2006 Jul 13;34(12):e83.
217. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley III CP, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SK, Blakesley RW, Prange C, Myers RM, Green ED, Wagner K, Gerhard DS, Marra MA, Jones SJM, Holt RA. Sequencing and analysis of 10967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis. Genome Research. Jun 2006; 16: 796 – 803.
218. Quayle AP, Siddiqui AS, Jones SJM. Modeling network growth with assortative mixing. European Physical Journal B. 50(4), 617-630, 2006
219. Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang S-P, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AA, Marra MA, Wilson RK, Jones SJM. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Research. 2006 Jun.16 (6):768-775.
220. Ralph S, Oddy C, Cooper D, Yueh H, Jancsik S, Kolosova N, Philippe RN, Aeschliman D, White R, Huber D, Ritland CE, Benoit F, Rigby T, Nantel A, Butterfield YSN, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJM, Marra MA, Ellis BE, Douglas CJ, Ritland K, Bohlmann J. Genomics of hybrid poplar (Populus trichocarpa x deltoides) interacting with forest tent caterpillars (Malacosoma disstria): Normalized and full-length cDNA libraries, expressed sequence tags (ESTs), and a cDNA microarray for the study of insect-induced defenses in poplar. Molecular Ecology. Apr. 2006 15, 1275–1297.
221. Li YY, Jones SJM, Cherkasov A. Selective Targeting of Indel-Inferred Differences in Spatial Structures of Homologous Proteins. Journal of Bioinformatics and Computational Biology. 2006 Apr;4(2):403-14.
222. Ruzanov P, Jones SJ. An interactive tool for visualization of relationships between gene pression profiles. BMC Bioinformatics. 2006 Apr 6;7(1):193.
223. Sundaram B, Chapman BM, Li B, Mayo M, Siddiqui A, Jones S. Sun Grid Engine Package for OSCAR – A Google Summer of Code 2005 Project. Proceedings of 4th Annual OSCAR Symposium (OSCAR 2006).
224. Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ. ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics. 2006 Mar 1; 22(5):637-40.
225. Robertson G, Bilenky M., Lin K, He A, Yuen W, Dagpinar M, Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M., Sleumer MC, Pan W, Pleasance ED, Chuang M., Hao H, Li YY, Robertson N, Fjell C, Li B, Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS, Jones SJM. cisRED: A Database System for Genome Scale Computational Discovery of Regulatory Elements. Nucleic Acids Research. 2006 Jan 1;34(Database issue):D68-73.
226. Wilson GM, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG, Holt RA. Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Research. 2006 Feb;16(2):173-81.
227. Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BY-L, Lee LLC, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu A-L, Pandoh P, Riggins GJ, Ruiz de Algara T, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, MK Wu, Xie Y-Y, Yang G, Zhang I, Hirst M, Jones SJM, Helgason CD, Simpson EM, Hoodless PA, Marra MA. A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proceedings of the National Academy of Science. 2005 102: 18485-18490; published online before print December 13 2005, 10.1073/pnas.0509455102.
228. Cherkasov A, Shi Z, Li Y, Jones SM, Fallahi M, Hammond GL. ‘Inductive’ Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand. Chem Inf Model. 2005 Nov 28;45(6):1842-1853.
229. Larraya LM, Boyce K, So A, Steen BR, Jones S, Marra M, Kronstad J. Serial Analysis of Gene Expression Reveals Conserved Links between Protein Kinase A, Ribosome Biogenesis, and Phosphate Metabolism in Ustilago maydis. Eukaryot Cell. 2005 Dec;4(12):2029-43.
230. Griffith OL, Pleasance ED, Fulton DL, Oveisi M, Ester M, Siddiqui AS, Jones SJ. Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses. Genomics. 2005 Oct;86(4):476-488.
231. Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJ, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchell LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics. 2005 Oct;86(4):396-404.
232. Montgomery SB, Fu T, Guan J, Lin K, Jones SJM. An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs. Nature Methods. 2005 Aug;2(8):563.
233. Blacque OE, Perens EA, Boroevich KA, Inglis PA, Li C, Warner A, Khattra J, Holt RA, Ou G, Mah AK, McKay SJ, Huang P, Swoboda P, Jones SJM, Marra MA, Baillie DL, Moerman DG, Shaham S, Leroux MR. Functional genomics of the cilium, a sensory organelle. Current Biology. 2005 May 24;15(10):935-41.
234. Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJM. Management and visualization of whole genome shotgun assemblies using SAM. Biotechniques. 2005 May;38(5):715-6, 718, 720.
235. Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJM, Marra MA, Brooks-Wilson AR, Riddle DL. Analysis of Long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Research. 2005 May;15(5):603-15. Epub 2005 Apr 18.
236. Lian T, Simmer MI, D’Souza CA, Steen BR, Zuyderduyn SD, Jones SJ, Marra MA, Kronstad JW. Iron-regulated transcription and capsule formation in the fungal pathogen Cryptococcus neoformans. Molecular Microbiology. 2005 Mar: 55 (5): 1452-72.
237. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, Roder M, Finell J, Hantsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gonczy P, Coulson A, Hyman AA, Echeverri CJ. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature. 2005 Mar 24;434(7032):462-9. Citation: 139
238. Bajdik CD, Kuo B, Rusaw S, Jones S, Brooks-Wilson A. CGMIM: Automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes. BMC Bioinformatics. 2005 Mar 29;6(1):78.
239. Loftus B, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamethevan J, Miranda M, Anderson I, Fraser JA, Allen J, Bosdet I, Brent MR, Chiu R, Doering TL, Donlin, MJ, D’Souza C, Fox DS, Grinberg V, Fu J, Fukushima M, Haas B, Huang JC, Janbon G, Jones S, Krzywinski MI, Kwon-Chung J, Lengeler KB, Maiti R, Marra M, Marra RE, Mathewson C, Mitchell TG, Pertea M, Riggs F, Salzberg SL, Schein J, Shvartsbeyn, Shin H, Specht C, Suh B, Tenny A, Utterback T, Wickes BL, Wye N, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CW, Hyman RW. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science. 2005 Feb 25;307(5713):1321-4. Epub 2005 Jan 13. Citation: 111
240. Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Research. 2005 Feb;15(2):302-11.
241. Sander J, Ng R, Sleumer MC, Yuen MS, Jones S. A Methodology for Analyzing SAGE Libraries For Cancer Profiling. ACM Transactions on Information and Systems. 2005 Jan; 23(1)35-60.
242. Hirst M, Astell C, Griffith M, Coughlin SM, Moksa M, Zeng T, Smailus DE, Holt RA, Jones S, Marra MA, Petric M, Krajden M, Lawrence D, Mak A, Chow R, Skowronski DM, Tweed A, Goh S, Brunham RC, Robinson J, Bowes V, Sojonky K, Byrne SK, Paetzel M. A novel avian influenza H7N3 strain associated with an Avian Influenza Outbreak in British Columbia. Emerging Infectious Diseases. 2004 Dec;10(12):2192-2195.
243. Warren R, Hsiao WW, Kudo H, Myhre M, Donsanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Holt R, Jones S, Mohn WW, Brinkman FSL, Fukuda M, Davies J, Eltis LD. Functional Characterization of a Catabolic Plasmid from PCB-Degrading Rhodococcus sp. RHA1. J Bacteriol. 2004 Nov;186(22):7783-95.
244. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40.
245. The MGC Project Team. The Status, Quality and Expansion of the NIH Full-length cDNA project (MGC). Genome Research. 2004 Oct;14(10B):2121-7.
246. Baross A, Butterfield Y, Coughlin S, Zeng T, Griffith M, Griffith O, Petrescu A, Smailus D, Khattra J, McDonald H, McKay S, Moksa M, Siddiqui A, Jones S, Holt R, Marra M. Systematic Recovery and Analysis of Full-ORF Human cDNA Clones. Genome Research. 2004 Oct 14;(10B):2003-2092
247. Cherkasov A, Ho Sui SJ, Brunham RC, Jones SJ. Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics. BMC Bioinformatics. 2004 Jul 26;5(1):101.
248. Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Tsai M, Albertson D, Lam W, Choy C-O, Osoegawa K, Zhao S, de Jong P, Schein J, Jones S, Marra M. A Set of BAC Clones Spanning the Human Genome. Nucleic Acid Research. 2004 Jul 9; 32(12):3651-60.
249. Cherkasov AR, Jones SJ. An approach to large scale identification of non-obvious structural similarities between proteins. BMC Bioinformatics. 2004 May 17;5(1):61.
250. Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson G, Sleumer M, Siddiqui AS, Jones SJM. Sockeye: A 3D Environment for Comparative Genomics. Genome Research. 2004 May; 14(5):956-62.
251. MacAulayC, Lonergan K, Chi B, Zuyderduyn S, Schein J, Tsao M, LeRiche J, Jones S, Marra M, Lam S, Lam WL. Serial analysis of gene expression profiles of developmental stages in no-small cell lung carcinoma. Chest, 2004 May: 125 (5 Suppl): 97S
252. Krzywinski M, Wallis J, Gösele C, Bosdet I, Chiu R, Graves T, Hummel O, Layman D, Mathewson C, Wye N, Zhu B, Albracht D, Asano J, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Davito J, Fjell C, Gaige T, Ganten D, Girn N, Guggenheimer K, Himmelbauer H, Kreitler T, Leach S, Lee D, Lehrach H, Mayo M, Mead K, Olson T, Pandoh P, Prabhu A-L, Shin H, Tänzer S, Thompson J, Tsai M, Walker J, Yang G, Sekhon M, Hillier L, Zimdahl H, Marziali A, Osoegawa K, Zhao S, Siddiqui A, de Jong, P, Warren W, Mardis E, McPherson J, Wilson R, Hűbner N, Jones S, Marra M, Schein J. Integrated and Sequence-Ordered BAC and YAC-based Physical Maps for the Rat Genome. Genome Research. 2004 Apr;14(4):766-79.
253. Cherkasov AR, Jones SJ. Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinformatics. 2004 Apr 3;5(1):37.
254. The Rat Genome Project Consortium. Genome Sequence of the Brown Norway Rat Yields Insights into Mammalian Evolution. Nature. 2004. Apr 1;428(6982):493-521.
255. Baross A, Schertzer M, Zuyderduyn SD, Jones SJM, Marra MA, Lansdorp PL. Effect of TERT and ATM on gene expression profiles in human fibroblasts. Genes Chromosomes Cancer. 2004 Apr;39(4):298-310.
256. Rise ML, von Schalburg KR, Brown GD, Mawer, MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SRM, Smailus DE, Jones SJM, Schein J, Marra MA, Butterfield YSN, Stott J, Ng SHS, Davidson WS, Koop BF. Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics. Genome Research, 2004 March:14:478-490. Citation: 92
257. McKay SJ, Johnsen R, Khattra J, Asano J, Baillie DL, Chan S, Dube N, Fang L, Goszczynski B, Ha E, Halfnight E, Hollebakken R, Huang P, Hung K, Jensen V, Jones SJM, Kai H, Li D, Mah A, Marra M, McGhee J, Newbury R, Pouzyrev A, Riddle DL, Sonnhammer E, Tian H, Tu D, Tyson JR, Vatcher G, Warner A, Wong K, Zhao Z, and Moerman DG. Gene Expression Profiling of Cells, Tissues and Developmental Stages of the Nematode c. elegans. Cold Spring Harbor Symposia on Quantitative Biology. 2004 Jan: 159-169. Citation: 40
258. Steen BR, Zuyderduyn S, Toffaletti DL, Marra M, Jones SJM, Perfect JR, Kronstad J. Analysis of Cryptococcus neoformans gene expression during experimental cryptococcal meningitis. Eukaryot Cell. 2003 Dec;2(6):1336-49.
259. Kiger AA, Baum B, Jones S, Jones MR, Coulson A, Echeverri C, Perrimon N. A functional genomic analysis of cell morphology using RNA interference. Journal of Biology. 2003;2(4):27.
260. Pleasance ED, Marra MA, Jones SJM. Assessment of SAGE in transcript identification. Genome Research. 2003;June13(6A):1203-15.
261. Fjell CD, Bosdet I, Schein JE, Jones SJM, Marra MA. Internet Contig Explorer (iCE) - A tool for visualizing clone fingerprint maps. Genome Research. 2003 June;13(6A):1244-9.
262. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL. The genome sequence of the SARS-associated coronavirus. Science. 2003 May 30;300(5624):1399-1404. Citation: 772
263. Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJM, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Research, 2003 May; 13(5):940-53.
264. Gorski SM, Chittaranjan S, Pleasance ED, Freeman JD, Anderson CL, Varhol RJ, Coughlin SM, Jones SJM, Marra MA. A SAGE Approach to Discovery of Genes Involved in Autophagic Cell Death. Current Biology. 2003 Feb 18;13(4):358-63. Citation: 50
265. Phan J, Ng R, Yuen M, Jones S. GEA: a Toolkit for Gene Expression Analysis. Proceedings of 2002 ACM SIGMOD, 2002: 628. (Longer version appears in: Proceedings of BIOKDD 2002 Workshop on Data Mining in Bioinformatics, August 2002.)
266. Hsiao W, Wan I, Jones SJ, Brinkman FSL. IslandPath: Aiding detection of genomic islands in prokaryotes. Bioinformatics. 2002; 19(3):418-420.
267. Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the Nationall Academy of Science USA. 2002 Dec 24;99(26):16899-903. Citation: 600
268. McKay SJ, Jones SJM. AcePrimer: automation of PCR primer design based on gene structure. Bioinformatics. 2002; 18(0):1-2.
269. Guiliano DB, Hall N, Jones SJM, Clark LN, Corton CH, Barrell BG, Blaxter ML. Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biology. 2002; 3(10): research0057.1-0057.14.
270. Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR. A physical map of the mouse genome. Nature. 2002; 418(6899):743-50.
271. Vatcher G, Smailus D, Krzywinski M, Guin R, Stott J, Tsai M, Chan S, Pandoh P, Yang G, Asano J, Olson T, Prabhu A, Coope R, Marziali A, Schein J, Jones S, Marra M. Resuspension of DNA sequencing reaction products in agarose increases sequence quality on the MegaBACE 1000 automated sequencer. Biotechniques. 2002; 33(3):532-539.
272. Brinkman FSL, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BFF, Keeling PJ, Hancock REW, Rose AM, Jones SJM. Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria and the chloroplast. Genome Research. 2002; 12(8):1159-1167.
273. Mattman A, Huntsman D, Lockitch G, Langlois S, Buskard N, Ralston D, Butterfield Y, Rodrigues P, Jones S, Porto G, Marra M, De Sousa M, Vatcher G. Transferrin Receptor 2 (TFR2) and HFE Mutational Analysis in Non-C282Y Iron Overload:Identification of a Novel TfR2 mutation associated with Iron Overload and Leukopenia. Blood. 2002; 100(3):1075-7.
274. Steen BR, Lian T, Zuyderduyn S, MacDonald K, Marra M, Jones SJM, Kronstad JW. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Research. 2002; 12(9):1386-400.
275. Schein J, Tangen K, Chiu R, Shin H, Lengeler KB, MacDonald K, Bosdet I, Heitman J, Jones SJM, Marra M, Kronstad JW. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Research. 2002 Sep;12(9):1445-53.
276. Butterfield YSN, Marra MA, Chan SY, Guin R, Kryzwinski MI, Lee SS, MacDonald KWK, Mathewson CA, Olson TE, Pandoh PK, Prabhu A, Schnerch A, Skalska U, Smailus DE, Stott JM, Tsai MI, Yang GS, Zuyderduyn SD, Schein JE, Jones SJM. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Research. 2002 Jun 1; 30(11):2460-2468.
277. Shevchenko Y, Bouffard GG, Butterfield YSN, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJM, Touchman JW, Green ED. Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Research. 2002 Jun 1;30(11):2469-2477.
278. Ness SR, Terpstra W, Krzywinski M, Marra MA, Jones SJM. Assembly of fingerprint contigs: parallelized FPC. Bioinformatics. 2002 Mar;18(3):484-485.
279. Jones SJM, Riddle DL, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, Stricklin SL, Baillie DL, Waterston R, Marra MA. Changes in gene expression associated with developmental arrest and longevity in C. elegans. Genome Research. 2001; 11:1346-1352. Citation: 78
280. Brinkman FSL, Wan I, Hancock REW, Rose AM, Jones SJ. PhyloBLAST: A tool facilitating phylogenetic analysis of BLAST results. Bioinformatics. 2001; 17(4):385-387.
281. McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, Fulton R, Kucaba TA, Wagner-McPherson C, Barbazuk WB, Gregory SG, Humphray SJ, French L, Evans RS, Bethel G, Whittaker A, Holden JL, McCann OT, Dunham A, Soderlund C, Scott CE, Bentley DR, Schuler G, Chen HC, Jang W, Green ED, Idol JR, Maduro VV, Montgomery KT, Lee E, Miller A, Emerling S, Kucherlapati, Gibbs R, Scherer S, Gorrell JH, Sodergren E, Clerc-Blankenburg K, Tabor P, Naylor S, Garcia D, de Jong PJ, Catanese JJ, Nowak N, Osoegawa K, Qin S, Rowen L, Madan A, Dors M, Hood L, Trask B, Friedman C, Massa H, Cheung VG, Kirsch IR, Reid T, Yonescu R, Weissenbach J, Bruls T, Heilig R, Branscomb E, Olsen A, Doggett N, Cheng JF, Hawkins T, Myers RM, Shang J, Ramirez L, Schmutz J, Velasquez O, Dixon K, Stone NE, Cox DR, Haussler D, Kent WJ, Furey T, Rogic S, Kennedy S, Jones S, Rosenthal A, Wen G, Schilhabel M, Gloeckner G, Nyakatura G, Siebert R, Schlegelberger B, Korenberg J, Chen XN, Fujiyama A, Hattori M, Toyoda A, Yada T, Park HS, Sakaki Y, Shimizu N, Asakawa S, Kawasaki K, Sasaki T, Shintani A, Shimizu A, Shibuya K, Kudoh J, Minoshima S, Ramser J, Seranski P, Hoff C, Poustka A, Reinhardt R, Lehrach H. A physical map of the human genome. Nature. 2001; 409:934-941.
282. Gönczy P, Echeverri C, Oegema K, Coulson A, Jones SJM, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Özlü N, Bork P, Hyman AA. Functional genomic screen of cell division processes in C. elegans using RNAi: analysis of chromosome III. Nature. 2000; 408(6810):331-336. Citation: 441
283. Reinke V, Smith HE, Nance J, Wang J, Van Doren C, Begley R, Jones SJ, Davis EB, Scherer S, Ward S, Kim SK. A global profile of germline expression in C. elegans. Molecular Cell. 2000; 6(3):605-616.
284. de Koning AP, Brinkman F, Jones S, Keeling PJ. Evidence of a Laterally Transferred Gene in Trichomonas vaginalis. Molecular Biology and Evolution. 2000; 17(11):1769-1773.
285. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Zhong F, Zhong W, Gibbs R, Venter JC, Adams MD, Lewis S. Comparative genomics of the eukaryotes. Science. 2000; 287(5461):2204-2215. Citation: 756>
286. Johnsen R, Jones SJM, Rose A. Mutational accessibility of essential genes on chromasome l(left) in Caenorhabditis elegans. Molecular & General Genetics. 2000; 263(2):239-252.
287. Simmen MW, Leitgeb S, Charlton J, Jones SJ, Harris BR, Clark VH, Bird A. Nonmethylated transposable elements and methylated genes in a chordate genome. Science. 1999; 283(5405):1164-1167. Citation: 54
288. The C. elegans Sequencing Consortium. How the worm was won: The C. elegans Sequencing Project. Trends in Genetics. 1999; 15:51-58.
289. The C. elegans Sequencing Consortium. Genome Sequence of the Nematode C. elegans: A platform for Investigating Biology. Science. 1998; 282(5396):2012-2018.
290. Simmen MW, Leitgeb S, Clark VH, Jones SJ, Bird A. Gene number in an invertebrate chordate, Ciona intestinalis. Proceedings of the National Academy of Science USA. 1998 Apr 14;95(8):4437-40. Citation: 88
291. van Wageningen AM, Kirkpatrick PN, Williams DH, Harris BR, Kershaw JK, Lennard NJ, Jones M, Jones SJ, Solenberg PJ. Sequencing and analysis of genes involved in the biosynthesis of a vancomycin group antibiotic. Chemical Biology. 1998; 3:155-62. Citation: 148
292. Jones SJM. An update and lessons from whole genome sequencing projects. Current Opinions in Genetics and Development. 1995; 5:349-353.
293. Jones SJM, Baillie DL. Characterisation of the let-653 gene in Caenorhabditis elegans. Molecular and General Genetics. 1995; 248:719-726.

Book Chapters and Review Articles

1. Li YY, Jones SJ. Drug repositioning for personalized medicine. Genome Med. 2012 Mar 30;4(3):27.
2. Kasaian K, Jones SJ. A new frontier in personalized cancer therapy: mapping molecular changes. Future Oncol. 2011 Jul;7(7):873-94. Review.
3. Montgomery SB, Kasaian K, Jones SJ, Griffith OL. Annotating the regulatory genome. Methods Mol Biol. 2010. 674: p. 313-49. Review.
4. Griffith Ol, Melck A, Jones SJM, Wiseman SM. Thyroid Cancer: Identification of Gene Expression Markers for Diagnosis. Methods of Cancer Diagnosis, Therapy and Prognosis. Hyat MA, editor, Springer Publishing Company, New York, NY. 7(3):353-377, DOI: 10.1007/978-90-481-3186-0_24. Published: January 3, 2010.
5. Hoffman BG, Jones SJM. Genome-wide identification of DNA-protein interactions using Chromatin Immunoprecipitatio coupled with flow cell Sequencing. Journal of Endocrinology. 2009 Jan: 201,1-13.
6. Fejes AP, Jones SJM. Chapter contribution to "Next generation genome sequencing – toward personalized medicine" Wiley-VCH. Ed. Janitz. 978-3-527-32090-5. Published Oct. 2008.
7. Griffith OL, Chiu CG, Gown AM, Jones SJ, Wiseman SM. Biomarker panel diagnosis of thyroid cancer: a critical review. Expert Rev Anticancer Ther. 2008 Sep;8(9):1399-413.
8. Holt RA, Jones SJM. The new paradigm of flow cell sequencing. Genome Research. Invited review article. 2008 Jun;18(6):839-46
9. Jones SJM. "Prediction of Genomic Functional Elements." Annual Review of Genomics and Human Genetics: Vol 7. 2006;7:315-38.
10. Pleasance ED, Jones SJM. "Evaluation of SAGE tags for transcriptome study". SAGE Technologies: Current Technologies and Applications.Ed San Ming Wang. Norwich, UK: Horizon Bioscience, 2005.
11. Siddiqui A, Jones S. "Contig Mapping and Analysis." Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Ed. A Kuspa. Chichester, UK: John Wiley & Sons, Ltd, 2004.
12. Astell CR, Holt RA, Jones SJM, Marra MA. "Genome Organization and Structural Aspects of the SARS-related Virus." Birkhauser Advances in Infectious Diseases: Vol I. Eds A. Schmidt, M.H. Wolff, S.H.E. Kaufman. Basel, CHE: Birkhauser, 2004. 101-128pp.
13. Bird D, Opperman CH, Jones SJM, Baillie DL. "The Caenorhabditis elegans genome: A guide in the post genomics age." Annual Review of Phytopathology: Vol 37. Palo Alto, CA, 1999. 247-265pp.
14. Jones SJM, Hodgson D. "Internet resources for invertebrates." Internet for the Molecular Biologist. Eds S.R. Swindell, R.R. Miller, G.S.A. Myers. Norwich, UK: Horizon Scientific Press, 1996.2