Steven Jm Jones

InstitutionCanadian COVID Genomics Network
AddressCanada
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    Publication Timeline
    COVID-19 publications
    Bar chart showing 1 Covid-19 publications, with a maximum of 1 publications in July 2021
    All Publications
    Bar chart showing 221 publications over 19 distinct years, with a maximum of 18 publications in 2011
    These graphs show COVID-19 publications by month since August 2019 and all publications written by authors of COVID-19 publications over the past 30 years.

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    Publication Field Summary
    This graph shows the number and percent of publications by field. Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications. Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written. To see the data as text, click here.
    Publication List
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Citations: 14     Fields:    Translation:Humans
    2. Reisle C, Mungall KL, Choo C, Paulino D, Bleile DW, Muhammadzadeh A, Mungall AJ, Moore RA, Shlafman I, Coope R, Pleasance S, Ma Y, Jones SJM. MAVIS: merging, annotation, validation, and illustration of structural variants. Bioinformatics. 2019 02 01; 35(3):515-517. PMID: 30016509.
      Citations: 8     Fields:    Translation:HumansCells
    3. Jackman SD, Coombe L, Chu J, Warren RL, Vandervalk BP, Yeo S, Xue Z, Mohamadi H, Bohlmann J, Jones SJM, Birol I. Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinformatics. 2018 Oct 26; 19(1):393. PMID: 30367597.
      Citations: 21     Fields:    Translation:HumansCells
    4. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 10 01; 9(1):4001. PMID: 30275490.
      Citations: 40     Fields:    Translation:HumansCells
    5. Thibodeau ML, Reisle C, Zhao E, Martin LA, Alwelaie Y, Mungall KL, Ch'ng C, Thomas R, Ng T, Yip S, Lim H, Sun S, Young SS, Karsan A, Zhao Y, Mungall AJ, Moore RA, Renouf D, Gelmon K, Ma YP, Hayes M, Laskin J, Marra MA, Schrader KA, Jones SJM. Corrigendum: Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma. Cold Spring Harb Mol Case Stud. 2018 08; 4(4). PMID: 30068734.
      Citations:    Fields:    
    6. Ronsley R, Rassekh SR, Shen Y, Lee AF, Jantzen C, Halparin J, Albert C, Hawkins DS, Amed S, Rothstein R, Mungall AJ, Dix D, Blair G, Nadel H, Jones SJM, Laskin J, Marra MA, J Deyell R. Application of genomics to identify therapeutic targets in recurrent pediatric papillary thyroid carcinoma. Cold Spring Harb Mol Case Stud. 2018 04; 4(2). PMID: 29610391.
      Citations: 5     Fields:    Translation:Humans
    7. Owen DR, Wong HL, Bonakdar M, Jones M, Hughes CS, Morin GB, Jones SJM, Renouf DJ, Lim H, Laskin J, Marra M, Yip S, Schaeffer DF. Molecular characterization of ERBB2-amplified colorectal cancer identifies potential mechanisms of resistance to targeted therapies: a report of two instructive cases. Cold Spring Harb Mol Case Stud. 2018 04; 4(2). PMID: 29438965.
      Citations: 3     Fields:    Translation:HumansCells
    8. Thibodeau ML, Bonakdar M, Zhao E, Mungall KL, Reisle C, Zhang W, Bye MH, Thiessen N, Bleile D, Mungall AJ, Ma YP, Jones MR, Renouf DJ, Lim HJ, Yip S, Ng T, Ho C, Laskin J, Marra MA, Schrader KA, Jones SJM. Whole genome and whole transcriptome genomic profiling of a metastatic eccrine porocarcinoma. NPJ Precis Oncol. 2018; 2(1):8. PMID: 29872726.
      Citations: 2     
    9. Merk DJ, Ohli J, Merk ND, Thatikonda V, Morrissy S, Schoof M, Schmid SN, Harrison L, Filser S, Ahlfeld J, Erkek S, Raithatha K, Andreska T, Weißhaar M, Launspach M, Neumann JE, Shakarami M, Plenker D, Marra MA, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJM, Lutz B, Ertl-Wagner B, Rossi A, Wagener R, Siebert R, Jung A, Eberhart CG, Lach B, Sendtner M, Pfister SM, Taylor MD, Chavez L, Kool M, Schüller U. Opposing Effects of CREBBP Mutations Govern the Phenotype of Rubinstein-Taybi Syndrome and Adult SHH Medulloblastoma. Dev Cell. 2018 03 26; 44(6):709-724.e6. PMID: 29551561.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    10. Feau N, Beauseigle S, Bergeron MJ, Bilodeau GJ, Birol I, Cervantes-Arango S, Dhillon B, Dale AL, Herath P, Jones SJM, Lamarche J, Ojeda DI, Sakalidis ML, Taylor G, Tsui CKM, Uzunovic A, Yueh H, Tanguay P, Hamelin RC. Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. PeerJ. 2018; 6:e4392. PMID: 29492338.
      Citations: 4     
    11. Lever J, Gakkhar S, Gottlieb M, Rashnavadi T, Lin S, Siu C, Smith M, Jones MR, Krzywinski M, Jones SJM, Wren J. A collaborative filtering-based approach to biomedical knowledge discovery. Bioinformatics. 2018 02 15; 34(4):652-659. PMID: 29028901.
      Citations: 7     Fields:    
    12. Wong HL, Yang KC, Shen Y, Zhao EY, Loree JM, Kennecke HF, Kalloger SE, Karasinska JM, Lim HJ, Mungall AJ, Feng X, Davies JM, Schrader K, Zhou C, Karsan A, Jones SJM, Laskin J, Marra MA, Schaeffer DF, Gorski SM, Renouf DJ. Molecular characterization of metastatic pancreatic neuroendocrine tumors (PNETs) using whole-genome and transcriptome sequencing. Cold Spring Harb Mol Case Stud. 2018 02; 4(1). PMID: 29092957.
      Citations: 15     Fields:    Translation:HumansCells
    13. Velazquez-Torres G, Shoshan E, Ivan C, Huang L, Fuentes-Mattei E, Paret H, Kim SJ, Rodriguez-Aguayo C, Xie V, Brooks D, Jones SJM, Robertson AG, Calin G, Lopez-Berenstein G, Sood A, Bar-Eli M. A-to-I miR-378a-3p editing can prevent melanoma progression via regulation of PARVA expression. Nat Commun. 2018 01 31; 9(1):461. PMID: 29386624.
      Citations: 21     Fields:    Translation:HumansAnimalsCells
    14. Lee JJY, Gottlieb MM, Lever J, Jones SJM, Blau N, van Karnebeek CDM, Wasserman WW. Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis. J Inherit Metab Dis. 2018 05; 41(3):555-562. PMID: 29340838.
      Citations:    Fields:    Translation:Humans
    15. Zhao EY, Shen Y, Pleasance E, Kasaian K, Leelakumari S, Jones M, Bose P, Ch'ng C, Reisle C, Eirew P, Corbett R, Mungall KL, Thiessen N, Ma Y, Schein JE, Mungall AJ, Zhao Y, Moore RA, Den Brok W, Wilson S, Villa D, Shenkier T, Lohrisch C, Chia S, Yip S, Gelmon K, Lim H, Renouf D, Sun S, Schrader KA, Young S, Bosdet I, Karsan A, Laskin J, Marra MA, Jones SJM. Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer. Clin Cancer Res. 2017 Dec 15; 23(24):7521-7530. PMID: 29246904.
      Citations: 48     Fields:    Translation:Humans
    16. Jones SJ, Haulena M, Taylor GA, Chan S, Bilobram S, Warren RL, Hammond SA, Mungall KL, Choo C, Kirk H, Pandoh P, Ally A, Dhalla N, Tam AKY, Troussard A, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Jones SJM. The Genome of the Northern Sea Otter (Enhydra lutris kenyoni). Genes (Basel). 2017 Dec 11; 8(12). PMID: 29232880.
      Citations: 6     Fields:    
    17. Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA, Bilobram S, Mordecai G, Suttle CA, Miller KM, Schulze A, Chan AM, Jones SJ, Tse K, Li I, Cheung D, Mungall KL, Choo C, Ally A, Dhalla N, Tam AKY, Troussard A, Kirk H, Pandoh P, Paulino D, Coope RJN, Mungall AJ, Moore R, Zhao Y, Birol I, Ma Y, Marra M, Haulena M. The Genome of the Beluga Whale (Delphinapterus leucas). Genes (Basel). 2017 Dec 11; 8(12). PMID: 29232881.
      Citations: 9     Fields:    
    18. Grewal JK, Eirew P, Jones M, Chiu K, Tessier-Cloutier B, Karnezis AN, Karsan A, Mungall A, Zhou C, Yip S, Tinker AV, Laskin J, Marra M, Jones SJM. Detection and genomic characterization of a mammary-like adenocarcinoma. Cold Spring Harb Mol Case Stud. 2017 Nov; 3(6). PMID: 28877932.
      Citations: 4     Fields:    Translation:HumansCells
    19. Yakovenko O, Jones SJM. Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations. J Comput Aided Mol Des. 2018 01; 32(1):299-311. PMID: 29134430.
      Citations: 1     Fields:    Translation:HumansCells
    20. Chang EY, Novoa CA, Aristizabal MJ, Coulombe Y, Segovia R, Chaturvedi R, Shen Y, Keong C, Tam AS, Jones SJM, Masson JY, Kobor MS, Stirling PC. RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability. J Cell Biol. 2017 12 04; 216(12):3991-4005. PMID: 29042409.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    21. Mazor T, Chesnelong C, Pankov A, Jalbert LE, Hong C, Hayes J, Smirnov IV, Marshall R, Souza CF, Shen Y, Viswanath P, Noushmehr H, Ronen SM, Jones SJM, Marra MA, Cairncross JG, Perry A, Nelson SJ, Chang SM, Bollen AW, Molinaro AM, Bengtsson H, Olshen AB, Weiss S, Phillips JJ, Luchman HA, Costello JF. Clonal expansion and epigenetic reprogramming following deletion or amplification of mutant IDH1. Proc Natl Acad Sci U S A. 2017 10 03; 114(40):10743-10748. PMID: 28916733.
      Citations: 46     Fields:    Translation:HumansCells
    22. Hasan NA, Warren RL, Epperson LE, Malecha A, Alexander DC, Turenne CY, MacMillan D, Birol I, Pleasance S, Coope R, Jones SJM, Romney MG, Ng M, Chan T, Rodrigues M, Tang P, Gardy JL, Strong M. Complete Genome Sequence of Mycobacterium chimaera SJ42, a Nonoutbreak Strain from an Immunocompromised Patient with Pulmonary Disease. Genome Announc. 2017 Sep 14; 5(37). PMID: 28912319.
      Citations: 2     
    23. Thibodeau ML, Peters CH, Townsend KN, Shen Y, Hendson G, Adam S, Selby K, Macleod PM, Gershome C, Ruben P, Jones SJM, Friedman JM, Gibson WT, Horvath GA. Compound heterozygous TRPV4 mutations in two siblings with a complex phenotype including severe intellectual disability and neuropathy. Am J Med Genet A. 2017 Nov; 173(11):3087-3092. PMID: 28898540.
      Citations: 4     Translation:Humans
    24. Thibodeau ML, Reisle C, Zhao E, Martin LA, Alwelaie Y, Mungall KL, Ch'ng C, Thomas R, Ng T, Yip S, J Lim H, Sun S, Young SS, Karsan A, Zhao Y, Mungall AJ, Moore RA, J Renouf D, Gelmon K, Ma YP, Hayes M, Laskin J, Marra MA, Schrader KA, Jones SJM. Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma. Cold Spring Harb Mol Case Stud. 2017 Sep; 3(5). PMID: 28514723.
      Citations: 4     Fields:    Translation:HumansCells
    25. Siu C, Wiseman S, Gakkhar S, Heravi-Moussavi A, Bilenky M, Carles A, Sierocinski T, Tam A, Zhao E, Kasaian K, Moore RA, Mungall AJ, Walker B, Thomson T, Marra MA, Hirst M, Jones SJM. Characterization of the human thyroid epigenome. J Endocrinol. 2017 Nov; 235(2):153-165. PMID: 28808080.
      Citations: 4     Fields:    Translation:HumansCells
    26. Tech K, Tikunov AP, Farooq H, Morrissy AS, Meidinger J, Fish T, Green SC, Liu H, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJM, Marra MA, Vander Heiden MG, Taylor MD, Macdonald JM, Gershon TR. Pyruvate Kinase Inhibits Proliferation during Postnatal Cerebellar Neurogenesis and Suppresses Medulloblastoma Formation. Cancer Res. 2017 06 15; 77(12):3217-3230. PMID: 28515149.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    27. Morrissy AS, Cavalli FMG, Remke M, Ramaswamy V, Shih DJH, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DTW, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka JT, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJM, Das S, Malkin D, Jabado N, Marra MA, Taylor MD. Spatial heterogeneity in medulloblastoma. Nat Genet. 2017 May; 49(5):780-788. PMID: 28394352.
      Citations: 45     Fields:    Translation:HumansCells
    28. Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Coarfa C, Ma Y, Moore RA, Schein JE, Mungall AJ, Liu J, Pecot CV, Sood AK, Jones SJ, Marra MA, Gunaratne PH. Correction: miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget. 2017 03 07; 8(10):17406. PMID: 28403581.
      Citations: 2     Fields:    
    29. Segovia R, Shen Y, Lujan SA, Jones SJ, Stirling PC. Hypermutation signature reveals a slippage and realignment model of translesion synthesis by Rev3 polymerase in cisplatin-treated yeast. Proc Natl Acad Sci U S A. 2017 03 07; 114(10):2663-2668. PMID: 28223526.
      Citations: 8     Fields:    Translation:AnimalsCells
    30. Cohen AS, Tuysuz B, Shen Y, Bhalla SK, Jones SJ, Gibson WT. Corrigendum: A novel mutation in EED associated with overgrowth. J Hum Genet. 2017 Feb; 62(2):341-342. PMID: 28119537.
      Citations:    Fields:    
    31. 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 01; 24(1):53-69. PMID: 27872141.
      Citations: 14     Fields:    Translation:HumansCells
    32. Pellacani D, Bilenky M, Kannan N, Heravi-Moussavi A, Knapp DJHF, Gakkhar S, Moksa M, Carles A, Moore R, Mungall AJ, Marra MA, Jones SJM, 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 11 15; 17(8):2060-2074. PMID: 27851968.
      Citations: 38     Fields:    Translation:HumansCells
    33. 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 11; 6(11). PMID: 27906134.
      Citations: 12     Fields:    Translation:HumansCells
    34. 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 Dec; 10:85-88. PMID: 27752469.
      Citations: 11     
    35. 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; 11(9):e0163059. PMID: 27632164.
      Citations: 9     Fields:    Translation:AnimalsCells
    36. Younesy H, Nielsen CB, Lorincz MC, Jones SJ, Karimi MM, Möller T. ChAsE: chromatin analysis and exploration tool. Bioinformatics. 2016 11 01; 32(21):3324-3326. PMID: 27378294.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    37. 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 05 10; 9(1):52. PMID: 27164903.
      Citations: 20     Fields:    Translation:AnimalsCells
    38. Pan Y, Robertson G, Pedersen L, Lim E, Hernandez-Herrera A, Rowat AC, Patil SL, Chan CK, Wen Y, Zhang X, Basu-Roy U, Mansukhani A, Chu A, Sipahimalani P, Bowlby R, Brooks D, Thiessen N, Coarfa C, Ma Y, Moore RA, Schein JE, Mungall AJ, Liu J, Pecot CV, Sood AK, Jones SJ, Marra MA, Gunaratne PH. miR-509-3p is clinically significant and strongly attenuates cellular migration and multi-cellular spheroids in ovarian cancer. Oncotarget. 2016 May 03; 7(18):25930-48. PMID: 27036018.
      Citations: 22     Fields:    Translation:HumansCells
    39. 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. PMID: 27094764.
      Citations: 18     Fields:    Translation:HumansCells
    40. 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, Våge DI, 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 05 12; 533(7602):200-5. PMID: 27088604.
      Citations: 269     Fields:    Translation:AnimalsCells
    41. 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. PMID: 27366170.
      Citations: 2     
    42. Chun HE, Lim EL, Heravi-Moussavi A, Saberi S, Mungall KL, Bilenky M, Carles A, Tse K, Shlafman I, Zhu K, Qian JQ, Palmquist DL, 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.
      Citations: 45     Fields:    Translation:HumansCells
    43. 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. PMID: 27148585.
      Citations: 4     Fields:    
    44. 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 08; 8(1):29-41. PMID: 26645680.
      Citations: 14     Fields:    Translation:AnimalsCells
    45. Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res. 2016 Jan 04; 44(D1):D126-32. PMID: 26578589.
      Citations: 48     Fields:    Translation:Cells
    46. 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 Dec 15; 142(24):4340-50. PMID: 26525672.
      Citations: 23     Fields:    Translation:AnimalsCells
    47. 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 Dec; 100(12):E1512-22. PMID: 26485220.
      Citations: 3     Fields:    Translation:HumansCells
    48. Younesy H, Möller T, Lorincz MC, Karimi MM, Jones SJ. VisRseq: R-based visual framework for analysis of sequencing data. BMC Bioinformatics. 2015; 16 Suppl 11:S2. PMID: 26328469.
      Citations: 17     Fields:    Translation:AnimalsCells
    49. 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. PMID: 26204903.
      Citations: 4     Fields:    Translation:AnimalsCells
    50. 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-ß pathway genes through formation of RNA-DNA triplex structures. Nat Commun. 2015 Jul 24; 6:7743. PMID: 26205790.
      Citations: 219     Fields:    Translation:HumansCells
    51. Warren RL, Keeling CI, Yuen MM, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, 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 Jul; 83(2):189-212. PMID: 26017574.
      Citations: 54     Fields:    Translation:AnimalsCells
    52. 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.
      Citations: 3     Fields:    Translation:Humans
    53. 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; 10(3):e0119689. PMID: 25798586.
      Citations: 19     Fields:    Translation:Humans
    54. Cohen AS, Tuysuz B, Shen Y, Bhalla SK, Jones SJ, Gibson WT. A novel mutation in EED associated with overgrowth. J Hum Genet. 2015 Jun; 60(6):339-42. PMID: 25787343.
      Citations: 24     Fields:    Translation:Humans
    55. 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; discussion 889. PMID: 25852009.
      Citations: 4     Fields:    Translation:HumansCells
    56. 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. PMID: 25690954.
      Citations: 25     Fields:    Translation:HumansCells
    57. 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, Robertson AG, 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.
      Citations: 84     Fields:    Translation:HumansAnimalsCells
    58. Li-Chang HH, Kasaian K, Ng Y, Lum A, Kong E, Lim H, Jones SJ, 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 06; 15:32. PMID: 25656989.
      Citations: 13     Fields:    Translation:Humans
    59. 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.
      Citations: 7     Fields:    Translation:HumansCells
    60. 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; 13:167-77. PMID: 25506199.
      Citations: 4     
    61. De La Torre AR, Birol I, Bousquet J, Ingvarsson PK, Jansson S, Jones SJ, Keeling CI, MacKay J, Nilsson O, Ritland K, Street N, Yanchuk A, Zerbe P, Bohlmann J. Insights into conifer giga-genomes. Plant Physiol. 2014 Dec; 166(4):1724-32. PMID: 25349325.
      Citations: 37     Fields:    Translation:Animals
    62. Alder O, Cullum R, Lee S, Kan AC, Wei W, Yi Y, Garside VC, Bilenky M, Griffith M, Morrissy AS, Robertson GA, Thiessen N, Zhao Y, Chen Q, Pan D, Jones SJM, Marra MA, Hoodless PA. Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation. Cell Rep. 2014 Oct 09; 9(1):261-271. PMID: 25263553.
      Citations: 35     Fields:    Translation:AnimalsCells
    63. Dean RA, Fam HK, An J, Choi K, Shimizu Y, Jones SJ, Boerkoel CF, Interthal H, Pfeifer TA. Identification of a putative Tdp1 inhibitor (CD00509) by in vitro and cell-based assays. J Biomol Screen. 2014 Dec; 19(10):1372-82. PMID: 25117203.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    64. Butterfield YS, Kreitzman M, Thiessen N, Corbett RD, Li Y, Pang J, Ma YP, Jones SJ, Birol I. JAGuaR: junction alignments to genome for RNA-seq reads. PLoS One. 2014; 9(7):e102398. PMID: 25062255.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    65. van den Berg S, Shen Y, Jones SJ, Gibson WT. Genetic counseling in direct-to-consumer exome sequencing: a case report. J Genet Couns. 2014 Oct; 23(5):742-53. PMID: 24954083.
      Citations: 3     Fields:    Translation:Humans
    66. Vanner RJ, Remke M, Gallo M, Selvadurai HJ, Coutinho F, Lee L, Kushida M, Head R, Morrissy S, Zhu X, Aviv T, Voisin V, Clarke ID, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJ, Marra MA, Malkin D, Northcott PA, Kool M, Pfister SM, Bader G, Hochedlinger K, Korshunov A, Taylor MD, Dirks PB. Quiescent sox2(+) cells drive hierarchical growth and relapse in sonic hedgehog subgroup medulloblastoma. Cancer Cell. 2014 Jul 14; 26(1):33-47. PMID: 24954133.
      Citations: 124     Fields:    Translation:AnimalsCells
    67. Cohen AS, Townsend KN, Xiang QS, Attariwala R, Borchers C, Senger C, Picker W, Levi J, Yewchuk L, Tan J, Eydoux P, Lum A, Yong SL, McKinnon ML, Lear SA, Everett R, Jones SJ, Yip S, Gibson WT. Somatic mosaicism for the p.His1047Arg mutation in PIK3CA in a girl with mesenteric lipomatosis. Am J Med Genet A. 2014 Sep; 164A(9):2360-4. PMID: 24903541.
      Citations: 5     Translation:Humans
    68. Jamshidi F, Pleasance E, Li Y, Shen Y, Kasaian K, Corbett R, Eirew P, Lum A, Pandoh P, Zhao Y, Schein JE, Moore RA, Rassekh R, Huntsman DG, Knowling M, Lim H, Renouf DJ, Jones SJ, Marra MA, Nielsen TO, Laskin J, Yip S. Diagnostic value of next-generation sequencing in an unusual sphenoid tumor. Oncologist. 2014 Jun; 19(6):623-30. PMID: 24807916.
      Citations: 11     Fields:    Translation:Humans
    69. Chang AC, Garside VC, Fournier M, Smrz J, Vrljicak P, Umlandt P, Fuller M, Robertson G, Zhao Y, Tam A, Jones SJ, Marra MA, Hoodless PA, Karsan A. A Notch-dependent transcriptional hierarchy promotes mesenchymal transdifferentiation in the cardiac cushion. Dev Dyn. 2014 Jul; 243(7):894-905. PMID: 24633789.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    70. Zovoilis A, Mungall AJ, Moore R, Varhol R, Chu A, Wong T, Marra M, Jones SJ. The expression level of small non-coding RNAs derived from the first exon of protein-coding genes is predictive of cancer status. EMBO Rep. 2014 Apr; 15(4):402-10. PMID: 24534129.
      Citations: 7     Fields:    Translation:HumansCells
    71. Demos MK, van Karnebeek CD, Ross CJ, Adam S, Shen Y, Zhan SH, Shyr C, Horvath G, Suri M, Fryer A, Jones SJ, Friedman JM. A novel recurrent mutation in ATP1A3 causes CAPOS syndrome. Orphanet J Rare Dis. 2014 Jan 28; 9:15. PMID: 24468074.
      Citations: 74     Fields:    Translation:Humans
    72. Younesy H, Möller T, Heravi-Moussavi A, Cheng JB, Costello JF, Lorincz MC, Karimi MM, Jones SJ. ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics. 2014 04 15; 30(8):1172-1174. PMID: 24371156.
      Citations: 7     Fields:    Translation:HumansAnimals
    73. Stirling PC, Shen Y, Corbett R, Jones SJ, Hieter P. Genome destabilizing mutator alleles drive specific mutational trajectories in Saccharomyces cerevisiae. Genetics. 2014 Feb; 196(2):403-12. PMID: 24336748.
      Citations: 11     Fields:    Translation:Animals
    74. Johnson BE, Mazor T, Hong C, Barnes M, Aihara K, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao Y, Moore RA, Mungall AJ, Jones SJM, Hirst M, Marra MA, Saito N, Aburatani H, Mukasa A, Berger MS, Chang SM, Taylor BS, Costello JF. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science. 2014 Jan 10; 343(6167):189-193. PMID: 24336570.
      Citations: 518     Fields:    Translation:Humans
    75. Greenway SC, McLeod R, Hume S, Roslin NM, Alvarez N, Giuffre M, Zhan SH, Shen Y, Preuss C, Andelfinger G, Jones SJ, Gerull B. Exome sequencing identifies a novel variant in ACTC1 associated with familial atrial septal defect. Can J Cardiol. 2014 Feb; 30(2):181-7. PMID: 24461919.
      Citations: 9     Fields:    Translation:Humans
    76. Schmouth JF, Castellarin M, Laprise S, Banks KG, Bonaguro RJ, McInerny SC, Borretta L, Amirabbasi M, Korecki AJ, Portales-Casamar E, Wilson G, Dreolini L, Jones SJ, Wasserman WW, Goldowitz D, Holt RA, Simpson EM. Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice. BMC Biol. 2013 Oct 14; 11:106. PMID: 24124870.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    77. Kasaian K, Wiseman SM, Thiessen N, Mungall KL, Corbett RD, Qian JQ, Nip KM, He A, Tse K, Chuah E, Varhol RJ, Pandoh P, McDonald H, Zeng T, Tam A, Schein J, Birol I, Mungall AJ, Moore RA, Zhao Y, Hirst M, Marra MA, Walker BA, Jones SJ. Complete genomic landscape of a recurring sporadic parathyroid carcinoma. J Pathol. 2013 Jul; 230(3):249-60. PMID: 23616356.
      Citations: 20     Fields:    Translation:HumansCells
    78. Maksakova IA, Thompson PJ, Goyal P, Jones SJ, Singh PB, Karimi MM, Lorincz MC. Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. Epigenetics Chromatin. 2013 Jun 04; 6(1):15. PMID: 23735015.
      Citations: 63     Fields:    
    79. Hadj Khodabakhshi A, Fejes AP, Birol I, Jones SJ. Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline. BMC Bioinformatics. 2013 May 28; 14:167. PMID: 23714400.
      Citations: 1     Fields:    Translation:Humans
    80. Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, Taylor GA, Yuen MM, Keeling CI, Brand D, Vandervalk BP, Kirk H, Pandoh P, Moore RA, Zhao Y, Mungall AJ, Jaquish B, Yanchuk A, Ritland C, Boyle B, Bousquet J, Ritland K, Mackay J, Bohlmann J, Jones SJ. Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics. 2013 Jun 15; 29(12):1492-7. PMID: 23698863.
      Citations: 114     Fields:    Translation:AnimalsCells
    81. Hall DE, Yuen MM, Jancsik S, Quesada AL, Dullat HK, Li M, Henderson H, Arango-Velez A, Liao NY, Docking RT, Chan SK, Cooke JE, Breuil C, Jones SJ, Keeling CI, Bohlmann J. Transcriptome resources and functional characterization of monoterpene synthases for two host species of the mountain pine beetle, lodgepole pine (Pinus contorta) and jack pine (Pinus banksiana). BMC Plant Biol. 2013 May 16; 13:80. PMID: 23679205.
      Citations: 19     Fields:    Translation:AnimalsCells
    82. 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 messenger RNA profiling in rodent liver development implicates mir302b and mir20a in repressing transforming growth factor-beta signaling. Hepatology. 2013 Jun; 57(6):2491-501. PMID: 23315977.
      Citations: 7     Fields:    Translation:AnimalsCells
    83. Keeling CI, Yuen MM, Liao NY, Docking TR, Chan SK, Taylor GA, Palmquist DL, Jackman SD, Nguyen A, Li M, Henderson H, Janes JK, Zhao Y, Pandoh P, Moore R, Sperling FA, Huber DP, Birol I, Jones SJ, Bohlmann J. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biol. 2013 Mar 27; 14(3):R27. PMID: 23537049.
      Citations: 99     Fields:    Translation:AnimalsCells
    84. Trinh DL, Scott DW, Morin RD, Mendez-Lago M, An J, Jones SJ, Mungall AJ, Zhao Y, Schein J, Steidl C, Connors JM, Gascoyne RD, Marra MA. Analysis of FOXO1 mutations in diffuse large B-cell lymphoma. Blood. 2013 May 02; 121(18):3666-74. PMID: 23460611.
      Citations: 45     Fields:    Translation:HumansCells
    85. Reipas KM, Law JH, Couto N, Islam S, Li Y, Li H, Cherkasov A, Jung K, Cheema AS, Jones SJ, Hassell JA, Dunn SE. Luteolin is a novel p90 ribosomal S6 kinase (RSK) inhibitor that suppresses Notch4 signaling by blocking the activation of Y-box binding protein-1 (YB-1). Oncotarget. 2013 Feb; 4(2):329-45. PMID: 23593654.
      Citations: 24     Fields:    Translation:HumansCells
    86. 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. PMID: 23363597.
      Citations: 16     Fields:    Translation:AnimalsCells
    87. 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, Guidry 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. PMID: 23334666.
      Citations: 440     Fields:    Translation:HumansCells
    88. Qin ZS, Bilenky M, Su G, Jones SJ. MotifOrganizer: a scalable model-based motif clustering tool for mammalian genomes. Front Biosci (Elite Ed). 2013 01 01; 5(2):785-97. PMID: 23277033.
      Citations:    Fields:    Translation:HumansAnimalsCells
    89. 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. PMID: 23184418.
      Citations: 74     Fields:    Translation:HumansCells
    90. 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. PMID: 23131835.
      Citations: 50     Fields:    Translation:Humans
    91. 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. PMID: 23086925.
      Citations: 86     Fields:    Translation:HumansCells
    92. Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ, Jones SJ. Spark: a navigational paradigm for genomic data exploration. Genome Res. 2012 Nov; 22(11):2262-9. PMID: 22960372.
      Citations: 19     Fields:    Translation:HumansCells
    93. 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. PMID: 22927308.
      Citations: 23     Fields:    Translation:HumansCells
    94. Vrljicak P, Cullum R, Xu E, Chang AC, Wederell ED, Bilenky M, Jones SJ, Marra MA, Karsan A, Hoodless PA. Twist1 transcriptional targets in the developing atrio-ventricular canal of the mouse. PLoS One. 2012; 7(7):e40815. PMID: 22815831.
      Citations: 3     Fields:    Translation:AnimalsCells
    95. Shankar J, Wiseman SM, Meng F, Kasaian K, Strugnell S, Mofid A, Gown A, Jones SJ, Nabi IR. Coordinated expression of galectin-3 and caveolin-1 in thyroid cancer. J Pathol. 2012 Sep; 228(1):56-66. PMID: 22513979.
      Citations: 14     Fields:    Translation:HumansCells
    96. 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, Triggs-Raine B, Zelinski T. GPSM2 mutations cause the brain malformations and hearing loss in Chudley-McCullough syndrome. Am J Hum Genet. 2012 Jun 08; 90(6):1088-93. PMID: 22578326.
      Citations: 50     Fields:    Translation:Humans
    97. Simonis M, Atanur SS, Linsen S, 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. PMID: 22541052.
      Citations: 15     Fields:    Translation:AnimalsCells
    98. Keeling CI, Henderson H, Li M, Yuen M, Clark EL, Fraser JD, Huber DP, Liao NY, Docking TR, Birol I, Chan SK, Taylor GA, Palmquist D, Jones SJ, Bohlmann J. Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests. Insect Biochem Mol Biol. 2012 Aug; 42(8):525-36. PMID: 22516182.
      Citations: 41     Fields:    Translation:AnimalsCells
    99. Li YY, Jones SJ. Drug repositioning for personalized medicine. Genome Med. 2012; 4(3):27. PMID: 22494857.
      Citations: 62     Fields:    
    100. 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. PMID: 22294438.
      Citations: 31     Fields:    Translation:HumansCells
    101. Chiu CG, Chan SK, Fang ZA, Masoudi H, Wood-Baker R, Jones SJM, 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):654-659. PMID: 22402266.
      Citations: 11     Fields:    Translation:Humans
    102. Chu JS, Johnsen RC, Chua SY, Tu D, Dennison M, Marra M, Jones SJ, Baillie DL, Rose AM. Allelic ratios and the mutational landscape reveal biologically significant heterozygous SNVs. Genetics. 2012 Apr; 190(4):1225-33. PMID: 22267497.
      Citations: 9     Fields:    Translation:AnimalsCells
    103. 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. PMID: 22223660.
      Citations: 63     Fields:    Translation:HumansCells
    104. Heravi-Moussavi A, Anglesio MS, Cheng SW, Senz J, Yang W, Prentice L, Fejes AP, Chow C, Tone A, Kalloger SE, Hamel N, Roth A, Ha G, Wan AN, Maines-Bandiera S, Salamanca C, Pasini B, Clarke BA, Lee AF, Lee CH, Zhao C, Young RH, Aparicio SA, Sorensen PH, Woo MM, Boyd N, Jones SJ, Hirst M, Marra MA, Gilks B, Shah SP, Foulkes WD, Morin GB, Huntsman DG. Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers. N Engl J Med. 2012 Jan 19; 366(3):234-42. PMID: 22187960.
      Citations: 131     Fields:    Translation:Humans
    105. Gibson WT, Hood RL, Zhan SH, Bulman DE, Fejes AP, Moore R, Mungall AJ, Eydoux P, Babul-Hirji R, An J, Marra MA, Chitayat D, Boycott KM, Weaver DD, Jones SJ. Mutations in EZH2 cause Weaver syndrome. Am J Hum Genet. 2012 Jan 13; 90(1):110-8. PMID: 22177091.
      Citations: 94     Fields:    Translation:HumansCells
    106. Krzywinski M, Birol I, Jones SJ, Marra MA. Hive plots--rational approach to visualizing networks. Brief Bioinform. 2012 Sep; 13(5):627-44. PMID: 22155641.
      Citations: 62     Fields:    Translation:HumansCells
    107. 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 Y, Mungall AJ, Jones SJ, 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. PMID: 22072542.
      Citations: 118     Fields:    Translation:HumansCells
    108. Liang B, Luo M, Scott-Herridge J, Semeniuk C, Mendoza M, Capina R, Sheardown B, Ji H, Kimani J, Ball BT, Van Domselaar G, Graham M, Tyler S, Jones SJ, Plummer FA. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1. PLoS One. 2011; 6(10):e26745. PMID: 22039546.
      Citations: 17     Fields:    Translation:Cells
    109. 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. PMID: 21923906.
      Citations: 11     Fields:    Translation:AnimalsCells
    110. Li YY, An J, Jones SJ. A computational approach to finding novel targets for existing drugs. PLoS Comput Biol. 2011 Sep; 7(9):e1002139. PMID: 21909252.
      Citations: 37     Fields:    Translation:HumansCells
    111. Schrader KA, Heravi-Moussavi A, Waters PJ, Senz J, Whelan J, Ha G, Eydoux P, Nielsen T, Gallagher B, Oloumi A, Boyd N, Fernandez BA, Young TL, Jones SJ, 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; 225(1):12-8. PMID: 21792934.
      Citations: 14     Fields:    Translation:Humans
    112. 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. PMID: 21796119.
      Citations: 627     Fields:    Translation:HumansCells
    113. Kasaian K, Jones SJ. A new frontier in personalized cancer therapy: mapping molecular changes. Future Oncol. 2011 Jul; 7(7):873-94. PMID: 21732758.
      Citations: 6     Fields:    Translation:HumansAnimals
    114. Yakovenko OY, Li YY, Oliferenko AA, Vashchenko GM, Bdzhola VG, Jones SJ. Ab initio parameterization of YFF1, a universal force field for drug-design applications. J Mol Model. 2012 Feb; 18(2):663-73. PMID: 21562826.
      Citations: 1     Fields:    
    115. Wiseman SM, Griffith OL, Gown A, Walker B, Jones SJ. Immunophenotyping of thyroid tumors identifies molecular markers altered during transformation of differentiated into anaplastic carcinoma. Am J Surg. 2011 May; 201(5):580-6. PMID: 21545903.
      Citations: 5     Fields:    Translation:Humans
    116. 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. PMID: 21547704.
      Citations: 13     Fields:    Translation:Humans
    117. Fejes AP, Khodabakhshi AH, Birol I, Jones SJ. Human variation database: an open-source database template for genomic discovery. Bioinformatics. 2011 Apr 15; 27(8):1155-6. PMID: 21367872.
      Citations: 7     Fields:    Translation:Humans
    118. Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I, Jones SJ, Cronk QC, Douglas CJ. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Mol Ecol Resour. 2011 Mar; 11 Suppl 1:81-92. PMID: 21429165.
      Citations: 35     Fields:    Translation:Animals
    119. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, 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. PMID: 21345102.
      Citations: 332     Fields:    Translation:HumansCellsPHPublic Health
    120. Shin H, Lee H, Fejes AP, Baillie DL, Koo HS, 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 Feb 08; 4:34. PMID: 21303547.
      Citations: 16     Fields:    
    121. DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Alamouti SM, Tsui CK, Docking RT, Levasseur A, Haridas S, Robertson G, Birol I, Holt RA, Marra MA, Hamelin RC, Hirst M, Jones SJ, 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 U S A. 2011 Feb 08; 108(6):2504-9. PMID: 21262841.
      Citations: 67     Fields:    Translation:AnimalsCells
    122. McLarren KW, Severson TM, du Souich C, Stockton DW, Kratz LE, Cunningham D, Hendson G, Morin RD, Wu D, Paul JE, An J, Nelson TN, Chou A, DeBarber AE, Merkens LS, Michaud JL, Waters PJ, Yin J, McGillivray B, Demos M, Rouleau GA, Grzeschik KH, Smith R, Tarpey PS, Shears D, Schwartz CE, Gecz J, Stratton MR, Arbour L, Hurlburt J, Van Allen MI, Herman GE, Zhao Y, Moore R, Kelley RI, Jones SJ, Steiner RD, Raymond FL, Marra MA, Boerkoel CF. Hypomorphic temperature-sensitive alleles of NSDHL cause CK syndrome. Am J Hum Genet. 2010 Dec 10; 87(6):905-14. PMID: 21129721.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    123. 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. PMID: 20935650.
      Citations: 374     Fields:    Translation:Animals
    124. 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 04; 11:536. PMID: 20920358.
      Citations: 13     Fields:    Translation:AnimalsCells
    125. 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; 11(9):403. PMID: 20887641.
      Citations: 104     Fields:    Translation:AnimalsCells
    126. Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJ, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing. Nat Methods. 2010 Oct; 7(10):843-7. PMID: 20835245.
      Citations: 143     Fields:    Translation:HumansCells
    127. 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):1532-43. PMID: 20942669.
      Citations: 604     Fields:    Translation:HumansCells
    128. 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. PMID: 20807748.
      Citations: 39     Fields:    Translation:HumansAnimalsCells
    129. Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, Butterfield YS, Cezard T, Chuah E, Corbett R, Fejes AP, Griffith M, Yee J, Martin M, Mayo M, Melnyk N, Morin RD, Pugh TJ, Severson T, Shah SP, Sutcliffe M, Tam A, Terry J, Thiessen N, Thomson T, Varhol R, Zeng T, Zhao Y, Moore RA, Huntsman DG, Birol I, Hirst M, Holt RA, Marra MA. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010; 11(8):R82. PMID: 20696054.
      Citations: 79     Fields:    Translation:Humans
    130. 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. PMID: 20651839.
      Citations: 2     Fields:    Translation:HumansCells
    131. 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, Thiessen N, 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 Jul 08; 466(7303):253-7. PMID: 20613842.
      Citations: 728     Fields:    Translation:HumansAnimalsCells
    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; 11:279. PMID: 20433749.
      Citations: 43     Fields:    Translation:AnimalsCells
    133. Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ. The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res. 2010 Jun; 20(6):791-803. PMID: 20430781.
      Citations: 54     Fields:    Translation:AnimalsCells
    134. 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. PMID: 20363921.
      Citations: 46     Fields:    Translation:HumansCells
    135. Malhis N, Jones SJ. High quality SNP calling using Illumina data at shallow coverage. Bioinformatics. 2010 Apr 15; 26(8):1029-35. PMID: 20190250.
      Citations: 22     Fields:    
    136. Rose AM, O'Neil NJ, Bilenky M, Butterfield YS, Malhis N, Flibotte S, Jones MR, Marra M, Baillie DL, Jones SJ. Genomic sequence of a mutant strain of Caenorhabditis elegans with an altered recombination pattern. BMC Genomics. 2010 Feb 23; 11:131. PMID: 20178641.
      Citations: 7     Fields:    Translation:AnimalsCells
    137. Sleumer MC, Mah AK, Baillie DL, Jones SJ. Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. Nucleic Acids Res. 2010 May; 38(9):2990-3004. PMID: 20100800.
      Citations: 1     Fields:    Translation:AnimalsCells
    138. Montgomery SB, Kasaian K, Jones SJ, Griffith OL. Annotating the regulatory genome. Methods Mol Biol. 2010; 674:313-49. PMID: 20827601.
      Citations:    Fields:    Translation:HumansAnimalsCells
    139. 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. PMID: 19834150.
      Citations: 13     Fields:    Translation:Cells
    140. Romanuik TL, Wang G, Holt RA, Jones SJ, Marra MA, Sadar MD. Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries. BMC Genomics. 2009 Oct 15; 10:476. PMID: 19832994.
      Citations: 41     Fields:    Translation:HumansAnimalsCells
    141. Diguistini S, Liao NY, Platt D, Robertson G, Seidel M, Chan SK, Docking TR, Birol I, Holt RA, Hirst M, Mardis E, Marra MA, Hamelin RC, Bohlmann J, Breuil C, Jones SJ. De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol. 2009; 10(9):R94. PMID: 19747388.
      Citations: 60     Fields:    Translation:Animals
    142. 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 Res. 2009 Jul; 29(7):2437-44. PMID: 19596911.
      Citations: 1     Fields:    Translation:Humans
    143. 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 SJ, Marra MA, Moerman DG. An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans. PLoS Genet. 2009 Jun; 5(6):e1000537. PMID: 19557190.
      Citations: 58     Fields:    Translation:AnimalsCells
    144. Birol I, Jackman SD, Nielsen CB, 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 01; 25(21):2872-7. PMID: 19528083.
      Citations: 200     Fields:    
    145. 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. J Med Chem. 2009 May 14; 52(9):2667-72. PMID: 19419201.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    146. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res. 2009 Jun; 19(6):1117-23. PMID: 19251739.
      Citations: 1436     Fields:    Translation:HumansAnimalsCells
    147. Sleumer MC, Bilenky M, He A, Robertson G, Thiessen N, Jones SJ. Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. Nucleic Acids Res. 2009 Mar; 37(4):1323-34. PMID: 19151087.
      Citations: 11     Fields:    Translation:AnimalsCells
    148. Hoffman BG, Jones SJ. Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing. J Endocrinol. 2009 Apr; 201(1):1-13. PMID: 19136617.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    149. McGhee JD, Fukushige T, Krause MW, Minnema SE, Goszczynski B, Gaudet J, Kohara Y, Bossinger O, Zhao Y, 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. Dev Biol. 2009 Mar 15; 327(2):551-65. PMID: 19111532.
      Citations: 72     Fields:    Translation:AnimalsCells
    150. 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 01; 25(1):6-13. PMID: 18974170.
      Citations: 16     Fields:    Translation:HumansCells
    151. 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; 9:484. PMID: 18854048.
      Citations: 49     Fields:    Translation:AnimalsCells
    152. Robertson AG, Bilenky M, Tam A, Zhao Y, 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 SJ. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res. 2008 Dec; 18(12):1906-17. PMID: 18787082.
      Citations: 99     Fields:    Translation:HumansAnimalsCells
    153. 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. PMID: 18759692.
      Citations: 15     Fields:    Translation:Humans
    154. D'Souza CA, Chopra V, Varhol R, Xie YY, Bohacec S, Zhao Y, Lee LL, Bilenky M, Portales-Casamar E, He A, Wasserman WW, Goldowitz D, Marra MA, Holt RA, Simpson EM, Jones SJ. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci. 2008 Jul 14; 9:66. PMID: 18625066.
      Citations: 11     Fields:    Translation:AnimalsCells
    155. Wiseman SM, Melck A, Masoudi H, Ghaidi F, Goldstein L, Gown A, Jones SJ, Griffith OL. Molecular phenotyping of thyroid tumors identifies a marker panel for differentiated thyroid cancer diagnosis. Ann Surg Oncol. 2008 Oct; 15(10):2811-26. PMID: 18612701.
      Citations: 15     Fields:    Translation:Humans
    156. Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJ. Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags. BMC Biol. 2008 Jul 08; 6:30. PMID: 18611272.
      Citations: 29     Fields:    Translation:AnimalsCells
    157. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics. 2008 Aug 01; 24(15):1729-30. PMID: 18599518.
      Citations: 151     Fields:    Translation:Cells
    158. Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones SJ, Marra MA, Helgason CD. Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol. 2008; 9(6):R99. PMID: 18554416.
      Citations: 24     Fields:    Translation:Animals
    159. Holt RA, Jones SJ. The new paradigm of flow cell sequencing. Genome Res. 2008 Jun; 18(6):839-46. PMID: 18519653.
      Citations: 75     Fields:    
    160. Wiseman SM, Griffith OL, Melck A, Masoudi H, Gown A, Nabi IR, Jones SJ. Evaluation of type 1 growth factor receptor family expression in benign and malignant thyroid lesions. Am J Surg. 2008 May; 195(5):667-73; discussion 673. PMID: 18424286.
      Citations: 6     Fields:    Translation:Humans
    161. Chan SK, Griffith OL, Tai IT, Jones SJ. Meta-analysis of colorectal cancer gene expression profiling studies identifies consistently reported candidate biomarkers. Cancer Epidemiol Biomarkers Prev. 2008 Mar; 17(3):543-52. PMID: 18349271.
      Citations: 72     Fields:    Translation:Humans
    162. Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM. Text-mining assisted regulatory annotation. Genome Biol. 2008; 9(2):R31. PMID: 18271954.
      Citations: 15     Fields:    Translation:HumansAnimals
    163. Griffith M, Tang MJ, Griffith OL, Morin RD, Chan SY, Asano JK, Zeng T, Flibotte S, Ally A, Baross A, Hirst M, Jones SJ, Morin GB, Tai IT, Marra MA. ALEXA: a microarray design platform for alternative expression analysis. Nat Methods. 2008 Feb; 5(2):118. PMID: 18235430.
      Citations: 9     Fields:    
    164. 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; 9:57. PMID: 18230180.
      Citations: 25     Fields:    Translation:AnimalsCells
    165. Kneller JM, Ehlen T, Matisic JP, Miller D, Van Niekerk D, Lam WL, Marra M, Richards-Kortum R, Follen M, Macaulay C, Jones SJ. Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling. Biomark Insights. 2007 Dec 11; 2:447-61. PMID: 19662225.
      Citations: 4     
    166. Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, 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 SJ. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 2008 Jan; 36(Database issue):D107-13. PMID: 18006570.
      Citations: 133     Fields:    Translation:HumansAnimalsCells
    167. Melck A, Masoudi H, Griffith OL, Rajput A, Wilkins G, Bugis S, Jones SJ, Wiseman SM. Cell cycle regulators show diagnostic and prognostic utility for differentiated thyroid cancer. Ann Surg Oncol. 2007 Dec; 14(12):3403-11. PMID: 17882495.
      Citations: 16     Fields:    Translation:HumansCells
    168. 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. PMID: 17712020.
      Citations: 29     Fields:    Translation:AnimalsCells
    169. Hou J, Charters AM, Lee SC, Zhao Y, Wu MK, Jones SJ, Marra MA, Hoodless PA. A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE). BMC Dev Biol. 2007 Aug 02; 7:92. PMID: 17683524.
      Citations: 24     Fields:    Translation:Animals
    170. Wiseman SM, Griffith OL, Deen S, Rajput A, Masoudi H, Gilks B, Goldstein L, Gown A, Jones SJ. Identification of molecular markers altered during transformation of differentiated into anaplastic thyroid carcinoma. Arch Surg. 2007 Aug; 142(8):717-27; discussion 727-9. PMID: 17709725.
      Citations: 22     Fields:    Translation:Humans
    171. 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 J. 2007 Jun; 50(6):1063-78. PMID: 17488239.
      Citations: 27     Fields:    Translation:AnimalsCells
    172. Montgomery SB, Griffith OL, Schuetz JM, Brooks-Wilson A, Jones SJ. A survey of genomic properties for the detection of regulatory polymorphisms. PLoS Comput Biol. 2007 Jun; 3(6):e106. PMID: 17559298.
      Citations: 16     Fields:    Translation:Cells
    173. Quayle AP, Siddiqui AS, Jones SJ. Perturbation of interaction networks for application to cancer therapy. Cancer Inform. 2007; 5:45-65. PMID: 19390668.
      Citations: 2     
    174. Quayle SN, Hare H, Delaney AD, Hirst M, Hwang D, Schein JE, Jones SJ, Marra MA, Sadar MD. Novel expressed sequences identified in a model of androgen independent prostate cancer. BMC Genomics. 2007 Jan 26; 8:32. PMID: 17257419.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    175. Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, 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, Jann O, Jones SJ, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TP, Sonstegard TS, Taylor JF, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol. 2007; 8(8):R165. PMID: 17697342.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    176. Warren RL, Sutton GG, Jones SJ, Holt RA. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 2007 Feb 15; 23(4):500-1. PMID: 17158514.
      Citations: 150     Fields:    Translation:Cells
    177. Griffith OL, Melck A, Jones SJ, Wiseman SM. Meta-analysis and meta-review of thyroid cancer gene expression profiling studies identifies important diagnostic biomarkers. J Clin Oncol. 2006 Nov 01; 24(31):5043-51. PMID: 17075124.
      Citations: 111     Fields:    Translation:Humans
    178. McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJ, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol. 2007 Feb 15; 302(2):627-45. PMID: 17113066.
      Citations: 90     Fields:    Translation:AnimalsCells
    179. Elnitski L, Jin VX, Farnham PJ, Jones SJ. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res. 2006 Dec; 16(12):1455-64. PMID: 17053094.
      Citations: 90     Fields:    Translation:HumansAnimalsCells
    180. Bainbridge MN, Warren RL, He A, Bilenky M, Robertson AG, Jones SJ. THOR: targeted high-throughput ortholog reconstructor. Bioinformatics. 2007 Oct 01; 23(19):2622-4. PMID: 17038343.
      Citations: 3     Fields:    Translation:HumansCells
    181. McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A. 2006 Oct 17; 103(42):15582-7. PMID: 17030794.
      Citations: 207     Fields:    Translation:Cells
    182. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJ. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics. 2006 Sep 29; 7:246. PMID: 17010196.
      Citations: 61     Fields:    Translation:HumansCells
    183. Ralph SG, Yueh H, Friedmann M, Aeschliman D, Zeznik JA, Nelson CC, Butterfield YS, Kirkpatrick R, Liu J, Jones SJ, Marra MA, 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 Environ. 2006 Aug; 29(8):1545-70. PMID: 16898017.
      Citations: 68     Fields:    Translation:AnimalsCells
    184. Friedman JM, Baross A, Delaney AD, Ally A, Arbour L, Armstrong 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 SJ, 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, Zahir F, Eydoux P, Marra MA. Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am J Hum Genet. 2006 Sep; 79(3):500-13. PMID: 16909388.
      Citations: 79     Fields:    Translation:Humans
    185. Siddiqui AS, Delaney AD, Schnerch A, Griffith OL, Jones SJ, Marra MA. Sequence biases in large scale gene expression profiling data. Nucleic Acids Res. 2006 Jul 13; 34(12):e83. PMID: 16840527.
      Citations: 28     Fields:    Translation:HumansAnimals
    186. Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang SP, Kronstad JW, Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE, Siddiqui AS, Marra MA, Wilson RK, Jones SJ. Physical map-assisted whole-genome shotgun sequence assemblies. Genome Res. 2006 Jun; 16(6):768-75. PMID: 16741162.
      Citations: 13     Fields:    Translation:AnimalsCells
    187. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Chow W, 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 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 SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, Holt RA. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res. 2006 Jun; 16(6):796-803. PMID: 16672307.
      Citations: 40     Fields:    Translation:AnimalsCells
    188. Ruzanov P, Jones SJ. An interactive tool for visualization of relationships between gene expression profiles. BMC Bioinformatics. 2006 Apr 06; 7:193. PMID: 16600045.
      Citations:    Fields:    Translation:HumansAnimalsCells
    189. Li YY, Jones SJ, Cherkasov A. Selective targeting of indel-inferred differences in spatial structures of homologous proteins. J Bioinform Comput Biol. 2006 Apr; 4(2):403-14. PMID: 16819791.
      Citations: 1     Fields:    Translation:AnimalsCells
    190. 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 YS, Kirkpatrick R, Chun E, Liu J, Palmquist D, Wynhoven B, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJ, Marra MA, Ellis BE, Douglas CJ, Ritland K, Bohlmann J. Genomics of hybrid poplar (Populus trichocarpax deltoides) interacting with forest tent caterpillars (Malacosoma disstria): normalized and full-length cDNA libraries, expressed sequence tags, and a cDNA microarray for the study of insect-induced defences in poplar. Mol Ecol. 2006 Apr; 15(5):1275-97. PMID: 16626454.
      Citations: 50     Fields:    Translation:AnimalsCells
    191. Jones SJ. Prediction of genomic functional elements. Annu Rev Genomics Hum Genet. 2006; 7:315-38. PMID: 16824019.
      Citations: 20     Fields:    Translation:Animals
    192. Li YY, An J, Jones SJ. A large-scale computational approach to drug repositioning. Genome Inform. 2006; 17(2):239-47. PMID: 17503396.
      Citations: 9     Fields:    Translation:HumansCells
    193. 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, Lee LL, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJ, 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. Proc Natl Acad Sci U S A. 2005 Dec 20; 102(51):18485-90. PMID: 16352711.
      Citations: 58     Fields:    Translation:AnimalsCells
    194. Cherkasov A, Shi Z, Li Y, Jones SJ, 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. J Chem Inf Model. 2005 Nov-Dec; 45(6):1842-53. PMID: 16309292.
      Citations: 1     Fields:    Translation:Humans
    195. 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):476-88. PMID: 16098712.
      Citations: 22     Fields:    Translation:Humans
    196. 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. PMID: 16026963.
      Citations: 50     Fields:    Translation:Animals
    197. Montgomery SB, Fu T, Guan J, Lin K, Jones SJ. An application of peer-to-peer technology to the discovery, use and assessment of bioinformatics programs. Nat Methods. 2005 Aug; 2(8):563. PMID: 16094378.
      Citations: 1     Fields:    
    198. Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJ. Management and visualization of whole genome shotgun assemblies using SAM. Biotechniques. 2005 May; 38(5):715-6, 718, 720. PMID: 15945370.
      Citations: 2     Fields:    
    199. Halaschek-Wiener J, Khattra JS, McKay S, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJ, Marra MA, Brooks-Wilson AR, Riddle DL. Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Res. 2005 May; 15(5):603-15. PMID: 15837805.
      Citations: 94     Fields:    Translation:AnimalsCells
    200. 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. Mol Microbiol. 2005 Mar; 55(5):1452-72. PMID: 15720553.
      Citations: 58     Fields:    Translation:AnimalsCells
    201. 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 Res. 2005 Feb; 15(2):302-11. PMID: 15687294.
      Citations: 29     Fields:    Translation:AnimalsCells
    202. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science. 2005 Feb 25; 307(5713):1321-4. PMID: 15653466.
      Citations: 318     Fields:    Translation:HumansAnimalsCells
    203. Warren R, Hsiao WW, Kudo H, Myhre M, Dosanjh M, Petrescu A, Kobayashi H, Shimizu S, Miyauchi K, Masai E, Yang G, Stott JM, Schein JE, Shin H, Khattra J, Smailus D, Butterfield YS, Siddiqui A, Holt R, Marra MA, Jones SJ, Mohn WW, Brinkman FS, Fukuda M, Davies J, Eltis LD. Functional characterization of a catabolic plasmid from polychlorinated- biphenyl-degrading Rhodococcus sp. strain RHA1. J Bacteriol. 2004 Nov; 186(22):7783-95. PMID: 15516593.
      Citations: 16     Fields:    Translation:CellsPHPublic Health
    204. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct; 14(10B):2121-7. PMID: 15489334.
      Citations: 220     Fields:    Translation:HumansAnimals
    205. 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; 5:101. PMID: 15274750.
      Citations: 3     Fields:    Translation:Cells
    206. Cherkasov A, Jones SJ. An approach to large scale identification of non-obvious structural similarities between proteins. BMC Bioinformatics. 2004 May 17; 5:61. PMID: 15147578.
      Citations:    Fields:    Translation:HumansCells
    207. Montgomery SB, Astakhova T, Bilenky M, Birney E, Fu T, Hassel M, Melsopp C, Rak M, Robertson AG, Sleumer M, Siddiqui AS, Jones SJ. Sockeye: a 3D environment for comparative genomics. Genome Res. 2004 May; 14(5):956-62. PMID: 15123592.
      Citations: 11     Fields:    Translation:HumansAnimals
    208. Cherkasov A, Jones SJ. Structural characterization of genomes by large scale sequence-structure threading. BMC Bioinformatics. 2004 Apr 03; 5:37. PMID: 15061866.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    209. Baross A, Schertzer M, Zuyderduyn SD, Jones SJ, Marra MA, Lansdorp PM. Effect of TERT and ATM on gene expression profiles in human fibroblasts. Genes Chromosomes Cancer. 2004 Apr; 39(4):298-310. PMID: 14978791.
      Citations: 5     Fields:    Translation:HumansCells
    210. 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 SR, Smailus DE, Jones SJ, Schein JE, Marra MA, Butterfield YS, Stott JM, Ng SH, Davidson WS, Koop BF. Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. Genome Res. 2004 Mar; 14(3):478-90. PMID: 14962987.
      Citations: 100     Fields:    Translation:Animals
    211. Zuyderduyn SD, Jones SJ. A knowledge discovery object model API for Java. BMC Bioinformatics. 2003 Oct 28; 4:51. PMID: 14583100.
      Citations: 1     Fields:    
    212. Fjell CD, Bosdet I, Schein JE, Jones SJ, Marra MA. Internet Contig Explorer (iCE)--a tool for visualizing clone fingerprint maps. Genome Res. 2003 Jun; 13(6A):1244-9. PMID: 12799356.
      Citations: 10     Fields:    Translation:HumansAnimals
    213. Pleasance ED, Marra MA, Jones SJ. Assessment of SAGE in transcript identification. Genome Res. 2003 Jun; 13(6A):1203-15. PMID: 12743019.
      Citations: 31     Fields:    Translation:AnimalsCells
    214. 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):1399-404. PMID: 12730501.
      Citations: 847     Fields:    Translation:HumansAnimalsCells
    215. Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LW, Waterston RH, McPherson JD, Jones SJ, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Res. 2003 May; 13(5):940-53. PMID: 12727910.
      Citations: 13     Fields:    Translation:AnimalsCells
    216. Gorski SM, Chittaranjan S, Pleasance ED, Freeman JD, Anderson CL, Varhol RJ, Coughlin SM, Zuyderduyn SD, Jones SJ, Marra MA. A SAGE approach to discovery of genes involved in autophagic cell death. Curr Biol. 2003 Feb 18; 13(4):358-63. PMID: 12593804.
      Citations: 87     Fields:    Translation:AnimalsCells
    217. 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. Proc Natl Acad Sci U S A. 2002 Dec 24; 99(26):16899-903. PMID: 12477932.
      Citations: 561     Fields:    Translation:HumansAnimals
    218. McKay SJ, Jones SJ. AcePrimer: automation of PCR primer design based on gene structure. Bioinformatics. 2002 Nov; 18(11):1538-9. PMID: 12424127.
      Citations: 9     Fields:    Translation:AnimalsCells
    219. Schein JE, Tangen KL, Chiu R, Shin H, Lengeler KB, MacDonald WK, Bosdet I, Heitman J, Jones SJ, Marra MA, Kronstad JW. Physical maps for genome analysis of serotype A and D strains of the fungal pathogen Cryptococcus neoformans. Genome Res. 2002 Sep; 12(9):1445-53. PMID: 12213782.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    220. Steen BR, Lian T, Zuyderduyn S, MacDonald WK, Marra M, Jones SJ, Kronstad JW. Temperature-regulated transcription in the pathogenic fungus Cryptococcus neoformans. Genome Res. 2002 Sep; 12(9):1386-400. PMID: 12213776.
      Citations: 33     Fields:    Translation:AnimalsCells
    221. Brinkman FS, Blanchard JL, Cherkasov A, Av-Gay Y, Brunham RC, Fernandez RC, Finlay BB, Otto SP, Ouellette BF, Keeling PJ, Rose AM, Hancock RE, Jones SJ, Greberg H. Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Res. 2002 Aug; 12(8):1159-67. PMID: 12176923.
      Citations: 51     Fields:    Translation:HumansAnimalsCells
    222. Shevchenko Y, Bouffard GG, Butterfield YS, Blakesley RW, Hartley JL, Young AC, Marra MA, Jones SJ, Touchman JW, Green ED. Systematic sequencing of cDNA clones using the transposon Tn5. Nucleic Acids Res. 2002 Jun 01; 30(11):2469-77. PMID: 12034835.
      Citations: 32     Fields:    Translation:Cells
    223. Butterfield YS, Marra MA, Asano JK, Chan SY, Guin R, Krzywinski MI, Lee SS, MacDonald KW, Mathewson CA, Olson TE, Pandoh PK, Prabhu AL, Schnerch A, Skalska U, Smailus DE, Stott JM, Tsai MI, Yang GS, Zuyderduyn SD, Schein JE, Jones SJ. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones. Nucleic Acids Res. 2002 Jun 01; 30(11):2460-8. PMID: 12034834.
      Citations: 16     Fields:    Translation:Cells