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Author Abbatiello, S.; Ackermann, B.L.; Borchers, C.; Bradshaw, R.A.; Carr, S.A.; Chalkley, R.; Choi, M.; Deutsch, E.; Domon, B.; Hoofnagle, A.N.; Keshishian, H.; Kuhn, E.; Liebler, D.C.; MacCoss, M.; MacLean, B.; Mani, D.R.; Neubert, H.; Smith, D.; Vitek, O.; Zimmerman, L. url  openurl
  Title New Guidelines for Publication of Manuscripts Describing Development and Application of Targeted Mass Spectrometry Measurements of Peptides and Proteins Type Journal Article
  Year 2017 Publication Abbreviated Journal Mol Cell Proteomics  
  Volume 16 Issue 3 Pages 327-328  
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  Series Volume Series Issue Edition  
  ISSN 1535-9476 ISBN Medium  
  Area Expedition Conference  
  Notes Approved no  
  Call Number UofT @ mathieu.lemaire @ Serial 45425  
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Author Abbosh, C.; Birkbak, N.J.; Wilson, G.A.; Jamal-Hanjani, M.; Constantin, T.; Salari, R.; Le Quesne, J.; Moore, D.A.; Veeriah, S.; Rosenthal, R.; Marafioti, T.; Kirkizlar, E.; Watkins, T.B.K.; McGranahan, N.; Ward, S.; Martinson, L.; Riley, J.; Fraioli, F.; Al Bakir, M.; Grönroos, E.; Zambrana, F.; Endozo, R.; Bi, W.L.; Fennessy, F.M.; Sponer, N.; Johnson, D.; Laycock, J.; Shafi, S.; Czyzewska-Khan, J.; Rowan, A.; Chambers, T.; Matthews, N.; Turajlic, S.; Hiley, C.; Lee, S.M.; Forster, M.D.; Ahmad, T.; Falzon, M.; Borg, E.; Lawrence, D.; Hayward, M.; Kolvekar, S.; Panagiotopoulos, N.; Janes, S.M.; Thakrar, R.; Ahmed, A.; Blackhall, F.; Summers, Y.; Hafez, D.; Naik, A.; Ganguly, A.; Kareht, S.; Shah, R.; Joseph, L.; Marie Quinn, A.; Crosbie, P.A.; Naidu, B.; Middleton, G.; Langman, G.; Trotter, S.; Nicolson, M.; Remmen, H.; Kerr, K.; Chetty, M.; Gomersall, L.; Fennell, D.A.; Nakas, A.; Rathinam, S.; Anand, G.; Khan, S.; Russell, P.; Ezhil, V.; Ismail, B.; Irvin-Sellers, M.; Prakash, V.; Lester, J.F.; Kornaszewska, M.; Attanoos, R.; Adams, H.; Davies, H.; Oukrif, D.; Akarca, A.U.; Hartley, J.A.; Lowe, H.L.; Lock, S.; Iles, N.; Bell, H.; Ngai, Y.; Elgar, G.; Szallasi, Z.; Schwarz, R.F.; Herrero, J.; Stewart, A.; Quezada, S.A.; Peggs, K.S.; Van Loo, P.; Dive, C.; Lin, C.J.; Rabinowitz, M.; Aerts, H.J.W.L.; Hackshaw, A.; Shaw, J.A.; Zimmermann, B.G.; TRACERx, consortium; PEACE, consortium; Swanton, C. url  openurl
  Title Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution Type Journal Article
  Year 2017 Publication Abbreviated Journal Nature  
  Volume 545 Issue 7655 Pages 446-451  
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  Abstract The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.  
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  ISSN 0028-0836 ISBN Medium  
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  Call Number UofT @ mathieu.lemaire @ Serial 45424  
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Author Abdel-Kader, K. url  openurl
  Title The Times, They Are A-Changin: Innovations in Health Care Delivery To Reduce CKD Progression Type Journal Article
  Year 2017 Publication Abbreviated Journal Clin J Am Soc Nephrol  
  Volume 12 Issue 9 Pages 1375-1376  
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  Series Volume Series Issue Edition  
  ISSN 1555-9041 ISBN Medium  
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  Notes Approved no  
  Call Number UofT @ mathieu.lemaire @ Serial 45429  
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Author Abou Sherif, S.; Ozden Tok, O.; Taşköylü, Ö.; Goktekin, O.; Kilic, I.D. openurl 
  Title Coronary Artery Aneurysms: A Review of the Epidemiology, Pathophysiology, Diagnosis, and Treatment Type Journal Article
  Year 2017 Publication Abbreviated Journal Front Cardiovasc Med  
  Volume 4 Issue Pages 24  
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  Abstract Coronary artery aneurysms (CAAs) are uncommon and describe a localized dilatation of a coronary artery segment more than 1.5-fold compared with adjacent normal segments. The incidence of CAAs varies from 0.3 to 5.3%. Ever since the dawn of the interventional era, CAAs have been increasingly diagnosed on coronary angiography. Causative factors include atherosclerosis, Takayasu arteritis, congenital disorders, Kawasaki disease (KD), and percutaneous coronary intervention. The natural history of CAAs remains unclear; however, several recent studies have postulated the underlying molecular mechanisms of CAAs, and genome-wide association studies have revealed several genetic predispositions to CAA. Controversies persist regarding the management of CAAs, and emerging findings support the importance of an early diagnosis in patients predisposed to CAAs, such as in children with KD. This review aims to summarize the present knowledge of CAAs and collate the recent advances regarding the epidemiology, etiology, pathophysiology, diagnosis, and treatment of this disease.  
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  Call Number UofT @ mathieu.lemaire @ Serial 45440  
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Author Achermann, J.C.; Schwabe, J.; Fairall, L.; Chatterjee, K. url  openurl
  Title Genetic disorders of nuclear receptors Type Journal Article
  Year 2017 Publication Abbreviated Journal J Clin Invest  
  Volume 127 Issue 4 Pages 1181-1192  
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  Abstract Following the first isolation of nuclear receptor (NR) genes, genetic disorders caused by NR gene mutations were initially discovered by a candidate gene approach based on their known roles in endocrine pathways and physiologic processes. Subsequently, the identification of disorders has been informed by phenotypes associated with gene disruption in animal models or by genetic linkage studies. More recently, whole exome sequencing has associated pathogenic genetic variants with unexpected, often multisystem, human phenotypes. To date, defects in 20 of 48 human NR genes have been associated with human disorders, with different mutations mediating phenotypes of varying severity or several distinct conditions being associated with different changes in the same gene. Studies of individuals with deleterious genetic variants can elucidate novel roles of human NRs, validating them as targets for drug development or providing new insights into structure-function relationships. Importantly, human genetic discoveries enable definitive disease diagnosis and can provide opportunities to therapeutically manage affected individuals. Here we review germline changes in human NR genes associated with “monogenic” conditions, including a discussion of the structural basis of mutations that cause distinctive changes in NR function and the molecular mechanisms mediating pathogenesis.  
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  ISSN 0021-9738 ISBN Medium  
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  Notes Approved no  
  Call Number UofT @ mathieu.lemaire @ Serial 45421  
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Author Acmg, B.O.D. url  openurl
  Title Genome editing in clinical genetics: points to consider-a statement of the American College of Medical Genetics and Genomics Type Journal Article
  Year 2017 Publication Abbreviated Journal Genet Med  
  Volume Issue Pages  
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  Abstract Disclaimer: These recommendations are designed primarily as an educational resource for medical geneticists and other health-care providers, to help them provide quality medical genetic services. Adherence to these recommendations does not necessarily assure a successful medical outcome. These recommendations should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the geneticist should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen. It may be prudent, however, to document in the patient’s record the rationale for any significant deviation from these recommendations.Genet Med advance online publication 26 January 2017Genetics in Medicine (2017); doi:10.1038/gim.2016.195.  
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  ISSN 1098-3600 ISBN Medium  
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  Notes Approved no  
  Call Number UofT @ mathieu.lemaire @ Serial 45423  
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Author Adan, A.; Alizada, G.; Kiraz, Y.; Baran, Y.; Nalbant, A. url  openurl
  Title Flow cytometry: basic principles and applications Type Journal Article
  Year 2017 Publication Abbreviated Journal Crit Rev Biotechnol  
  Volume 37 Issue 2 Pages 163-176  
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  Abstract Flow cytometry is a sophisticated instrument measuring multiple physical characteristics of a single cell such as size and granularity simultaneously as the cell flows in suspension through a measuring device. Its working depends on the light scattering features of the cells under investigation, which may be derived from dyes or monoclonal antibodies targeting either extracellular molecules located on the surface or intracellular molecules inside the cell. This approach makes flow cytometry a powerful tool for detailed analysis of complex populations in a short period of time. This review covers the general principles and selected applications of flow cytometry such as immunophenotyping of peripheral blood cells, analysis of apoptosis and detection of cytokines. Additionally, this report provides a basic understanding of flow cytometry technology essential for all users as well as the methods used to analyze and interpret the data. Moreover, recent progresses in flow cytometry have been discussed in order to give an opinion about the future importance of this technology.  
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  ISSN 0738-8551 ISBN Medium  
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  Notes Approved no  
  Call Number UofT @ mathieu.lemaire @ Serial 45928  
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Author Adhikari, K. openurl 
  Title The Genetic Diversity of the Americas Type Journal Article
  Year 2017 Publication Abbreviated Journal Annu Rev Genomics Hum Genet  
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  Abstract The history of the Americas involved the encounter of millions of Native Americans, Europeans, and Africans. A variable admixture of these three continental groups has taken place throughout the continent, influenced by demography and a range of social factors. This variable admixture has had a major influence on the genetic makeup of populations across the continent. Here, we summarize the demographic history of the region, highlight some social factors that affected historical admixture, and review major patterns of ancestry across the Western Hemisphere based on genetic data.  
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  Call Number UofT @ mathieu.lemaire @ Serial 45891  
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Author Agudelo, D.; Duringer, A.; Bozoyan, L.; Huard, C.C.; Carter, S.; Loehr, J.; Synodinou, D.; Drouin, M.; Salsman, J.; Dellaire, G.; Laganière, J.; Doyon, Y. url  openurl
  Title Marker-free coselection for CRISPR-driven genome editing in human cells Type Journal Article
  Year 2017 Publication Abbreviated Journal Nat Methods  
  Volume 14 Issue 6 Pages 615-620  
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  Abstract Targeted genome editing enables the creation of bona fide cellular models for biological research and may be applied to human cell-based therapies. Therefore, broadly applicable and versatile methods for increasing its efficacy in cell populations are highly desirable. We designed a simple and robust coselection strategy for enrichment of cells with either nuclease-driven nonhomologous end joining (NHEJ) or homology-directed repair (HDR) events by harnessing the multiplexing capabilities of CRISPR-Cas9 and Cpf1 systems. Selection for dominant alleles of the ubiquitous sodium/potassium pump (Na(+)/K(+) ATPase) that rendered cells resistant to ouabain was used to enrich for custom genetic modifications at another unlinked locus of interest, thereby effectively increasing the recovery of engineered cells. The process is readily adaptable to transformed and primary cells, including hematopoietic stem and progenitor cells. The use of universal CRISPR reagents and a commercially available small-molecule inhibitor streamlines the incorporation of marker-free genetic changes in human cells.  
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  ISSN 1548-7091 ISBN Medium  
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  Notes Approved no  
  Call Number UofT @ mathieu.lemaire @ Serial 45877  
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Author Aguet, F.; Ardlie, K.G.; Cummings, B.B.; Gelfand, E.T.; Getz, G.; Hadley, K.; Handsaker, R.E.; Huang, K.H.; Kashin, S.; Karczewski, K.J.; Lek, M.; Li, X.; MacArthur, D.G.; Nedzel, J.L.; Nguyen, D.T.; Noble, M.S.; Segrè, A.V.; Trowbridge, C.A.; Tukiainen, T.; Abell, N.S.; Balliu, B.; Barshir, R.; Basha, O.; Battle, A.; Bogu, G.K.; Brown, A.; Brown, C.D.; Castel, S.E.; Chen, L.S.; Chiang, C.; Conrad, D.F.; Cox, N.J.; Damani, F.N.; Davis, J.R.; Delaneau, O.; Dermitzakis, E.T.; Engelhardt, B.E.; Eskin, E.; Ferreira, P.G.; Frésard, L.; Gamazon, E.R.; Garrido-Martín, D.; Gewirtz, A.D.H.; Gliner, G.; Gloudemans, M.J.; Guigo, R.; Hall, I.M.; Han, B.; He, Y.; Hormozdiari, F.; Howald, C.; Kyung Im, H.; Jo, B.; Yong Kang, E.; Kim, Y.; Kim-Hellmuth, S.; Lappalainen, T.; Li, G.; Li, X.; Liu, B.; Mangul, S.; McCarthy, M.I.; McDowell, I.C.; Mohammadi, P.; Monlong, J.; Montgomery, S.B.; Muñoz-Aguirre, M.; Ndungu, A.W.; Nicolae, D.L.; Nobel, A.B.; Oliva, M.; Ongen, H.; Palowitch, J.J.; Panousis, N.; Papasaikas, P.; Park, Y.S.; Parsana, P.; Payne, A.J.; Peterson, C.B.; Quan, J.; Reverter, F.; Sabatti, C.; Saha, A.; Sammeth, M.; Scott, A.J.; Shabalin, A.A.; Sodaei, R.; Stephens, M.; Stranger, B.E.; Strober, B.J.; Sul, J.H.; Tsang, E.K.; Urbut, S.; van de Bunt, M.; Wang, G.; Wen, X.; Wright, F.A.; Xi, H.S.; Yeger-Lotem, E.; Zappala, Z.; Zaugg, J.B.; Zhou, Y.-H.; Akey, J.M.; Bates, D.; Chan, J.; Chen, L.S.; Claussnitzer, M.; Demanelis, K.; Diegel, M.; Doherty, J.A.; Feinberg, A.P.; Fernando, M.S.; Halow, J.; Hansen, K.D.; Haugen, E.; Hickey, P.F.; Hou, L.; Jasmine, F.; Jian, R.; Jiang, L.; Johnson, A.; Kaul, R.; Kellis, M.; Kibriya, M.G.; Lee, K.; Billy Li, J.; Li, Q.; Li, X.; Lin, J.; Lin, S.; Linder, S.; Linke, C.; Liu, Y.; Maurano, M.T.; Molinie, B.; Montgomery, S.B.; Nelson, J.; Neri, F.J.; Oliva, M.; Park, Y.; Pierce, B.L.; Rinaldi, N.J.; Rizzardi, L.F.; Sandstrom, R.; Skol, A.; Smith, K.S.; Snyder, M.P.; Stamatoyannopoulos, J.; Stranger, B.E.; Tang, H.; Tsang, E.K.; Wang, L.; Wang, M.; Van Wittenberghe, N.; Wu, F.; Zhang, R.; Nierras, C.R.; Branton, P.A.; Carithers, L.J.; Guan, P.; Moore, H.M.; Rao, A.; Vaught, J.B.; Gould, S.E.; Lockart, N.C.; Martin, C.; Struewing, J.P.; Volpi, S.; Addington, A.M.; Koester, S.E.; Little, A.R.; Brigham, L.E.; Hasz, R.; Hunter, M.; Johns, C.; Johnson, M.; Kopen, G.; Leinweber, W.F.; Lonsdale, J.T.; McDonald, A.; Mestichelli, B.; Myer, K.; Roe, B.; Salvatore, M.; Shad, S.; Thomas, J.A.; Walters, G.; Washington, M.; Wheeler, J.; Bridge, J.; Foster, B.A.; Gillard, B.M.; Karasik, E.; Kumar, R.; Miklos, M.; Moser, M.T.; Jewell, S.D.; Montroy, R.G.; Rohrer, D.C.; Valley, D.R.; Davis, D.A.; Mash, D.C.; Undale, A.H.; Smith, A.M.; Tabor, D.E.; Roche, N.V.; McLean, J.A.; Vatanian, N.; Robinson, K.L.; Sobin, L.; Barcus, M.E.; Valentino, K.M.; Qi, L.; Hunter, S.; Hariharan, P.; Singh, S.; Um, K.S.; Matose, T.; Tomaszewski, M.M.; Barker, L.K.; Mosavel, M.; Siminoff, L.A.; Traino, H.M.; Flicek, P.; Juettemann, T.; Ruffier, M.; Sheppard, D.; Taylor, K.; Trevanion, S.J.; Zerbino, D.R.; Craft, B.; Goldman, M.; Haeussler, M.; Kent, W.J.; Lee, C.M.; Paten, B.; Rosenbloom, K.R.; Vivian, J.; Zhu, J.; Aguet, F.; Brown, A.A.; Castel, S.E.; Davis, J.R.; He, Y.; Jo, B.; Mohammadi, P.; Park, Y.S.; Parsana, P.; Segrè, A.V.; Strober, B.J.; Zappala, Z.; Cummings, B.B.; Gelfand, E.T.; Hadley, K.; Huang, K.H.; Lek, M.; Li, X.; Nedzel, J.L.; Nguyen, D.Y.; Noble, M.S.; Sullivan, T.J.; Tukiainen, T.; MacArthur, D.G.; Getz, G.; Addington, A.; Guan, P.; Koester, S.; Little, A.R.; Lockhart, N.C.; Moore, H.M.; Rao, A.; Struewing, J.P.; Volpi, S.; Brigham, L.E.; Hasz, R.; Hunter, M.; Johns, C.; Johnson, M.; Kopen, G.; Leinweber, W.F.; Lonsdale, J.T.; McDonald, A.; Mestichelli, B.; Myer, K.; Roe, B.; Salvatore, M.; Shad, S.; Thomas, J.A.; Walters, G.; Washington, M.; Wheeler, J.; Bridge, J.; Foster, B.A.; Gillard, B.M.; Karasik, E.; Kumar, R.; Miklos, M.; Moser, M.T.; Jewell, S.D.; Montroy, R.G.; Rohrer, D.C.; Valley, D.; Mash, D.C.; Davis, D.A.; Sobin, L.; Barcus, M.E.; Branton, P.A.; Abell, N.S.; Balliu, B.; Delaneau, O.; Frésard, L.; Gamazon, E.R.; Garrido-Martín, D.; Gewirtz, A.D.H.; Gliner, G.; Gloudemans, M.J.; Han, B.; He, A.Z.; Hormozdiari, F.; Li, X.; Liu, B.; Kang, E.Y.; McDowell, I.C.; Ongen, H.; Palowitch, J.J.; Peterson, C.B.; Quon, G.; Ripke, S.; Saha, A.; Shabalin, A.A.; Shimko, T.C.; Sul, J.H.; Teran, N.A.; Tsang, E.K.; Zhang, H.; Zhou, Y.-H.; Bustamante, C.D.; Cox, N.J.; Guigó, R.; Kellis, M.; McCarthy, M.I.; Conrad, D.F.; Eskin, E.; Li, G.; Nobel, A.B.; Sabatti, C.; Stranger, B.E.; Wen, X.; Wright, F.A.; Ardlie, K.G.; Dermitzakis, E.T.; Lappalainen, T.; Battle, A.; Brown, C.D.; Engelhardt, B.E.; Montgomery, S.B. url  openurl
  Title Genetic effects on gene expression across human tissues Type Journal Article
  Year 2017 Publication Abbreviated Journal Nature  
  Volume 550 Issue 7675 Pages 204-213  
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  ISSN 0028-0836 ISBN Medium  
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  Notes Approved no  
  Call Number UofT @ mathieu.lemaire @ Serial 45917  
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