Timex - PMC

Mengyu Xie, Kyubum Lee, John H Lockhart, Scott D Cukras, Rodrigo Carvajal, Amer A Beg, Elsa R Flores, Mingxiang Teng, Christine H Chung, Aik Choon Tan

Bioinformatics. 2021 Oct 15; 37(20): 3681–3683. Published online 2021 Apr 26. doi: 10.1093/bioinformatics/btab244

PMCID:: PMC11025676

Abstract Article PDF–192K

Select item 96380554.

Temporal disambiguation of relative temporal expressions in clinical texts

Amy L. Olex, Bridget T. McInnes

Front Res Metr Anal. 2022; 7: 1001266. Published online 2022 Oct 24. doi: 10.3389/frma.2022.1001266

PMCID:: PMC9638055

Abstract Article PDF–3.2M

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Subchronic safety evaluation of hot-water extract from thinned immature mangos (Mangifera indica ‘Irwin’): 90-days oral toxicity study in rats

Hayato Tajiri, Wataru Tanaka, Masakatsu Takashima, Hiroki Matsuyama, Takuya Sugita, Kenta Hidaka, Hiroyuki Sakakibara

Toxicol Rep. 2021; 8: 1046–1053. Published online 2021 May 12. doi: 10.1016/j.toxrep.2021.05.005

PMCID:: PMC8142251

Abstract Article PDF–1.2M

Select item 40067246.

Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization

Rituparna Mukhopadhyay, Julien Lajugie, Nicolas Fourel, Ari Selzer, Michael Schizas, Boris Bartholdy, Jessica Mar, Chii Mei Lin, Melvenia M. Martin, Michael Ryan, Mirit I. Aladjem, Eric E. Bouhassira

PLoS Genet. 2014 May; 10(5): e1004319. Published online 2014 May 1. doi: 10.1371/journal.pgen.1004319

PMCID:: PMC4006724

Abstract Article PDF–2.3M

Select item 27921757.

Predictable dynamic program of timing of DNA replication in human cells

Romain Desprat, Danielle Thierry-Mieg, Nathalie Lailler, Julien Lajugie, Carl Schildkraut, Jean Thierry-Mieg, Eric E. Bouhassira

Genome Res. 2009 Dec; 19(12): 2288–2299. doi: 10.1101/gr.094060.109

PMCID:: PMC2792175

Abstract Article PDF–2.0M

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EGFR Inhibition by Cetuximab Modulates Hypoxia and IFN Response Genes in Head and Neck Squamous Cell Carcinoma

Ritu Chaudhary, Robbert J.C. Slebos, Leenil C. Noel, Feifei Song, Maria I. Poole, Dirk S. Hoening, Juan C. Hernandez-Prera, Jose R. Conejo-Garcia, Jose A. Guevara-Patino, Xuefeng Wang, Mengyu Xie, Aik Choon Tan, Christine H. Chung

Cancer Res Commun. 2023 May; 3(5): 896–907. Published online 2023 May 22. doi: 10.1158/2767-9764.CRC-22-0443

PMCID:: PMC10202124

Abstract Article PDF–8.5M

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An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge

Yan Xu, Yining Wang, Tianren Liu, Junichi Tsujii, Eric I-Chao Chang

J Am Med Inform Assoc. 2013 Sep; 20(5): 849–858. Published online 2013 Mar 6. doi: 10.1136/amiajnl-2012-001607

PMCID:: PMC3756267

Abstract Article PDF–686K

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Genomic patterns of transcription–replication interactions in mouse primary B cells

Commodore P St Germain, Hongchang Zhao, Vrishti Sinha, Lionel A Sanz, Frédéric Chédin, Jacqueline H Barlow

Nucleic Acids Res. 2022 Feb 28; 50(4): 2051–2073. Published online 2022 Jan 31. doi: 10.1093/nar/gkac035

PMCID:: PMC8887484

Abstract Article PDF–3.8M

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Deciphering the Tumor–Immune–Microbe Interactions in HPV-Negative Head and Neck Cancer

Min Hu, Samuel Coleman, Muhammad Zaki Hidayatullah Fadlullah, Daniel Spakowicz, Christine H. Chung, Aik Choon Tan

Genes (Basel) 2023 Aug; 14(8): 1599. Published online 2023 Aug 8. doi: 10.3390/genes14081599

PMCID:: PMC10454300

Abstract Article PDF–3.9M

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Improved prognosis and evidence of enhanced immunogenicity in tumor and circulation of high-risk melanoma patients with unknown primary

Ahmad A Tarhini, Sandra J Lee, Aik-Choon Tan, Issam M El Naqa, F Stephen Hodi, Lisa H Butterfield, William A LaFramboise, Walter J Storkus, Arivarasan D Karunamurthy, Jose R Conejo-Garcia, Patrick Hwu, Howard Streicher, Vernon K Sondak, John M Kirkwood

J Immunother Cancer. 2022; 10(1): e004310. Published online 2022 Jan 24. doi: 10.1136/jitc-2021-004310

PMCID:: PMC8788316

Abstract Article PDF–1.8M

Select item 108675913.

The Effects of Light on a Circadian Rhythm of Conidiation in Neurospora

Malcolm L. Sargent, Winslow R. Briggs

Plant Physiol. 1967 Nov; 42(11): 1504–1510. doi: 10.1104/pp.42.11.1504

PMCID:: PMC1086759

Summary Page Browse PDF–1.0M

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Premature Termination Codon of 1Dy12 Gene Improves Cookie Quality in Ningmai9 Wheat

Guangxiao Liu, Yujiao Gao, Huadun Wang, Yonggang Wang, Jianmin Chen, Pingping Zhang, Hongxiang Ma

Front Plant Sci. 2022; 13: 835164. Published online 2022 May 12. doi: 10.3389/fpls.2022.835164

PMCID:: PMC9134186

Abstract Article PDF–1.8M

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A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence

Sander Canisius, John W. M. Martens, Lodewyk F. A. Wessels

Genome Biol. 2016; 17: 261. Published online 2016 Dec 16. doi: 10.1186/s13059-016-1114-x

PMCID:: PMC5162102

Abstract Article PDF–1.1M

Select item 24977016.

Genetic Determinants of Circadian Rhythmicity in Neurospora

Malcolm L. Sargent, Dow O. Woodward

J Bacteriol. 1969 Feb; 97(2): 861–866. doi: 10.1128/jb.97.2.861-866.1969

PMCID:: PMC249770

Summary Page Browse PDF–890K

Select item 916432017.

Enhanced immune activation within the tumor microenvironment and circulation of female high-risk melanoma patients and improved survival with adjuvant CTLA4 blockade compared to males

Mariam Saad, Sandra J. Lee, Aik Choon Tan, Issam M. El Naqa, F. Stephen Hodi, Lisa H. Butterfield, William A. LaFramboise, Walter Storkus, Arivarasan D. Karunamurthy, Jose Conejo-Garcia, Patrick Hwu, Howard Streicher, Vernon K. Sondak, John M. Kirkwood, Ahmad A. Tarhini

J Transl Med. 2022; 20: 253. Published online 2022 Jun 3. doi: 10.1186/s12967-022-03450-3

PMCID:: PMC9164320

Abstract Article PDF–1.2M

Select item 659173518.

Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse

Anthony Tubbs, Sriram Sridharan, Niek van Wietmarschen, Yaakov Maman, Elsa Callen, Andre Stanlie, Wei Wu, Xia Wu, Amanda Day, Nancy Wong, Mianmian Yin, Andres Canela, Haiqing Fu, Christophe Redon, Steven C. Pruitt, Yan Jaszczyszyn, Mirit I. Aladjem, Peter D. Aplan, Olivier Hyrien, André Nussenzweig

Cell. Author manuscript; available in PMC 2019 Jun 25.

Published in final edited form as: Cell. 2018 Aug 23; 174(5): 1127–1142.e19. Published online 2018 Aug 2. doi: 10.1016/j.cell.2018.07.011

PMCID:: PMC6591735

Abstract Article PDF–2.9M

Select item 472011219.

Free electron laser-driven ultrafast rearrangement of the electronic structure in Ti

E. Principi, E. Giangrisostomi, R. Cucini, F. Bencivenga, A. Battistoni, A. Gessini, R. Mincigrucci, M. Saito, S. Di Fonzo, F. D'Amico, A. Di Cicco, R. Gunnella, A. Filipponi, A. Giglia, S. Nannarone, C. Masciovecchio

Struct Dyn. 2016 Mar; 3(2): 023604. Published online 2015 Nov 12. doi: 10.1063/1.4935687

PMCID:: PMC4720112

Abstract Article PDF–479K

Select item 1070177320.

Expression of cancer–testis antigens in the immune microenvironment of non‐small cell lung cancer

Feria Hikmet, Marc Rassy, Max Backman, Loren Méar, Johanna Sofia Margareta Mattsson, Dijana Djureinovic, Johan Botling, Hans Brunnström, Patrick Micke, Cecilia Lindskog

Mol Oncol. 2023 Dec; 17(12): 2603–2617. Published online 2023 Jun 27. doi: 10.1002/1878-0261.13474

PMCID:: PMC10701773

Abstract Article PDF–1.1M

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Figure 1

System result analysis. (A) EVENT distribution. (B) EVENT type distribution. (C) TIMEX distribution. (D) TIMEX type distribution. (E) Timex distribution. (F) Timex type distribution.

Evaluating temporal relations in clinical text: 2012 i2b2 Challenge

J Am Med Inform Assoc. 2013 Sep;20(5):806-813.
Figure 2

Structure of the TIMEX Extraction and Normalization System.

Normalization of relative and incomplete temporal expressions in clinical narratives

J Am Med Inform Assoc. 2015 Sep;22(5):1001-1008.
Figure 4

Effects of the consumption of a hot-water extract of thinned immature mangoes (TIMEx) on the serum concentrations of hormones in apolipoprotein E-deficient (ApoE^−/−) mice. ApoE^−/− mice were divided into three diet groups: an AIN-93M-based 20% fat diet containing 0%, 0.1%, or 1.0% TIMEx. Following 8-weeks consumption, mice were sacrificed without fasting. The data are mean ± SEM; n = 9. (a) Resistin, (b) leptin, and (c) glucose-dependent insulinotropic polypeptide (GIP), (d) Insulin. * p < 0.05 vs. the control group (0% TIMEx); Williams’s multiple comparison test.

Beneficial Effects of the Consumption of Hot-Water Extracts of Thinned Immature Mangos (Mangifera indica “Irwin”) on the Hypertriglyceridemia of Apolipoprotein E-Deficient Mice

Metabolites. 2022 Feb;12(2):116.
Figure 4Hi-resolution TimEX-seq analysis reveals the fine structure of the timing domains.

25-resolution TimEX profiles. Top panel: S/G1 ratios calculated every 1 kb are plotted. At this read depth, the shape of the timing domains can be distinguished without any smoothing. Middle and bottom panel: same data after Gaussian smoothing using sigma = 20 Kb or 100 kb. Smoothing at 100 kb, which was necessary to obtain reproducible profiles after read-depth at a low read depth or with micro-array based methods, reveals the major timing domains but smooth the details out. Inset: red curve: TimEX profile after 20 Kb Gaussian smoothing for individual FNY01 3_2; black curve: same data after 100 kb Gaussian smoothing; blue curve: TimEX profile for individual FNY01 3_3 after 20 kb Gaussian smoothing. Note the reproducibility sub-peaks or ripples in the profiles of FNY01 3_2 and 3_3 and how the 100 kb processing masks the details.

Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization

PLoS Genet. 2014 May;10(5):e1004319.