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Maternal BMI, IGF-I Levels, and Birth Weight in African American and White Infants.

International journal of pediatrics

Vidal AC, Murtha AP, Murphy SK, Fortner K, Overcash F, Henry N, Schildkraut JM, Forman MR, Demark-Wahnefried W, Kurtzberg J, Jirtle R, Hoyo C.
PMID: 23861689
Int J Pediatr. 2013;2013:191472. doi: 10.1155/2013/191472. Epub 2013 Jun 03.

At birth, elevated IGF-I levels have been linked to birth weight extremes; high birth weight and low birth weight are risk factors for adult-onset chronic diseases including obesity, cardiovascular disease, and type 2 diabetes. We examined associations between plasma...

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Vidal AC, Murtha AP, Murphy SK, et al. Maternal BMI, IGF-I Levels, and Birth Weight in African American and White Infants. Int J Pediatr. 2013;2013:191472doi: 10.1155/2013/191472.
Vidal, A. C., Murtha, A. P., Murphy, S. K., Fortner, K., Overcash, F., Henry, N., Schildkraut, J. M., Forman, M. R., Demark-Wahnefried, W., Kurtzberg, J., Jirtle, R., & Hoyo, C. (2013). Maternal BMI, IGF-I Levels, and Birth Weight in African American and White Infants. International journal of pediatrics, 2013191472. https://doi.org/10.1155/2013/191472
Vidal, Adriana C, et al. "Maternal BMI, IGF-I Levels, and Birth Weight in African American and White Infants." International journal of pediatrics vol. 2013 (2013): 191472. doi: https://doi.org/10.1155/2013/191472
Vidal AC, Murtha AP, Murphy SK, Fortner K, Overcash F, Henry N, Schildkraut JM, Forman MR, Demark-Wahnefried W, Kurtzberg J, Jirtle R, Hoyo C. Maternal BMI, IGF-I Levels, and Birth Weight in African American and White Infants. Int J Pediatr. 2013;2013:191472. doi: 10.1155/2013/191472. Epub 2013 Jun 03. PMID: 23861689; PMCID: PMC3686113.
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G1 Synchronization of CHO Cells by Isoleucine Deprivation.

CSH protocols

Galgano PJ, Schildkraut CL.
PMID: 22485889
CSH Protoc. 2006 Sep 01;2006(4). doi: 10.1101/pdb.prot4486.

INTRODUCTIONThis protocol provides a method for the synchronization of a monolayer culture of CHO cells in G(1) using isoleucine deprivation. Since CHO cells can also be adapted to grow in suspension culture, this procedure can be used to obtain...

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Galgano PJ, Schildkraut CL. G1 Synchronization of CHO Cells by Isoleucine Deprivation. CSH Protoc. 2006;2006(4)doi: 10.1101/pdb.prot4486.
Galgano, P. J., & Schildkraut, C. L. (2006). G1 Synchronization of CHO Cells by Isoleucine Deprivation. CSH protocols, 2006(4), . https://doi.org/10.1101/pdb.prot4486
Galgano, Paul J, and Schildkraut, Carl L. "G1 Synchronization of CHO Cells by Isoleucine Deprivation." CSH protocols vol. 2006,4 (2006). doi: https://doi.org/10.1101/pdb.prot4486
Galgano PJ, Schildkraut CL. G1 Synchronization of CHO Cells by Isoleucine Deprivation. CSH Protoc. 2006 Sep 01;2006(4). doi: 10.1101/pdb.prot4486. PMID: 22485889.
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Synchronization of Mammalian cell cultures in mitosis using selective detachment.

CSH protocols

Galgano PJ, Schildkraut CL.
PMID: 22485891
CSH Protoc. 2006 Sep 01;2006(4). doi: 10.1101/pdb.prot4489.

INTRODUCTIONThis protocol describes a method for synchronizing monolayer cells in mitosis using selective detachment from their substrate. During mitosis, cells become more spherical, causing them to become more loosely attached to their substrate. The "rounded up" cells are selectively...

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Galgano PJ, Schildkraut CL. Synchronization of Mammalian cell cultures in mitosis using selective detachment. CSH Protoc. 2006;2006(4)doi: 10.1101/pdb.prot4489.
Galgano, P. J., & Schildkraut, C. L. (2006). Synchronization of Mammalian cell cultures in mitosis using selective detachment. CSH protocols, 2006(4), . https://doi.org/10.1101/pdb.prot4489
Galgano, Paul J, and Schildkraut, Carl L. "Synchronization of Mammalian cell cultures in mitosis using selective detachment." CSH protocols vol. 2006,4 (2006). doi: https://doi.org/10.1101/pdb.prot4489
Galgano PJ, Schildkraut CL. Synchronization of Mammalian cell cultures in mitosis using selective detachment. CSH Protoc. 2006 Sep 01;2006(4). doi: 10.1101/pdb.prot4489. PMID: 22485891.
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The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of the IGF2 imprinted control regions in the offspring.

Clinical epigenetics

Soubry A, Murphy S, Huang Z, Murtha A, Schildkraut J, Jirtle R, Wang F, Kurtzberg J, Demark-Wahnefried W, Forman M, Hoyo C.
PMID: 22414206
Clin Epigenetics. 2011 Oct 26;3:2. doi: 10.1186/1868-7083-3-2.

In utero exposures to environmental factors may result in persistent epigenetic modifications affecting normal development and susceptibility to chronic diseases in later life. We explored the relationship between exposure of the growing fetus to maternal depression or antidepressants and...

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Soubry A, Murphy S, Huang Z, et al. The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of the IGF2 imprinted control regions in the offspring. Clin Epigenetics. 2011;3:2doi: 10.1186/1868-7083-3-2.
Soubry, A., Murphy, S., Huang, Z., Murtha, A., Schildkraut, J., Jirtle, R., Wang, F., Kurtzberg, J., Demark-Wahnefried, W., Forman, M., & Hoyo, C. (2011). The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of the IGF2 imprinted control regions in the offspring. Clinical epigenetics, 32. https://doi.org/10.1186/1868-7083-3-2
Soubry, A, et al. "The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of the IGF2 imprinted control regions in the offspring." Clinical epigenetics vol. 3 (2011): 2. doi: https://doi.org/10.1186/1868-7083-3-2
Soubry A, Murphy S, Huang Z, Murtha A, Schildkraut J, Jirtle R, Wang F, Kurtzberg J, Demark-Wahnefried W, Forman M, Hoyo C. The effects of depression and use of antidepressive medicines during pregnancy on the methylation status of the IGF2 imprinted control regions in the offspring. Clin Epigenetics. 2011 Oct 26;3:2. doi: 10.1186/1868-7083-3-2. PMID: 22414206; PMCID: PMC3257545.
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Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq.

Genome research

Yan B, Tzertzinis G, Schildkraut I, Ettwiller L.
PMID: 34815308
Genome Res. 2022 Jan;32(1):162-174. doi: 10.1101/gr.275784.121. Epub 2021 Nov 23.

Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the...

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Yan B, Tzertzinis G, Schildkraut I, et al. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2021;32(1):162-174doi: 10.1101/gr.275784.121.
Yan, B., Tzertzinis, G., Schildkraut, I., & Ettwiller, L. (2022). Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome research, 32(1), 162-174. https://doi.org/10.1101/gr.275784.121
Yan, Bo, et al. "Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq." Genome research vol. 32,1 (2022): 162-174. doi: https://doi.org/10.1101/gr.275784.121
Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2022 Jan;32(1):162-174. doi: 10.1101/gr.275784.121. Epub 2021 Nov 23. PMID: 34815308.
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Replication stress induces global chromosome breakage in the fragile X genome.

Cell reports

Chakraborty A, Jenjaroenpun P, Li J, El Hilali S, McCulley A, Haarer B, Hoffman EA, Belak A, Thorland A, Hehnly H, Schildkraut CL, Chen CL, Kuznetsov VA, Feng W.
PMID: 33761342
Cell Rep. 2021 Mar 23;34(12):108838. doi: 10.1016/j.celrep.2021.108838.

No abstract available.

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Chakraborty A, Jenjaroenpun P, Li J, et al. Replication stress induces global chromosome breakage in the fragile X genome. Cell Rep. 2021;34(12):108838doi: 10.1016/j.celrep.2021.108838.
Chakraborty, A., Jenjaroenpun, P., Li, J., El Hilali, S., McCulley, A., Haarer, B., Hoffman, E. A., Belak, A., Thorland, A., Hehnly, H., Schildkraut, C. L., Chen, C. L., Kuznetsov, V. A., & Feng, W. (2021). Replication stress induces global chromosome breakage in the fragile X genome. Cell reports, 34(12), 108838. https://doi.org/10.1016/j.celrep.2021.108838
Chakraborty, Arijita, et al. "Replication stress induces global chromosome breakage in the fragile X genome." Cell reports vol. 34,12 (2021): 108838. doi: https://doi.org/10.1016/j.celrep.2021.108838
Chakraborty A, Jenjaroenpun P, Li J, El Hilali S, McCulley A, Haarer B, Hoffman EA, Belak A, Thorland A, Hehnly H, Schildkraut CL, Chen CL, Kuznetsov VA, Feng W. Replication stress induces global chromosome breakage in the fragile X genome. Cell Rep. 2021 Mar 23;34(12):108838. doi: 10.1016/j.celrep.2021.108838. PMID: 33761342; PMCID: PMC8045960.
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Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites.

Proceedings of the National Academy of Sciences of the United States of America

Twayana S, Bacolla A, Barreto-Galvez A, De-Paula RB, Drosopoulos WC, Kosiyatrakul ST, Bouhassira EE, Tainer JA, Madireddy A, Schildkraut CL.
PMID: 34815340
Proc Natl Acad Sci U S A. 2021 Nov 30;118(48). doi: 10.1073/pnas.2106477118.

Common fragile sites (CFSs) are difficult-to-replicate genomic regions that form gaps and breaks on metaphase chromosomes under replication stress. They are hotspots for chromosomal instability in cancer. Repetitive sequences located at CFS loci are inefficiently copied by replicative DNA...

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Twayana S, Bacolla A, Barreto-Galvez A, et al. Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites. Proc Natl Acad Sci U S A. 2021;118(48)doi: 10.1073/pnas.2106477118.
Twayana, S., Bacolla, A., Barreto-Galvez, A., De-Paula, R. B., Drosopoulos, W. C., Kosiyatrakul, S. T., Bouhassira, E. E., Tainer, J. A., Madireddy, A., & Schildkraut, C. L. (2021). Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites. Proceedings of the National Academy of Sciences of the United States of America, 118(48), . https://doi.org/10.1073/pnas.2106477118
Twayana, Shyam, et al. "Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites." Proceedings of the National Academy of Sciences of the United States of America vol. 118,48 (2021). doi: https://doi.org/10.1073/pnas.2106477118
Twayana S, Bacolla A, Barreto-Galvez A, De-Paula RB, Drosopoulos WC, Kosiyatrakul ST, Bouhassira EE, Tainer JA, Madireddy A, Schildkraut CL. Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites. Proc Natl Acad Sci U S A. 2021 Nov 30;118(48). doi: 10.1073/pnas.2106477118. PMID: 34815340; PMCID: PMC8640788.
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The epidemiology of nontuberculous mycobacterial pulmonary disease in the Netherlands.

ERJ open research

Schildkraut JA, Zweijpfenning SMH, Nap M, He K, Dacheva E, Overbeek J, Tostmann A, Wertheim HFL, Hoefsloot W, van Ingen J.
PMID: 34262970
ERJ Open Res. 2021 Jul 12;7(3). doi: 10.1183/23120541.00207-2021. eCollection 2021 Jul.

BACKGROUND: Nontuberculous mycobacteria (NTM) are emerging opportunistic pathogens of humans. Because NTM pulmonary disease (PD) is not a notifiable disease in Europe, the epidemiology of NTM-PD is not well known. However, the prevalence of NTM-PD is thought to be...

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Schildkraut JA, Zweijpfenning SMH, Nap M, et al. The epidemiology of nontuberculous mycobacterial pulmonary disease in the Netherlands. ERJ Open Res. 2021;7(3)doi: 10.1183/23120541.00207-2021.
Schildkraut, J. A., Zweijpfenning, S. M. H., Nap, M., He, K., Dacheva, E., Overbeek, J., Tostmann, A., Wertheim, H. F. L., Hoefsloot, W., & van Ingen, J. (2021). The epidemiology of nontuberculous mycobacterial pulmonary disease in the Netherlands. ERJ open research, 7(3), . https://doi.org/10.1183/23120541.00207-2021
Schildkraut, Jodie Anne, et al. "The epidemiology of nontuberculous mycobacterial pulmonary disease in the Netherlands." ERJ open research vol. 7,3 (2021). doi: https://doi.org/10.1183/23120541.00207-2021
Schildkraut JA, Zweijpfenning SMH, Nap M, He K, Dacheva E, Overbeek J, Tostmann A, Wertheim HFL, Hoefsloot W, van Ingen J. The epidemiology of nontuberculous mycobacterial pulmonary disease in the Netherlands. ERJ Open Res. 2021 Jul 12;7(3). doi: 10.1183/23120541.00207-2021. eCollection 2021 Jul. PMID: 34262970; PMCID: PMC8273392.
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Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq.

Genome research

Yan B, Tzertzinis G, Schildkraut I, Ettwiller L.
PMID: 34815308
Genome Res. 2021 Nov 23; doi: 10.1101/gr.275784.121. Epub 2021 Nov 23.

Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the...

Cite
Yan B, Tzertzinis G, Schildkraut I, et al. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2021;doi: 10.1101/gr.275784.121.
Yan, B., Tzertzinis, G., Schildkraut, I., & Ettwiller, L. (2021). Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome research, . https://doi.org/10.1101/gr.275784.121
Yan, Bo, et al. "Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq." Genome research vol. (2021). doi: https://doi.org/10.1101/gr.275784.121
Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res. 2021 Nov 23; doi: 10.1101/gr.275784.121. Epub 2021 Nov 23. PMID: 34815308.
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A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA.

eLife

Yang W, Lin YC, Johnson W, Dai N, Vaisvila R, Weigele P, Lee YJ, Corrêa IR, Schildkraut I, Ettwiller L.
PMID: 34747693
Elife. 2021 Nov 08;10. doi: 10.7554/eLife.70021. Epub 2021 Nov 08.

Shotgun metagenomic sequencing is a powerful approach to study microbiomes in an unbiased manner and of increasing relevance for identifying novel enzymatic functions. However, the potential of metagenomics to relate from microbiome composition to function has thus far been...

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Yang W, Lin YC, Johnson W, et al. A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. Elife. 2021;10doi: 10.7554/eLife.70021.
Yang, W., Lin, Y. C., Johnson, W., Dai, N., Vaisvila, R., Weigele, P., Lee, Y. J., Corrêa, I. R., Schildkraut, I., & Ettwiller, L. (2021). A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. eLife, 10. https://doi.org/10.7554/eLife.70021
Yang, Weiwei, et al. "A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA." eLife vol. 10 (2021). doi: https://doi.org/10.7554/eLife.70021
Yang W, Lin YC, Johnson W, Dai N, Vaisvila R, Weigele P, Lee YJ, Corrêa IR, Schildkraut I, Ettwiller L. A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA. Elife. 2021 Nov 08;10. doi: 10.7554/eLife.70021. Epub 2021 Nov 08. PMID: 34747693.
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Publisher Correction: Mendelian randomisation study of the relationship between vitamin D and risk of glioma.

Scientific reports

Takahashi H, Cornish AJ, Sud A, Law PJ, Kinnersley B, Ostrom QT, Labreche K, Eckel-Passow JE, Armstrong GN, Claus EB, Il'yasova D, Schildkraut J, Barnholtz-Sloan JS, Olson SH, Bernstein JL, Lai RK, Schoemaker MJ, Simon M, Hoffmann P, Nöthen MM, Jöckel KH, Chanock S, Rajaraman P, Johansen C, Jenkins RB, Melin BS, Wrensch MR, Sanson M, Bondy ML, Turnbull C, Houlston RS.
PMID: 31118477
Sci Rep. 2019 May 23;9(1):7924. doi: 10.1038/s41598-019-43787-2.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

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Takahashi H, Cornish AJ, Sud A, et al. Publisher Correction: Mendelian randomisation study of the relationship between vitamin D and risk of glioma. Sci Rep. 2019;9(1):7924doi: 10.1038/s41598-019-43787-2.
Takahashi, H., Cornish, A. J., Sud, A., Law, P. J., Kinnersley, B., Ostrom, Q. T., Labreche, K., Eckel-Passow, J. E., Armstrong, G. N., Claus, E. B., Il'yasova, D., Schildkraut, J., Barnholtz-Sloan, J. S., Olson, S. H., Bernstein, J. L., Lai, R. K., Schoemaker, M. J., Simon, M., Hoffmann, P., Nöthen, M. M., Jöckel, K. H., Chanock, S., Rajaraman, P., Johansen, C., Jenkins, R. B., Melin, B. S., Wrensch, M. R., Sanson, M., Bondy, M. L., Turnbull, C., & Houlston, R. S. (2019). Publisher Correction: Mendelian randomisation study of the relationship between vitamin D and risk of glioma. Scientific reports, 9(1), 7924. https://doi.org/10.1038/s41598-019-43787-2
Takahashi, Hannah, et al. "Publisher Correction: Mendelian randomisation study of the relationship between vitamin D and risk of glioma." Scientific reports vol. 9,1 (2019): 7924. doi: https://doi.org/10.1038/s41598-019-43787-2
Takahashi H, Cornish AJ, Sud A, Law PJ, Kinnersley B, Ostrom QT, Labreche K, Eckel-Passow JE, Armstrong GN, Claus EB, Il'yasova D, Schildkraut J, Barnholtz-Sloan JS, Olson SH, Bernstein JL, Lai RK, Schoemaker MJ, Simon M, Hoffmann P, Nöthen MM, Jöckel KH, Chanock S, Rajaraman P, Johansen C, Jenkins RB, Melin BS, Wrensch MR, Sanson M, Bondy ML, Turnbull C, Houlston RS. Publisher Correction: Mendelian randomisation study of the relationship between vitamin D and risk of glioma. Sci Rep. 2019 May 23;9(1):7924. doi: 10.1038/s41598-019-43787-2. PMID: 31118477; PMCID: PMC6531429.
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RNA Sequencing Elucidates Drug-Specific Mechanisms of Antibiotic Tolerance and Resistance in Mycobacterium abscessus.

Antimicrobial agents and chemotherapy

Schildkraut JA, Coolen JPM, Burbaud S, Sangen JJN, Kwint MP, Floto RA, Op den Camp HJM, Te Brake LHM, Wertheim HFL, Neveling K, Hoefsloot W, van Ingen J.
PMID: 34633851
Antimicrob Agents Chemother. 2022 Jan 18;66(1):e0150921. doi: 10.1128/AAC.01509-21. Epub 2021 Oct 11.

Mycobacterium abscessus is an opportunistic pathogen notorious for its resistance to most classes of antibiotics and low cure rates. M. abscessus carries an array of mostly unexplored defense mechanisms. A deeper understanding of antibiotic resistance and tolerance mechanisms is...

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Schildkraut JA, Coolen JPM, Burbaud S, et al. RNA Sequencing Elucidates Drug-Specific Mechanisms of Antibiotic Tolerance and Resistance in Mycobacterium abscessus. Antimicrob Agents Chemother. 2021;66(1):e0150921doi: 10.1128/AAC.01509-21.
Schildkraut, J. A., Coolen, J. P. M., Burbaud, S., Sangen, J. J. N., Kwint, M. P., Floto, R. A., Op den Camp, H. J. M., Te Brake, L. H. M., Wertheim, H. F. L., Neveling, K., Hoefsloot, W., & van Ingen, J. (2022). RNA Sequencing Elucidates Drug-Specific Mechanisms of Antibiotic Tolerance and Resistance in Mycobacterium abscessus. Antimicrobial agents and chemotherapy, 66(1), e0150921. https://doi.org/10.1128/AAC.01509-21
Schildkraut, Jodie A, et al. "RNA Sequencing Elucidates Drug-Specific Mechanisms of Antibiotic Tolerance and Resistance in Mycobacterium abscessus." Antimicrobial agents and chemotherapy vol. 66,1 (2022): e0150921. doi: https://doi.org/10.1128/AAC.01509-21
Schildkraut JA, Coolen JPM, Burbaud S, Sangen JJN, Kwint MP, Floto RA, Op den Camp HJM, Te Brake LHM, Wertheim HFL, Neveling K, Hoefsloot W, van Ingen J. RNA Sequencing Elucidates Drug-Specific Mechanisms of Antibiotic Tolerance and Resistance in Mycobacterium abscessus. Antimicrob Agents Chemother. 2022 Jan 18;66(1):e0150921. doi: 10.1128/AAC.01509-21. Epub 2021 Oct 11. PMID: 34633851.
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