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Showing 1 to 12 of 31 entries
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Identification of alternative topological domains in chromatin.

Algorithms for molecular biology : AMB

Filippova D, Patro R, Duggal G, Kingsford C.
PMID: 24868242
Algorithms Mol Biol. 2014 May 03;9:14. doi: 10.1186/1748-7188-9-14. eCollection 2014.

Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since...

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Filippova D, Patro R, Duggal G, et al. Identification of alternative topological domains in chromatin. Algorithms Mol Biol. 2014;9:14doi: 10.1186/1748-7188-9-14.
Filippova, D., Patro, R., Duggal, G., & Kingsford, C. (2014). Identification of alternative topological domains in chromatin. Algorithms for molecular biology : AMB, 914. https://doi.org/10.1186/1748-7188-9-14
Filippova, Darya, et al. "Identification of alternative topological domains in chromatin." Algorithms for molecular biology : AMB vol. 9 (2014): 14. doi: https://doi.org/10.1186/1748-7188-9-14
Filippova D, Patro R, Duggal G, Kingsford C. Identification of alternative topological domains in chromatin. Algorithms Mol Biol. 2014 May 03;9:14. doi: 10.1186/1748-7188-9-14. eCollection 2014. PMID: 24868242; PMCID: PMC4019371.
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Glycolipid-Dependent, Protease Sensitive Internalization of Pseudomonas aeruginosa Into Cultured Human Respiratory Epithelial Cells.

The open microbiology journal

Emam A, Carter WG, Lingwood C.
PMID: 21270937
Open Microbiol J. 2010 Dec 13;4:106-15. doi: 10.2174/1874285801004010106.

Internalization of PAK strain Pseudomonas aeruginosa into human respiratory epithelial cell lines and HeLa cervical cancer cells in vitro was readily demonstrable via a gentamycin protection assay. Depletion of target cell glycosphingolipids (GSLs) using a glucosyl ceramide synthase inhibitor,...

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Emam A, Carter WG, Lingwood C. Glycolipid-Dependent, Protease Sensitive Internalization of Pseudomonas aeruginosa Into Cultured Human Respiratory Epithelial Cells. Open Microbiol J. 2010;4:106-15doi: 10.2174/1874285801004010106.
Emam, A., Carter, W. G., & Lingwood, C. (2010). Glycolipid-Dependent, Protease Sensitive Internalization of Pseudomonas aeruginosa Into Cultured Human Respiratory Epithelial Cells. The open microbiology journal, 4106-15. https://doi.org/10.2174/1874285801004010106
Emam, Aufaugh, et al. "Glycolipid-Dependent, Protease Sensitive Internalization of Pseudomonas aeruginosa Into Cultured Human Respiratory Epithelial Cells." The open microbiology journal vol. 4 (2010): 106-15. doi: https://doi.org/10.2174/1874285801004010106
Emam A, Carter WG, Lingwood C. Glycolipid-Dependent, Protease Sensitive Internalization of Pseudomonas aeruginosa Into Cultured Human Respiratory Epithelial Cells. Open Microbiol J. 2010 Dec 13;4:106-15. doi: 10.2174/1874285801004010106. PMID: 21270937; PMCID: PMC3026333.
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VariantStore: an index for large-scale genomic variant search.

Genome biology

Pandey P, Gao Y, Kingsford C.
PMID: 34412679
Genome Biol. 2021 Aug 19;22(1):231. doi: 10.1186/s13059-021-02442-8.

Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, a system that indexes genomic variants from multiple samples using a...

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Pandey P, Gao Y, Kingsford C. VariantStore: an index for large-scale genomic variant search. Genome Biol. 2021;22(1):231doi: 10.1186/s13059-021-02442-8.
Pandey, P., Gao, Y., & Kingsford, C. (2021). VariantStore: an index for large-scale genomic variant search. Genome biology, 22(1), 231. https://doi.org/10.1186/s13059-021-02442-8
Pandey, Prashant, et al. "VariantStore: an index for large-scale genomic variant search." Genome biology vol. 22,1 (2021): 231. doi: https://doi.org/10.1186/s13059-021-02442-8
Pandey P, Gao Y, Kingsford C. VariantStore: an index for large-scale genomic variant search. Genome Biol. 2021 Aug 19;22(1):231. doi: 10.1186/s13059-021-02442-8. PMID: 34412679; PMCID: PMC8375130.
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Clinical Characteristics of Subependymal Giant Cell Astrocytoma in Tuberous Sclerosis Complex.

Frontiers in neurology

Jansen AC, Belousova E, Benedik MP, Carter T, Cottin V, Curatolo P, Dahlin M, D'Amato L, d'Augères GB, de Vries PJ, Ferreira JC, Feucht M, Fladrowski C, Hertzberg C, Jozwiak S, Lawson JA, Macaya A, Marques R, Nabbout R, O'Callaghan F, Qin J, Sander V, Sauter M, Shah S, Takahashi Y, Touraine R, Youroukos S, Zonnenberg B, Kingswood JC.
PMID: 31333563
Front Neurol. 2019 Jul 03;10:705. doi: 10.3389/fneur.2019.00705. eCollection 2019.

No abstract available.

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Jansen AC, Belousova E, Benedik MP, et al. Clinical Characteristics of Subependymal Giant Cell Astrocytoma in Tuberous Sclerosis Complex. Front Neurol. 2019;10:705doi: 10.3389/fneur.2019.00705.
Jansen, A. C., Belousova, E., Benedik, M. P., Carter, T., Cottin, V., Curatolo, P., Dahlin, M., D'Amato, L., d'Augères, G. B., de Vries, P. J., Ferreira, J. C., Feucht, M., Fladrowski, C., Hertzberg, C., Jozwiak, S., Lawson, J. A., Macaya, A., Marques, R., Nabbout, R., O'Callaghan, F., Qin, J., Sander, V., Sauter, M., Shah, S., Takahashi, Y., Touraine, R., Youroukos, S., Zonnenberg, B., & Kingswood, J. C. (2019). Clinical Characteristics of Subependymal Giant Cell Astrocytoma in Tuberous Sclerosis Complex. Frontiers in neurology, 10705. https://doi.org/10.3389/fneur.2019.00705
Jansen, Anna C, et al. "Clinical Characteristics of Subependymal Giant Cell Astrocytoma in Tuberous Sclerosis Complex." Frontiers in neurology vol. 10 (2019): 705. doi: https://doi.org/10.3389/fneur.2019.00705
Jansen AC, Belousova E, Benedik MP, Carter T, Cottin V, Curatolo P, Dahlin M, D'Amato L, d'Augères GB, de Vries PJ, Ferreira JC, Feucht M, Fladrowski C, Hertzberg C, Jozwiak S, Lawson JA, Macaya A, Marques R, Nabbout R, O'Callaghan F, Qin J, Sander V, Sauter M, Shah S, Takahashi Y, Touraine R, Youroukos S, Zonnenberg B, Kingswood JC. Clinical Characteristics of Subependymal Giant Cell Astrocytoma in Tuberous Sclerosis Complex. Front Neurol. 2019 Jul 03;10:705. doi: 10.3389/fneur.2019.00705. eCollection 2019. PMID: 31333563; PMCID: PMC6616060.
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Analysis of the structural variability of topologically associated domains as revealed by Hi-C.

NAR genomics and bioinformatics

Sauerwald N, Singhal A, Kingsford C.
PMID: 31687663
NAR Genom Bioinform. 2020 Mar;2(1). doi: 10.1093/nargab/lqz008. Epub 2019 Sep 30.

Three-dimensional chromosome structure plays an integral role in gene expression and regulation, replication timing, and other cellular processes. Topologically associated domains (TADs), building blocks of chromosome structure, are genomic regions with higher contact frequencies within the region than outside...

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Sauerwald N, Singhal A, Kingsford C. Analysis of the structural variability of topologically associated domains as revealed by Hi-C. NAR Genom Bioinform. 2019;2(1)doi: 10.1093/nargab/lqz008.
Sauerwald, N., Singhal, A., & Kingsford, C. (2020). Analysis of the structural variability of topologically associated domains as revealed by Hi-C. NAR genomics and bioinformatics, 2(1), . https://doi.org/10.1093/nargab/lqz008
Sauerwald, Natalie, et al. "Analysis of the structural variability of topologically associated domains as revealed by Hi-C." NAR genomics and bioinformatics vol. 2,1 (2020). doi: https://doi.org/10.1093/nargab/lqz008
Sauerwald N, Singhal A, Kingsford C. Analysis of the structural variability of topologically associated domains as revealed by Hi-C. NAR Genom Bioinform. 2020 Mar;2(1). doi: 10.1093/nargab/lqz008. Epub 2019 Sep 30. PMID: 31687663; PMCID: PMC6824515.
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Context-aware seeds for read mapping.

Algorithms for molecular biology : AMB

Xin H, Shao M, Kingsford C.
PMID: 32489399
Algorithms Mol Biol. 2020 May 23;15:10. doi: 10.1186/s13015-020-00172-3. eCollection 2020.

MOTIVATION: Most modern seed-and-extend NGS read mappers employ a seeding scheme that requires extracting RESULTS: We propose a novel seeding framework, context-aware seeds (CAS). CAS guarantees finding all valid mappings but uses fewer (and longer) seeds, which reduces seed...

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Xin H, Shao M, Kingsford C. Context-aware seeds for read mapping. Algorithms Mol Biol. 2020;15:10doi: 10.1186/s13015-020-00172-3.
Xin, H., Shao, M., & Kingsford, C. (2020). Context-aware seeds for read mapping. Algorithms for molecular biology : AMB, 1510. https://doi.org/10.1186/s13015-020-00172-3
Xin, Hongyi, et al. "Context-aware seeds for read mapping." Algorithms for molecular biology : AMB vol. 15 (2020): 10. doi: https://doi.org/10.1186/s13015-020-00172-3
Xin H, Shao M, Kingsford C. Context-aware seeds for read mapping. Algorithms Mol Biol. 2020 May 23;15:10. doi: 10.1186/s13015-020-00172-3. eCollection 2020. PMID: 32489399; PMCID: PMC7245042.
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TuberOus SClerosis registry to increAse disease awareness (TOSCA) Post-Authorisation Safety Study of Everolimus in Patients With Tuberous Sclerosis Complex.

Frontiers in neurology

Kingswood JC, Belousova E, Benedik MP, Budde K, Carter T, Cottin V, Curatolo P, Dahlin M, D'Amato L, d'Augères GB, de Vries PJ, Ferreira JC, Feucht M, Fladrowski C, Hertzberg C, Jozwiak S, Lawson JA, Macaya A, Marques R, Nabbout R, O'Callaghan F, Qin J, Sander V, Sauter M, Shah S, Takahashi Y, Touraine R, Youroukos S, Zonnenberg B, Jansen AC.
PMID: 33833726
Front Neurol. 2021 Mar 23;12:630378. doi: 10.3389/fneur.2021.630378. eCollection 2021.

This non-interventional post-authorisation safety study (PASS) assessed the long-term safety of everolimus in patients with tuberous sclerosis complex (TSC) who participated in the TuberOus SClerosis registry to increase disease Awareness (TOSCA) clinical study and received everolimus for the licensed...

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Kingswood JC, Belousova E, Benedik MP, et al. TuberOus SClerosis registry to increAse disease awareness (TOSCA) Post-Authorisation Safety Study of Everolimus in Patients With Tuberous Sclerosis Complex. Front Neurol. 2021;12:630378doi: 10.3389/fneur.2021.630378.
Kingswood, J. C., Belousova, E., Benedik, M. P., Budde, K., Carter, T., Cottin, V., Curatolo, P., Dahlin, M., D'Amato, L., d'Augères, G. B., de Vries, P. J., Ferreira, J. C., Feucht, M., Fladrowski, C., Hertzberg, C., Jozwiak, S., Lawson, J. A., Macaya, A., Marques, R., Nabbout, R., O'Callaghan, F., Qin, J., Sander, V., Sauter, M., Shah, S., Takahashi, Y., Touraine, R., Youroukos, S., Zonnenberg, B., Jansen, A. C. (2021). TuberOus SClerosis registry to increAse disease awareness (TOSCA) Post-Authorisation Safety Study of Everolimus in Patients With Tuberous Sclerosis Complex. Frontiers in neurology, 12630378. https://doi.org/10.3389/fneur.2021.630378
Kingswood, J Chris, et al. "TuberOus SClerosis registry to increAse disease awareness (TOSCA) Post-Authorisation Safety Study of Everolimus in Patients With Tuberous Sclerosis Complex." Frontiers in neurology vol. 12 (2021): 630378. doi: https://doi.org/10.3389/fneur.2021.630378
Kingswood JC, Belousova E, Benedik MP, Budde K, Carter T, Cottin V, Curatolo P, Dahlin M, D'Amato L, d'Augères GB, de Vries PJ, Ferreira JC, Feucht M, Fladrowski C, Hertzberg C, Jozwiak S, Lawson JA, Macaya A, Marques R, Nabbout R, O'Callaghan F, Qin J, Sander V, Sauter M, Shah S, Takahashi Y, Touraine R, Youroukos S, Zonnenberg B, Jansen AC. TuberOus SClerosis registry to increAse disease awareness (TOSCA) Post-Authorisation Safety Study of Everolimus in Patients With Tuberous Sclerosis Complex. Front Neurol. 2021 Mar 23;12:630378. doi: 10.3389/fneur.2021.630378. eCollection 2021. PMID: 33833726; PMCID: PMC8021912.
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Exact transcript quantification over splice graphs.

Algorithms for molecular biology : AMB

Ma C, Zheng H, Kingsford C.
PMID: 33971903
Algorithms Mol Biol. 2021 May 10;16(1):5. doi: 10.1186/s13015-021-00184-7.

BACKGROUND: The probability of sequencing a set of RNA-seq reads can be directly modeled using the abundances of splice junctions in splice graphs instead of the abundances of a list of transcripts. We call this model graph quantification, which...

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Ma C, Zheng H, Kingsford C. Exact transcript quantification over splice graphs. Algorithms Mol Biol. 2021;16(1):5doi: 10.1186/s13015-021-00184-7.
Ma, C., Zheng, H., & Kingsford, C. (2021). Exact transcript quantification over splice graphs. Algorithms for molecular biology : AMB, 16(1), 5. https://doi.org/10.1186/s13015-021-00184-7
Ma, Cong, et al. "Exact transcript quantification over splice graphs." Algorithms for molecular biology : AMB vol. 16,1 (2021): 5. doi: https://doi.org/10.1186/s13015-021-00184-7
Ma C, Zheng H, Kingsford C. Exact transcript quantification over splice graphs. Algorithms Mol Biol. 2021 May 10;16(1):5. doi: 10.1186/s13015-021-00184-7. PMID: 33971903; PMCID: PMC8112020.
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Diffusion archeology for diffusion progression history reconstruction.

Knowledge and information systems

Sefer E, Kingsford C.
PMID: 27821901
Knowl Inf Syst. 2016 Nov;49(2):403-427. doi: 10.1007/s10115-015-0904-x. Epub 2015 Dec 11.

Diffusion through graphs can be used to model many real-world processes, such as the spread of diseases, social network memes, computer viruses, or water contaminants. Often, a real-world diffusion cannot be directly observed while it is occurring - perhaps...

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Sefer E, Kingsford C. Diffusion archeology for diffusion progression history reconstruction. Knowl Inf Syst. 2015;49(2):403-427doi: 10.1007/s10115-015-0904-x.
Sefer, E., & Kingsford, C. (2016). Diffusion archeology for diffusion progression history reconstruction. Knowledge and information systems, 49(2), 403-427. https://doi.org/10.1007/s10115-015-0904-x
Sefer, Emre, and Kingsford, Carl. "Diffusion archeology for diffusion progression history reconstruction." Knowledge and information systems vol. 49,2 (2016): 403-427. doi: https://doi.org/10.1007/s10115-015-0904-x
Sefer E, Kingsford C. Diffusion archeology for diffusion progression history reconstruction. Knowl Inf Syst. 2016 Nov;49(2):403-427. doi: 10.1007/s10115-015-0904-x. Epub 2015 Dec 11. PMID: 27821901; PMCID: PMC5095933.
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Renal Manifestations of Tuberous Sclerosis Complex: Key Findings From the Final Analysis of the TOSCA Study Focussing Mainly on Renal Angiomyolipomas.

Frontiers in neurology

Kingswood JC, Belousova E, Benedik MP, Carter T, Cottin V, Curatolo P, Dahlin M, D'Amato L, Beaure d'Augères G, de Vries PJ, Ferreira JC, Feucht M, Fladrowski C, Hertzberg C, Jozwiak S, Lawson JA, Macaya A, Marques R, Nabbout R, O'Callaghan F, Qin J, Sander V, Shah S, Takahashi Y, Touraine R, Youroukos S, Zonnenberg B, Jansen AC, Sauter M.
PMID: 33041968
Front Neurol. 2020 Sep 16;11:972. doi: 10.3389/fneur.2020.00972. eCollection 2020.

Renal angiomyolipomas are one of the most common renal manifestations in patients with tuberous sclerosis complex (TSC), with potentially life-threatening complications and a poor prognosis. Despite the considerable progress in understanding TSC-associated renal angiomyolipomas, there are no large scale...

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Kingswood JC, Belousova E, Benedik MP, et al. Renal Manifestations of Tuberous Sclerosis Complex: Key Findings From the Final Analysis of the TOSCA Study Focussing Mainly on Renal Angiomyolipomas. Front Neurol. 2020;11:972doi: 10.3389/fneur.2020.00972.
Kingswood, J. C., Belousova, E., Benedik, M. P., Carter, T., Cottin, V., Curatolo, P., Dahlin, M., D'Amato, L., Beaure d'Augères, G., de Vries, P. J., Ferreira, J. C., Feucht, M., Fladrowski, C., Hertzberg, C., Jozwiak, S., Lawson, J. A., Macaya, A., Marques, R., Nabbout, R., O'Callaghan, F., Qin, J., Sander, V., Shah, S., Takahashi, Y., Touraine, R., Youroukos, S., Zonnenberg, B., Jansen, A. C., & Sauter, M. (2020). Renal Manifestations of Tuberous Sclerosis Complex: Key Findings From the Final Analysis of the TOSCA Study Focussing Mainly on Renal Angiomyolipomas. Frontiers in neurology, 11972. https://doi.org/10.3389/fneur.2020.00972
Kingswood, J Chris, et al. "Renal Manifestations of Tuberous Sclerosis Complex: Key Findings From the Final Analysis of the TOSCA Study Focussing Mainly on Renal Angiomyolipomas." Frontiers in neurology vol. 11 (2020): 972. doi: https://doi.org/10.3389/fneur.2020.00972
Kingswood JC, Belousova E, Benedik MP, Carter T, Cottin V, Curatolo P, Dahlin M, D'Amato L, Beaure d'Augères G, de Vries PJ, Ferreira JC, Feucht M, Fladrowski C, Hertzberg C, Jozwiak S, Lawson JA, Macaya A, Marques R, Nabbout R, O'Callaghan F, Qin J, Sander V, Shah S, Takahashi Y, Touraine R, Youroukos S, Zonnenberg B, Jansen AC, Sauter M. Renal Manifestations of Tuberous Sclerosis Complex: Key Findings From the Final Analysis of the TOSCA Study Focussing Mainly on Renal Angiomyolipomas. Front Neurol. 2020 Sep 16;11:972. doi: 10.3389/fneur.2020.00972. eCollection 2020. PMID: 33041968; PMCID: PMC7526256.
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A cost-aggregating integer linear program for motif finding.

Journal of discrete algorithms (Amsterdam, Netherlands)

Kingsford C, Zaslavsky E, Singh M.
PMID: 22081765
J Discrete Algorithms (Amst). 2011 Dec 01;9(4):326-334. doi: 10.1016/j.jda.2011.04.001.

In the motif finding problem one seeks a set of mutually similar substrings within a collection of biological sequences. This is an important and widely-studied problem, as such shared motifs in DNA often correspond to regulatory elements. We study...

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Kingsford C, Zaslavsky E, Singh M. A cost-aggregating integer linear program for motif finding. J Discrete Algorithms (Amst). 2011;9(4):326-334doi: 10.1016/j.jda.2011.04.001.
Kingsford, C., Zaslavsky, E., & Singh, M. (2011). A cost-aggregating integer linear program for motif finding. Journal of discrete algorithms (Amsterdam, Netherlands), 9(4), 326-334. https://doi.org/10.1016/j.jda.2011.04.001
Kingsford, Carl, et al. "A cost-aggregating integer linear program for motif finding." Journal of discrete algorithms (Amsterdam, Netherlands) vol. 9,4 (2011): 326-334. doi: https://doi.org/10.1016/j.jda.2011.04.001
Kingsford C, Zaslavsky E, Singh M. A cost-aggregating integer linear program for motif finding. J Discrete Algorithms (Amst). 2011 Dec 01;9(4):326-334. doi: 10.1016/j.jda.2011.04.001. PMID: 22081765; PMCID: PMC3212737.
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Historical Patterns of Diagnosis, Treatments, and Outcome of Epilepsy Associated With Tuberous Sclerosis Complex: Results From TOSCA Registry.

Frontiers in neurology

Nabbout R, Belousova E, Benedik MP, Carter T, Cottin V, Curatolo P, Dahlin M, D'Amato L, Beaure d'Augères G, de Vries PJ, Ferreira JC, Feucht M, Fladrowski C, Hertzberg C, Jozwiak S, Lawson JA, Macaya A, Marques R, O'Callaghan F, Qin J, Sauter M, Shah S, Takahashi Y, Touraine R, Youroukos S, Zonnenberg B, Jansen AC, Kingswood JC.
PMID: 34566842
Front Neurol. 2021 Sep 08;12:697467. doi: 10.3389/fneur.2021.697467. eCollection 2021.

No abstract available.

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Nabbout R, Belousova E, Benedik MP, et al. Historical Patterns of Diagnosis, Treatments, and Outcome of Epilepsy Associated With Tuberous Sclerosis Complex: Results From TOSCA Registry. Front Neurol. 2021;12:697467doi: 10.3389/fneur.2021.697467.
Nabbout, R., Belousova, E., Benedik, M. P., Carter, T., Cottin, V., Curatolo, P., Dahlin, M., D'Amato, L., Beaure d'Augères, G., de Vries, P. J., Ferreira, J. C., Feucht, M., Fladrowski, C., Hertzberg, C., Jozwiak, S., Lawson, J. A., Macaya, A., Marques, R., O'Callaghan, F., Qin, J., Sauter, M., Shah, S., Takahashi, Y., Touraine, R., Youroukos, S., Zonnenberg, B., Jansen, A. C., & Kingswood, J. C. (2021). Historical Patterns of Diagnosis, Treatments, and Outcome of Epilepsy Associated With Tuberous Sclerosis Complex: Results From TOSCA Registry. Frontiers in neurology, 12697467. https://doi.org/10.3389/fneur.2021.697467
Nabbout, Rima, et al. "Historical Patterns of Diagnosis, Treatments, and Outcome of Epilepsy Associated With Tuberous Sclerosis Complex: Results From TOSCA Registry." Frontiers in neurology vol. 12 (2021): 697467. doi: https://doi.org/10.3389/fneur.2021.697467
Nabbout R, Belousova E, Benedik MP, Carter T, Cottin V, Curatolo P, Dahlin M, D'Amato L, Beaure d'Augères G, de Vries PJ, Ferreira JC, Feucht M, Fladrowski C, Hertzberg C, Jozwiak S, Lawson JA, Macaya A, Marques R, O'Callaghan F, Qin J, Sauter M, Shah S, Takahashi Y, Touraine R, Youroukos S, Zonnenberg B, Jansen AC, Kingswood JC. Historical Patterns of Diagnosis, Treatments, and Outcome of Epilepsy Associated With Tuberous Sclerosis Complex: Results From TOSCA Registry. Front Neurol. 2021 Sep 08;12:697467. doi: 10.3389/fneur.2021.697467. eCollection 2021. PMID: 34566842; PMCID: PMC8455825.
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Showing 1 to 12 of 31 entries