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Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well.

Ground water

Cihan A, Petrusak R, Bhuvankar P, Alumbaugh D, Trautz R, Birkholzer JT.
PMID: 34388260
Ground Water. 2021 Aug 13; doi: 10.1111/gwat.13127. Epub 2021 Aug 13.

Migration of clay fines can be a concern when less saline fluids are injected into brine-saturated sandstone formations containing clays. If the salinity near fluid injection wells decreases below a critical value, the clay fines near the injection may...

Cite
Cihan A, Petrusak R, Bhuvankar P, et al. Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well. Ground Water. 2021;doi: 10.1111/gwat.13127.
Cihan, A., Petrusak, R., Bhuvankar, P., Alumbaugh, D., Trautz, R., & Birkholzer, J. T. (2021). Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well. Ground water, . https://doi.org/10.1111/gwat.13127
Cihan, Abdullah, et al. "Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well." Ground water vol. (2021). doi: https://doi.org/10.1111/gwat.13127
Cihan A, Petrusak R, Bhuvankar P, Alumbaugh D, Trautz R, Birkholzer JT. Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well. Ground Water. 2021 Aug 13; doi: 10.1111/gwat.13127. Epub 2021 Aug 13. PMID: 34388260.
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ArrayExpress update - from bulk to single-cell expression data.

Nucleic acids research

Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A.
PMID: 30357387
Nucleic Acids Res. 2019 Jan 08;47:D711-D715. doi: 10.1093/nar/gky964.

ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter occupancy. The number of experiments based on sequencing technologies, in particular RNA-seq experiments,...

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Athar A, Füllgrabe A, George N, et al. ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 2019;47:D711-D715doi: 10.1093/nar/gky964.
Athar, A., Füllgrabe, A., George, N., Iqbal, H., Huerta, L., Ali, A., Snow, C., Fonseca, N. A., Petryszak, R., Papatheodorou, I., Sarkans, U., & Brazma, A. (2019). ArrayExpress update - from bulk to single-cell expression data. Nucleic acids research, 47D711-D715. https://doi.org/10.1093/nar/gky964
Athar, Awais, et al. "ArrayExpress update - from bulk to single-cell expression data." Nucleic acids research vol. 47 (2019): D711-D715. doi: https://doi.org/10.1093/nar/gky964
Athar A, Füllgrabe A, George N, Iqbal H, Huerta L, Ali A, Snow C, Fonseca NA, Petryszak R, Papatheodorou I, Sarkans U, Brazma A. ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 2019 Jan 08;47:D711-D715. doi: 10.1093/nar/gky964. PMID: 30357387; PMCID: PMC6323929.
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UniChem: a unified chemical structure cross-referencing and identifier tracking system.

Journal of cheminformatics

Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP.
PMID: 23317286
J Cheminform. 2013 Jan 14;5(1):3. doi: 10.1186/1758-2946-5-3.

UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based resources. In the past, the creation and maintenance of such links...

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Chambers J, Davies M, Gaulton A, et al. UniChem: a unified chemical structure cross-referencing and identifier tracking system. J Cheminform. 2013;5(1):3doi: 10.1186/1758-2946-5-3.
Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S., & Overington, J. P. (2013). UniChem: a unified chemical structure cross-referencing and identifier tracking system. Journal of cheminformatics, 5(1), 3. https://doi.org/10.1186/1758-2946-5-3
Chambers, Jon, et al. "UniChem: a unified chemical structure cross-referencing and identifier tracking system." Journal of cheminformatics vol. 5,1 (2013): 3. doi: https://doi.org/10.1186/1758-2946-5-3
Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP. UniChem: a unified chemical structure cross-referencing and identifier tracking system. J Cheminform. 2013 Jan 14;5(1):3. doi: 10.1186/1758-2946-5-3. PMID: 23317286; PMCID: PMC3616875.
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Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in .

NPJ genomic medicine

Steward CA, Roovers J, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF, Ceulemans B, Leroy P, Nava C, Lepine A, Tapanari E, Keiller D, Abbs S, Sanchis-Juan A, Grozeva D, Rogers AS, Diekhans M, Guigó R, Petryszak R, Minassian BA, Cavalleri G, Vitsios D, Petrovski S, Harrow J, Flicek P, Lucy Raymond F, Lench NJ, Jonghe P, Mudge JM, Weckhuysen S, Sisodiya SM, Frankish A.
PMID: 31814998
NPJ Genom Med. 2019 Dec 02;4:31. doi: 10.1038/s41525-019-0106-7. eCollection 2019.

The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60-65% of patients without a molecular diagnosis. Here, we explore the incompleteness of transcript models used for...

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Steward CA, Roovers J, Suner MM, et al. Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in . NPJ Genom Med. 2019;4:31doi: 10.1038/s41525-019-0106-7.
Steward, C. A., Roovers, J., Suner, M. M., Gonzalez, J. M., Uszczynska-Ratajczak, B., Pervouchine, D., Fitzgerald, S., Viola, M., Stamberger, H., Hamdan, F. F., Ceulemans, B., Leroy, P., Nava, C., Lepine, A., Tapanari, E., Keiller, D., Abbs, S., Sanchis-Juan, A., Grozeva, D., Rogers, A. S., Diekhans, M., Guigó, R., Petryszak, R., Minassian, B. A., Cavalleri, G., Vitsios, D., Petrovski, S., Harrow, J., Flicek, P., Lucy Raymond, F., Lench, N. J., Jonghe, P., Mudge, J. M., Weckhuysen, S., Sisodiya, S. M., & Frankish, A. (2019). Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in . NPJ genomic medicine, 431. https://doi.org/10.1038/s41525-019-0106-7
Steward, Charles A, et al. "Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in ." NPJ genomic medicine vol. 4 (2019): 31. doi: https://doi.org/10.1038/s41525-019-0106-7
Steward CA, Roovers J, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF, Ceulemans B, Leroy P, Nava C, Lepine A, Tapanari E, Keiller D, Abbs S, Sanchis-Juan A, Grozeva D, Rogers AS, Diekhans M, Guigó R, Petryszak R, Minassian BA, Cavalleri G, Vitsios D, Petrovski S, Harrow J, Flicek P, Lucy Raymond F, Lench NJ, Jonghe P, Mudge JM, Weckhuysen S, Sisodiya SM, Frankish A. Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in . NPJ Genom Med. 2019 Dec 02;4:31. doi: 10.1038/s41525-019-0106-7. eCollection 2019. PMID: 31814998; PMCID: PMC6889285.
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Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well.

Ground water

Cihan A, Petrusak R, Bhuvankar P, Alumbaugh D, Trautz R, Birkholzer JT.
PMID: 34388260
Ground Water. 2022 Jan;60(1):87-98. doi: 10.1111/gwat.13127. Epub 2021 Aug 26.

Migration of clay fines can be a concern when less saline fluids are injected into brine-saturated sandstone formations containing clays. If the salinity near fluid injection wells decreases below a critical value, the clay fines near the injection may...

Cite
Cihan A, Petrusak R, Bhuvankar P, et al. Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well. Ground Water. 2021;60(1):87-98doi: 10.1111/gwat.13127.
Cihan, A., Petrusak, R., Bhuvankar, P., Alumbaugh, D., Trautz, R., & Birkholzer, J. T. (2022). Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well. Ground water, 60(1), 87-98. https://doi.org/10.1111/gwat.13127
Cihan, Abdullah, et al. "Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well." Ground water vol. 60,1 (2022): 87-98. doi: https://doi.org/10.1111/gwat.13127
Cihan A, Petrusak R, Bhuvankar P, Alumbaugh D, Trautz R, Birkholzer JT. Permeability Decline by Clay Fines Migration around a Low-Salinity Fluid Injection Well. Ground Water. 2022 Jan;60(1):87-98. doi: 10.1111/gwat.13127. Epub 2021 Aug 26. PMID: 34388260.
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Open Targets: a platform for therapeutic target identification and validation.

Nucleic acids research

Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.
PMID: 27899665
Nucleic Acids Res. 2017 Jan 04;45:D985-D994. doi: 10.1093/nar/gkw1055. Epub 2016 Nov 29.

We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up....

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Koscielny G, An P, Carvalho-Silva D, et al. Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 2016;45:D985-D994doi: 10.1093/nar/gkw1055.
Koscielny, G., An, P., Carvalho-Silva, D., Cham, J. A., Fumis, L., Gasparyan, R., Hasan, S., Karamanis, N., Maguire, M., Papa, E., Pierleoni, A., Pignatelli, M., Platt, T., Rowland, F., Wankar, P., Bento, A. P., Burdett, T., Fabregat, A., Forbes, S., Gaulton, A., Gonzalez, C. Y., Hermjakob, H., Hersey, A., Jupe, S., Kafkas, �. �., Keays, M., Leroy, C., Lopez, F. J., Magarinos, M. P., Malone, J., McEntyre, J., Munoz-Pomer Fuentes, A., O'Donovan, C., Papatheodorou, I., Parkinson, H., Palka, B., Paschall, J., Petryszak, R., Pratanwanich, N., Sarntivijal, S., Saunders, G., Sidiropoulos, K., Smith, T., Sondka, Z., Stegle, O., Tang, Y. A., Turner, E., Vaughan, B., Vrousgou, O., Watkins, X., Martin, M. J., Sanseau, P., Vamathevan, J., Birney, E., Barrett, J., & Dunham, I. (2017). Open Targets: a platform for therapeutic target identification and validation. Nucleic acids research, 45D985-D994. https://doi.org/10.1093/nar/gkw1055
Koscielny, Gautier, et al. "Open Targets: a platform for therapeutic target identification and validation." Nucleic acids research vol. 45 (2017): D985-D994. doi: https://doi.org/10.1093/nar/gkw1055
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I. Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 2017 Jan 04;45:D985-D994. doi: 10.1093/nar/gkw1055. Epub 2016 Nov 29. PMID: 27899665; PMCID: PMC5210543.
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ArrayExpress update--simplifying data submissions.

Nucleic acids research

Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A.
PMID: 25361974
Nucleic Acids Res. 2015 Jan;43:D1113-6. doi: 10.1093/nar/gku1057. Epub 2014 Oct 31.

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains data from over 7000 public...

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Kolesnikov N, Hastings E, Keays M, et al. ArrayExpress update--simplifying data submissions. Nucleic Acids Res. 2014;43:D1113-6doi: 10.1093/nar/gku1057.
Kolesnikov, N., Hastings, E., Keays, M., Melnichuk, O., Tang, Y. A., Williams, E., Dylag, M., Kurbatova, N., Brandizi, M., Burdett, T., Megy, K., Pilicheva, E., Rustici, G., Tikhonov, A., Parkinson, H., Petryszak, R., Sarkans, U., & Brazma, A. (2015). ArrayExpress update--simplifying data submissions. Nucleic acids research, 43D1113-6. https://doi.org/10.1093/nar/gku1057
Kolesnikov, Nikolay, et al. "ArrayExpress update--simplifying data submissions." Nucleic acids research vol. 43 (2015): D1113-6. doi: https://doi.org/10.1093/nar/gku1057
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A. ArrayExpress update--simplifying data submissions. Nucleic Acids Res. 2015 Jan;43:D1113-6. doi: 10.1093/nar/gku1057. Epub 2014 Oct 31. PMID: 25361974; PMCID: PMC4383899.
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Discovering and linking public omics data sets using the Omics Discovery Index.

Nature biotechnology

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.
PMID: 28486464
Nat Biotechnol. 2017 May 09;35(5):406-409. doi: 10.1038/nbt.3790.

No abstract available.

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Perez-Riverol Y, Bai M, da Veiga Leprevost F, et al. Discovering and linking public omics data sets using the Omics Discovery Index. Nat Biotechnol. 2017;35(5):406-409doi: 10.1038/nbt.3790.
Perez-Riverol, Y., Bai, M., da Veiga Leprevost, F., Squizzato, S., Park, Y. M., Haug, K., Carroll, A. J., Spalding, D., Paschall, J., Wang, M., Del-Toro, N., Ternent, T., Zhang, P., Buso, N., Bandeira, N., Deutsch, E. W., Campbell, D. S., Beavis, R. C., Salek, R. M., Sarkans, U., Petryszak, R., Keays, M., Fahy, E., Sud, M., Subramaniam, S., Barbera, A., Jiménez, R. C., Nesvizhskii, A. I., Sansone, S. A., Steinbeck, C., Lopez, R., Vizcaíno, J. A., Ping, P., & Hermjakob, H. (2017). Discovering and linking public omics data sets using the Omics Discovery Index. Nature biotechnology, 35(5), 406-409. https://doi.org/10.1038/nbt.3790
Perez-Riverol, Yasset, et al. "Discovering and linking public omics data sets using the Omics Discovery Index." Nature biotechnology vol. 35,5 (2017): 406-409. doi: https://doi.org/10.1038/nbt.3790
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Discovering and linking public omics data sets using the Omics Discovery Index. Nat Biotechnol. 2017 May 09;35(5):406-409. doi: 10.1038/nbt.3790. PMID: 28486464; PMCID: PMC5831141.
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Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.

Nucleic acids research

Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, Mclaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R.
PMID: 15608201
Nucleic Acids Res. 2005 Jan 01;33:D297-302. doi: 10.1093/nar/gki039.

Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes. For over 190 species, Integr8 provides access to general information, recent publications, and a detailed statistical overview of the genome and proteome of...

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Kersey P, Bower L, Morris L, et al. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res. 2005;33:D297-302doi: 10.1093/nar/gki039.
Kersey, P., Bower, L., Morris, L., Horne, A., Petryszak, R., Kanz, C., Kanapin, A., Das, U., Michoud, K., Phan, I., Gattiker, A., Kulikova, T., Faruque, N., Duggan, K., Mclaren, P., Reimholz, B., Duret, L., Penel, S., Reuter, I., & Apweiler, R. (2005). Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic acids research, 33D297-302. https://doi.org/10.1093/nar/gki039
Kersey, Paul, et al. "Integr8 and Genome Reviews: integrated views of complete genomes and proteomes." Nucleic acids research vol. 33 (2005): D297-302. doi: https://doi.org/10.1093/nar/gki039
Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, Mclaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Res. 2005 Jan 01;33:D297-302. doi: 10.1093/nar/gki039. PMID: 15608201; PMCID: PMC539993.
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Gramene Database: Navigating Plant Comparative Genomics Resources.

Current plant biology

Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P.
PMID: 28713666
Curr Plant Biol. 2016 Nov;7:10-15. doi: 10.1016/j.cpb.2016.12.005.

Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the...

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Gupta P, Naithani S, Tello-Ruiz MK, et al. Gramene Database: Navigating Plant Comparative Genomics Resources. Curr Plant Biol. 2016;7:10-15doi: 10.1016/j.cpb.2016.12.005.
Gupta, P., Naithani, S., Tello-Ruiz, M. K., Chougule, K., D'Eustachio, P., Fabregat, A., Jiao, Y., Keays, M., Lee, Y. K., Kumari, S., Mulvaney, J., Olson, A., Preece, J., Stein, J., Wei, S., Weiser, J., Huerta, L., Petryszak, R., Kersey, P., Stein, L. D., Ware, D., & Jaiswal, P. (2016). Gramene Database: Navigating Plant Comparative Genomics Resources. Current plant biology, 710-15. https://doi.org/10.1016/j.cpb.2016.12.005
Gupta, Parul, et al. "Gramene Database: Navigating Plant Comparative Genomics Resources." Current plant biology vol. 7 (2016): 10-15. doi: https://doi.org/10.1016/j.cpb.2016.12.005
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P. Gramene Database: Navigating Plant Comparative Genomics Resources. Curr Plant Biol. 2016 Nov;7:10-15. doi: 10.1016/j.cpb.2016.12.005. PMID: 28713666; PMCID: PMC5509230.
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