The CoreMarketplace: University of Alabama at Birmingham Biological Data Science Core

University of Alabama at Birmingham Biological Data Science Core (Bioinformatics) RRID:SCR_021766	University of Alabama at Birmingham Birmingham, AL 35233	Computational - High Performance Computing, Copy Number Variation (CNV), Genomics, RNA analysis, RNAseq, Sequencing - DNA Sequencing, Sequencing - Next Generation Sequencing (NGS), Single-Cell Analysis, Spatial Transcriptomics, Whole Genome Sequencing, R Shiny App Development, Pipeline Development, Training, Data Visualization	Last Updated: 10/20/2021

All Facilities >> University of Alabama at Birmingham >> University of Alabama at Birmingham Biological Data Science Core (Bioinformatics)

University of Alabama at Birmingham Biological Data Science Core (Bioinformatics)

Facility Details

About This Facility

Services and Equipment

Publications

Awards & Associations

Metadata

Other Facilities at this Institution:

University of Alabama at Birmingham

1719 6th Ave S

Birmingham, AL 35233

United States of America

https://www.uab.edu/cores/ircp/bds

cite this facility

Quicklinks:

https://coremarketplace.org/UAB_BDS https://coremarketplace.org/RRID:SCR_021766

Primary Contact:

Lara Ianov

Last Updated: 10/20/2021

Facility RRID

RRID:SCR_021766

Facility Details

The UAB Biological Data Science Core (U-BDS) offers access to computational biology capabilities.

U-BDS aims to provide services, foster long-term collaborations with the UAB research community, and provide training for biomedical investigators on a specific set of analysis tools and techniques.

We place special emphasis in the areas of genomics, transcriptomics, systems biology and translational medicine. Our services include data analysis, biological interpretation, grant assistance, and training.

Facility Policies

Services are offerred outside of University of Alabama at Birmingham

Consulting is offerred outside of University of Alabama at Birmingham

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Services offered:

Computational - High Performance Computing

Copy Number Variation (CNV)

Data Visualization

Genomics

Pipeline Development

R Shiny App Development

RNA analysis

RNAseq

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Single-Cell Analysis

Spatial Transcriptomics

Training

Whole Genome Sequencing

Facility Equipment

No additional equipment has been listed

(To see more facility information, click the in the upper right)

Publications

Publications associated with this facility (Click To View):

1.) Whitlock JH, Wilk EJ, Howton TC, Clark AD, Lasseigne BN (2024 Jan 2). The landscape of SETBP1 gene expression and transcription factor activity across human tissues PLOS ONE, 19(1), e0296328. . PMCID: 10760659.

2.) Fisher JL, Clark AD, Jones EF, Lasseigne BN (2024 Jan 2). Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes BMC Pharmacology & Toxicology, 25(), 5. . PMCID: 10763002.

3.) Monavarian M, Page EF, Rajkarnikar R, Kumari A, Macias LQ, Massicano F, Lee NY, Sahoo S, Hempel N, Jolly MK, Ianov L, Worthey E, Singh A, Broude EV, Mythreye K (2023 Dec 6). Development of adaptive anoikis resistance promotes metastasis that can be overcome by CDK8/19 Mediator kinase inhibition bioRxiv, (), 2023.12.04.569970. . PMCID: 10723298.

4.) Monavarian M, Page EF, Rajkarnikar R, Kumari A, Macias LQ, Massicano F, Lee NY, Sahoo S, Hempel N, Jolly MK, Ianov L, Worthey E, Singh A, Broude EV, Mythreye K (2023 Dec 6). Development of adaptive anoikis resistance promotes metastasis that can be overcome by CDK8/19 Mediator kinase inhibition. bioRxiv : the preprint server for biology, (), . . PMID: 38106208.

5.) Soelter TM, Howton TC, Clark AD, Oza VH, Lasseigne BN (2023 Dec 1). Altered Glia-Neuron Communication in Alzheimer’s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq bioRxiv, (), 2023.11.29.569304. . PMCID: 10705421.

6.) Soelter TM, Howton TC, Clark AD, Oza VH, Lasseigne BN (2023 Dec 1). Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq. bioRxiv : the preprint server for biology, (), . . PMID: 38076822.

7.) Fisher JL, Clark AD, Jones EF, Lasseigne BN (2023 Nov 15). Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes bioRxiv, (), 2023.05.23.541950. . PMCID: 10290285.

8.) Fisher JL, Clark AD, Jones EF, Lasseigne BN (2023 Nov 15). Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes. bioRxiv : the preprint server for biology, (), . . PMID: 37362157.

9.) Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ (2023 Nov 8). Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer eLife, 12(), RP89993. . PMCID: 10631760.

10.) Phillips RA, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ (2023 Nov 8). Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. eLife, 12(), . . PMID: 37938195.

11.) Whitlock JH, Soelter TM, Howton TC, Wilk EJ, Oza VH, Lasseigne BN (2023 Nov). Cell-type-specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1(S858R) Schinzel Giedion Syndrome mice. Journal of cellular and molecular medicine, 27(22), 3565-3577. . PMID: 37872881.

12.) Whitlock JH, Soelter TM, Howton TC, Wilk EJ, Oza VH, Lasseigne BN (2023 Oct 23). Cell‐type‐specific gene expression and regulation in the cerebral cortex and kidney of atypical Setbp1 S858R Schinzel Giedion Syndrome mice Journal of Cellular and Molecular Medicine, 27(22), 3565-3577. . PMCID: 10660642.

13.) Whitlock JH, Wilk EJ, Howton TC, Clark AD, Lasseigne BN (2023 Oct 14). The landscape of SETBP1 gene expression and transcription factor activity across human tissues bioRxiv, (), 2023.08.08.551337. . PMCID: 10592643.

14.) Whitlock JH, Wilk EJ, Howton TC, Clark AD, Lasseigne BN (2023 Oct 14). The landscape of SETBP1 gene expression and transcription factor activity across human tissues. bioRxiv : the preprint server for biology, (), . . PMID: 37873221.

15.) Phillips RA 3rd, Wan E, Tuscher JJ, Reid D, Drake OR, Ianov L, Day JJ (2023 Aug 21). Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. bioRxiv : the preprint server for biology, (), . . PMID: 37333110.

16.) Phillips RA III, Wan E, Tuscher JJ, Reid D, Ianov L, Day JJ (2023 Jun 5). Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer bioRxiv, (), 2023.06.02.543489. . PMCID: 10274686.

17.) Bach SV, Bauman AJ, Hosein D, Tuscher JJ, Ianov L, Greathouse KM, Henderson BW, Herskowitz JH, Martinowich K, Day JJ (2023 Apr 5). Distinct roles of Bdnf I and Bdnf IV transcript variant expression in hippocampal neurons bioRxiv, (), 2023.04.05.535694. . PMCID: 10104043.

18.) Bach SV, Bauman AJ, Hosein D, Tuscher JJ, Ianov L, Greathouse KM, Henderson BW, Herskowitz JH, Martinowich K, Day JJ (2023 Apr 5). Distinct roles of Bdnf I and Bdnf IV transcript variant expression in hippocampal neurons. bioRxiv : the preprint server for biology, (), . . PMID: 37066216.

19.) Pandey S, Moyer AJ, Thyme SB (2023 Apr). A single-cell transcriptome atlas of the maturing zebrafish telencephalon Genome Research, 33(4), 658-671. . PMCID: 10234298.

20.) Pandey S, Moyer AJ, Thyme SB (2023 Apr). A single-cell transcriptome atlas of the maturing zebrafish telencephalon. Genome research, 33(4), 658-671. . PMID: 37072188.

21.) Phillips RA III, Tuscher JJ, Fitzgerald ND, Wan E, Zipperly ME, Duke CG, Ianov L, Day JJ (2023 Jan 13). Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine bioRxiv, (), 2023.01.12.523845. . PMCID: 9882178.

22.) Phillips RA 3rd, Tuscher JJ, Fitzgerald ND, Wan E, Zipperly ME, Duke CG, Ianov L, Day JJ (2023 Jan 13). Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine. bioRxiv : the preprint server for biology, (), . . PMID: 36711527.

23.) Oza VH, Whitlock JH, Wilk EJ, Uno-Antonison A, Wilk B, Gajapathy M, Howton TC, Trull A, Ianov L, Worthey EA, Lasseigne BN (2023 Jan 5). Ten simple rules for using public biological data for your research PLOS Computational Biology, 19(1), e1010749. . PMCID: 9815577.

24.) Oza VH, Whitlock JH, Wilk EJ, Uno-Antonison A, Wilk B, Gajapathy M, Howton TC, Trull A, Ianov L, Worthey EA, Lasseigne BN (2023 Jan). Ten simple rules for using public biological data for your research. PLoS computational biology, 19(1), e1010749. doi: 10.1371/journal.pcbi.1010749. PMID: 36602970.

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Associations

ABRF

Association of Biomolecular Resource Facilities

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Metadata

Links

All the links listed resolve to this core profile

https://coremarketplace.org/?FacilityID=1226
https://coremarketplace.org/RRID:SCR_021766

Institution

Institution ROR ID: https://ror.org/008s83205

SciCrunch Data Imports (data maintained by https://scicrunch.org)

Keywords:

USEDit, ABRF, genomics, transcriptomics, systems biology, translational medicine, data analysis, biological interpretation, grant assistance, training

Resource Type:

access service resource, service resource, core facility

Citation:

University of Alabama at Birmingham Biological Data Science Core (RRID:SCR_021766)

University of Alabama at Birmingham Biological Data Science Core (Bioinformatics)

Quicklinks:

Primary Contact:

Facility RRID

Facility Details

Facility Policies

(To see more facility information, click the in the upper right)

Services offered:

Facility Equipment

(To see more facility information, click the in the upper right)

Publications

(To see more facility information, click the in the upper right)

Associations

ABRF

(To see more facility information, click the in the upper right)

Metadata

SciCrunch Data Imports (data maintained by https://scicrunch.org)

(To see more facility information, click the in the upper right)

Contact Lara Ianov

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University of Alabama at Birmingham Biological Data Science Core

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