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

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

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

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.) Bahabry R, Hauser RM, Sánchez RG, Jago SS, Ianov L, Stuckey RJ, Parrish RR, Ver Hoef L, Lubin FD (2024 Oct 1). Alterations in DNA 5-hydroxymethylation patterns in the hippocampus of an experimental model of chronic epilepsy. Neurobiology of disease, 200(), 106638. doi: 10.1016/j.nbd.2024.106638. PMID: 39142613.

2.) Girkin CA, Strickland RG, Somerville MM, Anne Garner M, Grossman GH, Blake A, Kumar N, Ianov L, Fazio MA, Clark ME, Gross AK (2024 Oct). Acute ocular hypertension in the living human eye: Model description and initial cellular responses to elevated intraocular pressure. Vision research, 223(), 108465. . PMID: 39173459.

3.) Brida KL, Jorgensen ET, Phillips RA, Newman CE, Tuscher JJ, Morring EK, Zipperly ME, Ianov L, Montgomery KD, Tippani M, Hyde TM, Maynard KR, Martinowich K, Day JJ (2024 Jun 18). Reelin marks cocaine-activated striatal ensembles, promotes neuronal excitability, and regulates cocaine reward. bioRxiv : the preprint server for biology, (), . . PMID: 38948801.

4.) Soelter TM, Howton TC, Clark AD, Oza VH, Lasseigne BN (2024 Jun 7). Altered glia-neuron communication in Alzheimer's Disease affects WNT, p53, and NFkB Signaling determined by snRNA-seq. Cell communication and signaling : CCS, 22(1), 317. . PMID: 38849813.

5.) Andraka E, Phillips RA III, Brida KL, Day JJ (2024 Apr 18). Chst9 marks a spatially and transcriptionally unique population of Oprm1-expressing neurons in the nucleus accumbens Addiction neuroscience, 11(), 100153. . PMCID: 11218735.

6.) 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.

7.) 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.

8.) 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.

9.) 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.

10.) 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.

11.) 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.

12.) Bahabry R, Hauser RM, Sánchez RG, Jago SS, Ianov L, Stuckey RJ, Parrish RR, Hoef LV, Lubin FD (2023 Oct 5). Alterations in DNA 5-hydroxymethylation Patterns in the Hippocampus of an Experimental Model of Refractory Epilepsy. bioRxiv : the preprint server for biology, (), . . PMID: 37873276.

13.) 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.

14.) 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.

15.) 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.

16.) 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.

17.) 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.

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

Associations

ABRF

Association of Biomolecular Resource Facilities

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

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:

core facility, service resource, access service resource

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)

Facility Profile QR Code (links to this profile)

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

Contact Lara Ianov

Contact The CoreMarketplace

University of Alabama at Birmingham Biological Data Science Core

The CoreMarketplace is possible in part by collaborations with: