Palak Ahuja, Ph.D.
Postdoctoral Fellow
As a driven scientist I am excited to explore the biochemical secrets of heart pathophysiology. I hold expertise in various cell-based assays and in vivo studies.
I joined the Kraus lab in April 2022 and have taken up the role to study the functional role of PARP1 and NAD homeostasis in heart physiology. I will use biochemical assays, omics approaches and a conditional knockout mice model to decipher the molecular mechanisms involved in cardiovascular disorders.
Selected Publications
Ahuja P., Ng C.F., Pang B.P.S., Chan W.S., Tse M.C.L., Bi X., Kwan H.L.R., Brobst D., Pana O.H., Yang X., Du G., Saengnipanthkul S., Noh H.L., Jiao B., Kim J.K., Lee C.W., Ye K., Chan C.B. (2022) Muscle-generated BDNF (brain derived neurotrophic factor) maintains mitochondrial quality control in female mice. Autophagy 18(6):1367-1384.
Ahuja P., Bi X., Ng C.F., Tse M.C.L., Hang M., Pang B.P.S., Iu E.C.Y., Chan W.S., Ooi X.C., Sun A., Herlea-Pana O., Liu Z., Yang X., Jiao B., Ma X., Wu K.K.L., Lee L.T.O., Cheng K.K.Y., Lee C.W., Chanet C.B. (2022) Src homology 3 domain binding kinase 1 protects against hepatic steatosis and insulin resistance through the Nur77-FGF21 pathway. Hepatology
Marwa Aljardali, M.D.
Postdoctoral Fellow
I joined the Kraus Lab in January 2023. I completed my M.D. training in Lebanon in June 2022. As an aspiring obstetrician and gynecologist, I will focus my research on exploring different ways to enhance patient care. My main interests would be investigating novel therapies that could treat gynecologic cancers and finding biomarkers that could be used in clinics to direct the optimal treatment.
Selected Publications
- Farah S., Albaini O., Jardali M.A., Daccahe A., Jallad K. (2023) The Feasibility And Safety Of VNOTES Hysterectomy And Uterosacral Ligament Suspension: A Case Series. Journal of Minimally Invasive Gynecology S1553-4650(23)00005-5.
- Almekkawi A.K., AlJardali M.W., Daadaa H.M., Lane A.L., Worner A.R., Karim M.A., Scheck A.C., Frye R.E. (2022) Folate Pathway Gene Single Nucleotide Polymorphisms and Neural Tube Defects: A Systematic Review and Meta-Analysis. Journal of Personalized Medicine 12(10):1609.
Shehreen Amjad, Ph.D.
Postdoctoral Fellow
I joined the Kraus lab in August 2022. As a reproductive biologist, I am interested in studying the role of eRNAs in an estrogen regulated reproductive biological system (i.e., uterus) in primary cell lines and in vivo through omics, transgenic mice, and next generation sequencing.
Selected Publications
- Amjad S., Rahman M.S., Pang W.K., Ryu D.Y., Adegoke E.O., Park Y.J., Pang M.G. (2021) Effects of phthalates on the functions and fertility of mouse spermatozoa. Toxicology. 454:152746.
- Amjad S., Rahman M.S., Pang M.G. (2020) Role of Antioxidants in Alleviating Bisphenol A Toxicity. Biomolecules. 10(8):1105.
Andrea Edwards, Ph.D.
Postdoctoral Fellow
I joined the Kraus lab in March 2021. I am interested in the functional contribution of oncohistones to breast cancer tumorigenesis. I will be investigating histone mutations that target known/putative sites of ADP-ribosylation using various genomic strategies, cell-based/xenograft assays, CRISPR-Cas9, and other approaches. My studies propose that cancer utilizes mutations at sites of ADP-ribosylation to evade cell regulation, leading to enhanced proliferation and tumorigenesis.
I obtained my doctorate from the University of Arkansas for Medical Sciences in Interdisciplinary Biomedical Sciences. I investigated protein-DNA interactions between PARP-1 and oxidized G-Quadruplex DNA, highlighting a potentially novel repair mechanism that allows cancer cells to tolerate oxidative stress.
Selected Publications
- Huang D., Camacho C.V., Martire S., Nagari A., Setlem R., Gong X., Edwards A.D., Chiu S.P., Banaszynski L.A., Kraus W.L. (2022) Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation. Cancer Res. 82(13):2361-2377.
- Edwards A.D., Marecki J.C., Byrd A.K., Gao J., Raney K.D. (2021) G-Quadruplex loops regulate PARP-1 enzymatic activation. Nucleic Acids Research. 49(1):416–431.
Minjung Kwon, Ph.D.
Postdoctoral Fellow
With a variety of omics and biochemical tools, I investigate regulatory roles of TF ADP-ribosylation determining breast cancer subtype specificity. Final aims of the research are focused on connections between catalytic activity of PARP1, relevant TFs ADP-ribosylation, and therapeutic outcomes for subtype specific treatment.
Komal Pekhale, Ph.D.
Postdoctoral Fellow
I joined Kraus Lab in September 2022. I am broadly interested in gene regulation, ADP-ribosylation and NAD metabolism. In Kraus lab I am interested in role of PARPs in neurodegeneration. I would like to use a wide range of techniques including various genomic, proteomic, CRISPR-Cas9, cell-based assays and other approaches to understand the mechanisms.
Selected Publications
- Kadam D.A., Kalamkar S.D., Saraf A., Pathan I., Acharya J., Pekhale K., Shouche Y., Lole K., Ghaskadbi S., Ashma R. (2022) SNPs in the catalase promoter: a study based on Indian diabetic individuals. International Journal of Diabetes in Developing Countries.
- Perween N., Pekhale K., Haval G., Mittal S., Ghaskadbi S., Ghaskadbi S.S. (2022) Cloning and characterization of Thioredoxin 1 from the Cnidarian Hydra. The Journal of Biochemistry. 171(1):41-51.
Divya Reddy, Ph.D.
Assistant Instructor
As a broadly trained biochemist, I am interested in using my expertise in chromatin biology to understand 1. how various chromatin regulatory proteins function to facilitate a conducive environment for gene regulation in various cellular contexts including that of disease, and 2. how various metabolites directly regulate chromatin structure and function.
Selected Publications
- Reddy D., Bhattacharya S., Levy M., Zhang Y., Gogol M., Li H., Florens L., Workman J.L. (2023) Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep. 24(1):e55345.
- Bhattacharya S., Wang S., Reddy D., Shen S., Zhang Y., Zhang N., Li H., Washburn M.P., Florens L., Shi Y., Workman J.L., Li F. (2021) Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing. Nat Commun. 12(1):6452.
Xinrui Tan, M.D., Ph.D.
Visiting Instructor
I joined the Kraus lab in Feb 2022. I am interested in the function of mono(ADP-ribosyl)ation on ribosome protein during adipogenesis. I obtained my doctorate from Xi’an Jiaotong Univeristy, and then worked as pediatrician for 6 years in China. It is a precious experience for me to work at the bench with multiple advanced omics and biochemical tools, and to understand the mechanisms behind novel therapeutics.
Selected Publications
- Tan X., Cao Z., Li M., Xu E., Wang J., Xiao Y. (2016) TNF-α downregulates CIDEC via MEK/ERK-pathway in human adipocytes. Obesity 24(5):1070-1080.
- Tan X., Wang X., Chu H., Liu H., Yi X., Xiao Y. (2014) SFRP5 correlates with obesity and metabolic syndrome and increases after weight loss in children. Clinical Endocrinology 81(3):363–369.
Micah Thornton, Ph.D.
Computational Biology Postdoctoral Fellow
I am interested in the intersection of applied mathematics and statistical science and biology. To this end, I am seeking opportunities for developing and applying both predictive and descriptive models to biological processes of interest in medicine and general science. Specifically I am interested in the use of likelihood methods for the joint analysis of RNASeq and alternative sequencing data. Previously I have investigated phylogenetic distances using the Fourier coefficients of a genomic sequence, utilizing random forest classifiers for identifying the organism and the kind of library present in a raw sequencing reads file, and assisting in research on a three-nucleotide alignment algorithm that can be used in base-conversion sequence analysis. I also have experience and interest in applying nonparametric and semi-parametric models to other kinds of data including clinical outcomes data, glycosylation, and flow cytometry data.
Selected Publications
- Bennett C., Thornton M., Park C., Henry G., Zhang Y., Malladi V., Kim D. (2022) SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers. Bioinformatics 38(7):1830-1837.
- Zhang Y., Park C., Bennett C., Thornton M., Kim D. (2021) Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N. Genome Research 31(7):1290-1295.
Hyung Bum Kim
Graduate Student
I am interested in studying estrogen signaling in the context of breast cancer. I am using next generation sequencing techniques to understand how estrogen-receptor positive breast cancer cells respond to fluctuating concentrations of estrogen.
Weidan Song
Graduate Student
I am interested in understanding the effect of different activators, such as snoRNAs, on the poly(ADP-ribosyl)lation activity of poly(ADP-ribose) polymerases-1 (PARP1).
MiKayla Stokes
Graduate Student
Driven by my empathy towards those whose lives have been afflicted by disease, I found that biomedical research aligned this driving force with my curious and determined nature. Ultimately leading me to pursue research training at UT Southwestern under the guidance of Dr. W. Lee Kraus. As a graduate trainee, I am aiming to increase my ability to answer and explore basic science questions I believe are vital to the understanding and treatment of human disease. Currently I am interested in exploring transcriptional regulatory mechanisms that control adipogenesis and adipose tissue maintenance.
Selected Publications
- Parsons L.H.P., Challa S., Gibson B.A., Nandu T., Stokes M.S., Huang D., Lea J.S., Kraus W.L. (2021) Identification of PARP-7 substrates reveals a role for MARylation in microtubule control in ovarian cancer cells. eLife 10:e60481.
- Challa. S, Stokes M.S., Kraus W.L. (2021) MARTs and MARylation in the Cytosol: Biological Functions, Mechanisms of Action, and Therapeutic Potential. Cells 10(2): 313.
Amy Whitaker
Graduate Student
I am interested in understanding the role of poly(ADP-ribosyl)ation by nuclear poly(ADP-ribose) polymerases (PARPs) enzymes in signal-dependent control of transcription factor activity, enhancer formation, and target gene expression in adipogenesis and macrophage activation. My favorite transcription factor is C/EBPβ and I am dedicated to studying the role of PARylation of C/EBPβ within these biological systems. Additionally, I am interested in utilizing PAR-Trackers to detect fluctuating levels of PARylation in living mice.
Selected Publications
- Challa S*., Whitaker A.L.*, Kraus W.L. (2023) Detecting Poly(ADP-ribose) In Vitro and In Cells using PAR-Trackers. Methods in Molecular Biology 2609:75-90. *equal contribution
- Challa S., Ryu K.W., Whitaker A.L., Abshier J.C., Camacho C.V., Kraus W.L. (2022) Development and characterization of new tools for detecting poly(ADP-ribose) in vitro and in vivo. eLife 11:e72464.
Steven Blaine Holloway, M.D.
Gyn/Onc Clinical Fellow
I am excited to take the charge of advancing clinical care and the cutting edge as a growing physician scientist. My role in the Kraus lab is to investigate novel therapies and their mechanisms of action and resistance in gynecologic cancers, in order to better understand the underlying biology and explore new avenues of therapeutic strategy. The plethora of advanced basic science tools available in this lab and in collaboration with the Green Center and UTSW will allow for complex analysis and power to answer difficult questions.
I am a Gynecologic Oncology fellow, who completed my M.D. training at UT Southwestern in Obstetrics and Gynecology.
Christopher Walker, M.D.
Gyn/Onc Clinical Fellow
Selected Publications
- Walker C., Nguyen T.M., Jessel S., Alvero A.B., Silasi D.A., Rutherford T., Draghici S., Mor G. (2021) Automated Assay of a Four-Protein Biomarker Panel for Improved Detection of Ovarian Cancer. Cancers 13(2):325.
- Purandare N., Kramer K.J., Minchella P., Ottum S., Walker C., Rausch J., Chao C.R., Grossman L.I., Aras S., Recanati M.A. (2022) Intraperitoneal Triamcinolone Reduces Postoperative Adhesions, Possibly through Alteration of Mitochondrial Function. J Clin Med. 11(2):301.
Tulip Nandu, M.S.
Computational Biologist III
My expertise is in designing the data analysis pipelines, writing algorithms for sophisticated data analysis, and integration of various genomics assays to understand the complex regulation mechanisms of cancer, reproductive biology, endocrinology, and inflammation. As a computational biologist at UT Southwestern (2013-present), I have been working on various data-driven projects, which need efficient analysis and interpretation to have a better understanding of signal-regulated transcription using genomics. I am an expert in complex data analysis of Global Run-On Sequencing (GRO-seq), ATAC-seq, ChIP-seq, MeDIP-seq, RNA-seq, PRO-seq, ChIA-PET and various other next generation sequencing techniques and have automated the pipelines for some of them.
Selected Publications
- Kim D.S., Camacho C.V., Setlem R., Kim K., Malladi S., Hou T.Y., Nandu T., Gadad S.S., Kraus W.L. (2022) Functional Characterization of lncRNA152 as an Angiogenesis-Inhibiting Tumor Suppressor in Triple-Negative Breast Cancers. Mol Cancer Res. 20(11):1623-1635.
- Challa S., Khulpateea B.R., Nandu T., Camacho C.V., Ryu K.W., Chen H., Peng Y., Lea J.S., Kraus W.L. (2021) Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers. Cell 184(17):4531-4546.
Shu-Ping Chiu, M.S.
Research Associate
My work contributes to the successful flow of experimentation and research executed by postdoctoral fellows, graduate students, and research staff. I am interested in using my expertise in molecular biology for biochemical assays.
I am an AALAS-certified technician, RALAT, and participate in various studies involving animal models.
I obtained my Master of Science degree from Fu-Jen Catholic University in Taiwan.
Selected Publications
- Huang D., Camacho C.V., Martire S., Nagari A., Setlem R., Gong X., Edwards A.D., Chiu S.P., Banaszynski L.A., Kraus W.L. (2022) Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation. Cancer Res. 82(13):2361-2377.
Amy Gong, M.S.
Research Associate
Research areas that involve in DNA damage and repair, tumor microenvironment, cancer immunotherapy. General interests in pharmaceutical industry and drug development to discover transformative molecules through cutting-edge science and translate them into therapies for patients.
Selected Publications
- Huang D., Camacho C.V., Martire S., Nagari A., Setlem R., Gong X., Edwards A.D., Chiu S.P., Banaszynski L.A., Kraus W.L. (2022) Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation. Cancer Res. 82(13):2361-2377.
- Zhao K., Yang S.Y., Geng J., Gong X., Gong W., Shen L., Ning B. (2018) Combination of anginex gene therapy and radiation decelerates the growth and pulmonary metastasis of human osteosarcoma xenografts. Cancer Med. 7(6):2518-2529.
Charles Renshaw
Research Assistant I
My research interest lies in the areas of infection and immunity, specifically in the evasion of pathogens and the cumulative defects in microbial recognition and presentation by the innate immune system.
Luka Zrnic
Research Technician II
I am largely interested in cellular metabolism especially as it relates to adipogenesis, inflammation, and the immune system.
Josue Zuniga
Research Assistant I
My primary interest is in cell metabolism and differentiation as it pertains to adipose and cancer tissue.