プロフィール詳細

プロジェクトを作成

★★★★★

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Dr. Nashir U.に依頼

United States

RNA-seq & Cancer Bioinformatics Consultant | Translational Research | Biomarker Discovery | Data Analysist

プロフィール概要

I am an Assistant Professor in the Department of Radiation Oncology at UT Southwestern Medical Center with over 15 years of experience in cancer biology, translational research, molecular biology, and computational analysis. My research integrates experimental and bioinformatics approaches to investigate mechanisms of therapy resistance and identify biomarkers and therapeutic strategies for precision medicine. I hold a PhD in Medical Sciences and further strengthened my analytical background through a Data Science MicroMasters program through UC San Diego and edX. My scientific work spans molecular biology, cancer genomics, transcriptomics, radiation biology, immunology, and data-driven biomedical research. My expertise includes end-to-end RNA-seq and transcriptomic analysis workflows, including quality control, alignment, read quantification, differential gene expression analysis, pathway enrichment, and biological interpretation. I have hands-on experience with tools such as FastQC, MultiQC, STAR, FeatureCounts, DESeq2, GSEA, R, Python, Git/GitHub, and statistical analysis pipelines. I also develop reproducible computational workflows and integrate bioinformatics with experimental research questions. My current and previous research projects include investigating CDK4/6 inhibitor resistance in ER+ breast cancer, identifying mechanisms of radiotherapy resistance, studying tumor microenvironment remodeling, biomarker discovery, and developing therapeutic strategies involving immunotherapy and targeted agents. My work combines CRISPR-based approaches, transcriptomics, molecular assays, and machine learning methods to generate clinically relevant insights. Beyond data analysis, I provide support in experimental design, biological interpretation, manuscript preparation, grant development, publication-quality visualization, and scientific communication. I enjoy collaborating with academic laboratories, biotech companies, and researchers seeking high-quality scientific and RNA-seq analytical support. I am passionate about bridging biology and computational science to transform complex datasets into actionable discoveries.

専門分野

• ☆ Microbiology
• ☆ Microbiome Research
• ☆ Industrial Microbiology
• ☆ Microbiological Assays
• ☆ Biochemistry
• ☆ Immunoassay
• ☆ Biochemical Assays
• ☆ Structural Biology
• ☆ Apoptosis
• ☆ Oxidative Stress & Mitochondrial Function
• ☆ Antioxidants
• ☆ Enzyme Activity Assays
• ☆ Binding Assays
• ☆ Molecular Biology
• ☆ Biomarkers
• ☆ Genetics
• ☆ Microarrays
• ☆ Molecular Evolution
• ☆ Chromatin
• ☆ Epigenetics
• ☆ PCR
• ☆ Molecular Cloning
• ☆ Next Generation Sequencing (NGS)
• ☆ ATAC-Seq
• ☆ DNA Sequencing
• ☆ Synthetic Genomics
• ☆ Protein Sequencing
• ☆ Gene Expression Analysis
• ☆ Genome Sequencing
• ☆ Microinjection
• ☆ Mutagenesis
• ☆ Exome Sequencing
• ☆ Recombinant DNA
• ☆ RNA Synthesis
• ☆ RNA Sequencing
• ☆ DNA/Gene Synthesis
• ☆ Oligonucleotide Synthesis
• ☆ Plasmid DNA
• ☆ DNA Damage & Repair
• ☆ ChIP-Seq
• ☆ Kinases
• ☆ Monoclonal Antibody Production
• ☆ Molecular Ecology
• ☆ Basic Immunology
• ☆ Adjuvant & Antigen Research
• ☆ Data Analysis
• ☆ Image Processing
• ☆ Computer Simulation/Computational Modeling
• ☆ Algorithm Design
• ☆ Predictive Modeling & Analytics
• ☆ Data Processing
• ☆ Data Exploration
• ☆ Cluster Analysis
• ☆ Data Visualization
• ☆ Big Data Analytics
• ☆ Data Management
• ☆ Data Manipulation
• ☆ Machine Learning
• ☆ Text Mining & Analytics
• ☆ Data Mining
• ☆ Data Cleaning
• ☆ Natural Language Processing
• ☆ Data Architecture
• ☆ Neural Networks
• ☆ Pattern Recognition
• ☆ Artificial Intelligence
• ☆ Deep Learning
• ☆ Computer Vision
• ☆ Data Security
• ☆ Business Analytics
• ☆ Statistics
• ☆ Health Data Analysis
• ☆ Bioinformatics
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Structural Bioinformatics
• ☆ Food Microbiology
• ☆ Pathogenesis
• ☆ Clinical Microbiology
• ☆ Biomarker Discovery
• ☆ Blotting
• ☆ Immunohistochemistry
• ☆ Phylogenetics
• ☆ Population Genetics
• ☆ Python
• ☆ Excel
• ☆ R
• ☆ Tableau
• ☆ Drug Development
• ☆ Preclinical Research
• ☆ Clinical Trials
• ☆ Clinical Trials Data Analysis
• ☆ Allergy & Clinical Immunology
• ☆ Clinical Immunology
• ☆ HLA Typing/Tissue Typing
• ☆ Clinical Laboratory Science
• ☆ Clinical Biochemistry
• ☆ Cancer Research
• ☆ Technical & Scientific Writing
• ☆ Journal Selection
• ☆ Manuscript & Journal Article Writing
• ☆ Instructional Materials
• ☆ Release Notes
• ☆ Experimental Protocols
• ☆ SOP & Protocol Writing
• ☆ White Papers
• ☆ Spec Sheets
• ☆ Case Studies
• ☆ Textbook Content Writing
• ☆ Science Communication
• ☆ Grant Writing

サービス

• Writing
• Research
• Consulting
• Data & AI
• Product Development

Writing Clinical Trial Documentation, Medical Writing, Non-Medical Regulatory Writing, Technical Writing, Business & Legal Writing, Creative Writing, General Proofreading & Editing, Translation

Research Meta-Research, Feasibility Study, Fact Checking, Gap Analysis, Scientific and Technical Research, Secondary Data Collection

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Statistical Analysis, Image Processing, Image Analysis, Algorithm Design-ML, Data Visualization, Big Data Analytics, Text Mining & Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights

Product Development Product Evaluation, Concept Development

職務経験

Assistant Professor

The University of Texas Southwestern Medical Center

9月 2023 - 現在

Instructor

The University of Texas Southwestern Medical Center

5月 2018 - 8月 2023

Postdoctoral Researcher

The University of Texas Southwestern Medical Center

4月 2014 - 5月 2018

Graduate Student

Tohoku University

10月 2009 - 3月 2014

Research Investigator

ICDDR,B

10月 2005 - 3月 2009

Research Scholar / MS Thesis Student

ICDDR,B

3月 2004 - 9月 2005

学歴

MicroMasters in Data Science

UC San Diego & edX

8月 2022 - 4月 2023

Ph.D. (IDAC)

Tohoku University

10月 2009 - 3月 2014

MS (Biochemistry and Molecular Biology)

University of Dhaka

3月 2004 - 9月 2005

BS(Hons.) (Biochemistry and Molecular Biology)

University of Dhaka

7月 1998 - 2月 2004

認定資格

• Databases: Relational Databases and SQL

  StanfordOnline, Stanford University

  1月 2023 - 現在

• Microsoft SQL from A to Z

  Udemy

  12月 2022 - 現在

• Learning Python for Data Analysis and Visualization

  udemy

  8月 2022 - 現在

• Learn Python Programming Masterclass

  udemy

  7月 2022 - 現在

• R Programming A-ZTM: R For Data Science With Real Experience!

  udemy

  7月 2022 - 現在

• Postdoctoral Certificate in Advanced Research

  UT Southwestern Medical Center

  5月 2018 - 現在

• Postdoctoral Certificate in Research

  UT Southwestern Medical Center

  8月 2016 - 現在

出版物

PREPRINT

S M Nashir Udden, Baishan Jiang, Kamal Pandey, Cheryl M. Lewis, Sunati Sahoo, Noelle S. Williams, Prasanna G. Alluri (2025). The non-kinase function of CDK6 is a key driver of acquired resistance to CDK4/6 inhibitors in Estrogen Receptor-positive breast cancer .

JOURNAL ARTICLE

Avisankar Chini, Prarthana Guha, Ashcharya Rishi, Monira Obaid, SM Nashir Udden, Subhrangsu S. Mandal (2024). Discovery and functional characterization of LncRNAs associated with inflammation and macrophage activation . Methods.

S. M. Nashir Udden, GuemHee Baek, Kamal Pandey, Chantal Vidal, Yulun Liu, Asal S. Rahimi, D. Nathan Kim, Chika R. Nwachukwu, Ram S. Mani, Prasanna G. Alluri (2023). Towards precision radiation oncology: endocrine therapy response as a biomarker for personalization of breast radiotherapy . npj Precision Oncology.

Sm N. Udden, Qian Wang, Sunil Kumar, Venkat S. Malladi, Shwu-Yuan Wu, Shuguang Wei, Bruce A. Posner, Sophie Geboers, Noelle S. Williams, Yulun Liu, et al. (2022). Targeting ESR1 mutation–induced transcriptional addiction in breast cancer with BET inhibition . JCI Insight.

Monira Obaid, S. M. Nashir Udden, Prasanna Alluri, Subhrangsu S. Mandal (2021). LncRNA HOTAIR regulates glucose transporter Glut1 expression and glucose uptake in macrophages during inflammation . Scientific Reports.

Imran Hussain, Paromita Deb, Avisankar Chini, Monira Obaid, Arunoday Bhan, Khairul I. Ansari, Bibhu P. Mishra, Samara A. Bobzean, S. M. Nashir Udden, Prasanna G. Alluri, et al. (2020). HOXA5 Expression Is Elevated in Breast Cancer and Is Transcriptionally Regulated by Estradiol . Frontiers in Genetics.

(2019). NLRP12 suppresses hepatocellular carcinoma via downregulation of cJun N-terminal kinase activation in the hepatocyte . eLife.

Monira Obaid, S. M. Nashir Udden, Paromita Deb, Nadine Shihabeddin, Md. Hasan Zaki, Subhrangsu S. Mandal (2018). LncRNA HOTAIR regulates lipopolysaccharide-induced cytokine expression and inflammatory response in macrophages . Scientific Reports.

Abu Hena M. Kamal, Jayanta K. Chakrabarty, S. M. Nashir Udden, Md. Hasan Zaki, Saiful M. Chowdhury (2018). Inflammatory Proteomic Network Analysis of Statin-treated and Lipopolysaccharide-activated Macrophages . Scientific Reports.

(2017). NOD2 Suppresses Colorectal Tumorigenesis via Downregulation of the TLR Pathways . Cell reports.

(2017). The Ex Vivo Colon Organ Culture and Its Use in Antimicrobial Host Defense Studies . Journal of visualized experiments : JoVE.

(2013). c-ABL tyrosine kinase modulates p53-dependent p21 induction and ensuing cell fate decision in response to DNA damage . Cellular signalling.

M. Kamruzzaman, S. M. Nashir Udden, D. Ewen Cameron, Stephen B. Calderwood, G. Balakrish Nair, John J. Mekalanos, Shah M. Faruque (2010). Quorum-regulated biofilms enhance the development of conditionally viable, environmental <i>Vibrio cholerae</i> . Proceedings of the National Academy of Sciences.

M. Shamim Hasan Zahid, S. M. Nashir Udden, A. S. G. Faruque, Stephen B. Calderwood, John J. Mekalanos, Shah M. Faruque (2008). Effect of Phage on the Infectivity of <i>Vibrio cholerae</i> and Emergence of Genetic Variants . Infection and Immunity.

(2008). Acquisition of classical CTX prophage from Vibrio cholerae O141 by El Tor strains aided by lytic phages and chitin-induced competence . Proceedings of the National Academy of Sciences of the United States of America.

Shah M. Faruque, Kuntal Biswas, S. M. Nashir Udden, Qazi Shafi Ahmad, David A. Sack, G. Balakrish Nair, John J. Mekalanos (2006). Transmissibility of cholera: <i>In vivo</i> -formed biofilms and their relationship to infectivity and persistence in the environment . Proceedings of the National Academy of Sciences.