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-
- Description:
- Platelets are circulating anucleate discs derived from megakaryocytes, and play major roles in hemostasis, inflammation, thrombosis, and vascular biology. Multi-phase culture systems for inducing in vitro platelet production from mature megakaryocytes have been explored to allow progenitor expansion, megakaryocyte maturation, and promotion of platelet formation and shedding. In this thesis,...
- Keyword:
- gaussian mixture models, stem cell differentiation, machine learning, and megakaryocyte
- Subject:
- Bioengineering, Bioinformatics, and Biology
- Creator:
- WU, JIA JIE
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- etdadmin_upload_640286 and http://dissertations.umi.com/northwestern:14541
-
- Description:
- Wastewater and bioreactors in wastewater treatment plants (WWTPs) are reservoirs for antibiotic resistance genes (ARGs), which can pass through treatment processes and migrate into the environment as they are released in effluent. WWTPs harbor a variety of ARGs that can be spread by horizontal gene transfer facilitated by mobile genetic...
- Keyword:
- viruses, antibiotic resistance genes, biofilms, wastewater, and mobile genetic elements
- Subject:
- Microbiology, Environmental engineering, and Bioinformatics
- Creator:
- Petrovich, Morgan
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- etdadmin_upload_671878 and http://dissertations.umi.com/northwestern:14727
-
- Description:
- The critical importance of alternative mRNA splicing and the RNA binding proteins that orchestrate this essential layer of post-transcriptional gene regulation is increasingly recognized in gene regulatory programs. We and others have shown that alternative splicing plays a causal role during the Epithelial-Mesenchymal transition, a cell-developmental program that is hijacked...
- Keyword:
- splicing factor, RNA, EMT, alternative splicing, RNA binding protein, and metastasis
- Subject:
- Bioinformatics and Biology
- Creator:
- Harvey, Samuel
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:14663 and etdadmin_upload_662828
-
- Description:
- The embryonic neural crest is a unique vertebrate stem cell population that has the ability to retain its stem attributes while neighboring cells in the embryo undergo lineage restriction. These cells possess multi-germ layer developmental potential and can give rise to a diverse array of derivatives such as components of...
- Keyword:
- pluripotency, HDAC, Neural Crest, TSA, and stem cell
- Subject:
- Bioinformatics and Developmental biology
- Creator:
- Rao, Anjali Narsing
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- etdadmin_upload_663294 and http://dissertations.umi.com/northwestern:14684
-
- Description:
- Annual age-adjusted breast cancer incidence rates in the United States have been static for decades. More recently, the development of massively parallel, high throughput DNA sequencing has enabled the cataloging of somatic mutations in cancer. Mutations are non-random and occur within sequence motifs. These motifs provide us with evidence to...
- Keyword:
- Natural Language Processing, Electronic Health Records, Genomics, Mutational Processes, Breast Cancer, and Machine Learning
- Subject:
- Bioinformatics and Computer science
- Creator:
- Zeng, Zexian
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:14500 and etdadmin_upload_635668
-
- Description:
- Understanding and controlling microbial community assembly is critical to developing novel bioprocesses for nutrient and energy recovery from wastewater and preparing for global climate change. As molecular biology tools and DNA sequencing improve, microbial ecologists can progress from answering qualitative questions about “who is there, and what are they doing?”...
- Keyword:
- metagenomics, microbial electrochemical cells, microbial ecology, activated sludge, and amplicon sequencing
- Subject:
- Environmental engineering and Bioinformatics
- Creator:
- Grifin, James
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2018-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:14462 and etdadmin_upload_626962
-
- Description:
- Recent studies have shown that many high profile studies in biology could not be reproduced, calling into questions the legitimacy of their findings. These reports have the potential to greatly jeopardize the credibility of scientists in the field as well as erode public confidence in the scientific enterprise. Computational research...
- Keyword:
- Sequencing, Reproducibility, and Computational Biology
- Subject:
- Bioinformatics and Engineering
- Creator:
- Liu, Sophia Shou
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- etdadmin_upload_658807 and http://dissertations.umi.com/northwestern:14578
-
- Description:
- Frontotemporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS) are two devastating neurodegenerative diseases that affect 100,000s of people globally. They have a severe adverse impact on society, yet there are currently no early diagnostic tools or disease-modifying therapies available. Despite their clinical heterogeneity, evidence points to these diseases being on...
- Keyword:
- microRNA, Compositional Data Analysis, TDP-43 Proteinopathy, FUS Proteinopathy, RNA-Seq, and Mitochondria
- Subject:
- Molecular biology, Bioinformatics, and Neurosciences
- Creator:
- McGee, Warren A
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:14675 and etdadmin_upload_663037
-
- Description:
- Polycystic ovary syndrome (PCOS) is among the most common endocrine disorders of premenopausal women, affecting 5-15% of this population depending on the diagnostic criteria applied. It is characterized by hyperandrogenism, ovulatory dysfunction and polycystic ovarian morphology. PCOS is highly heritable, but only a small proportion of this heritability can be...
- Keyword:
- complex trait genetics, rare variants, DENND1A, PCOS, and sub-phenotyping
- Subject:
- Bioinformatics, Genetics, and Endocrinology
- Creator:
- Dapas, Matthew
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:14662 and etdadmin_upload_662808
-
- Description:
- The focus of this thesis is on evaluating, designing, and applying statistical methods that elucidate molecular mechanisms by seeking to understand the pathways that contribute to disease. Chapter 1 introduces the field and motivates the work in this thesis. Chapters 2, 3, and 4 describe original work. Chapter 5 recapitulates...
- Keyword:
- Gene expression, Algorithms, Pathways, Networks, and Systems biology
- Subject:
- Statistics and Bioinformatics
- Creator:
- Shah, Sahil D
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:14812 and etdadmin_upload_685626
-
- Description:
- Gene regulatory networks (GRNs) are important abstractions of the complex regulatory interplays between genes, proteins, metabolites, and other molecular-level entities. Comprehensive GRNs provide high-level overviews of the topology of gene-gene interactions and their purposes, thereby enabling a comprehensive understanding of their role in phenotypic variation, disease mechanisms, and other biological...
- Subject:
- Applied mathematics and Bioinformatics
- Creator:
- Nguyen, Phan
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:14495 and etdadmin_upload_634566
-
- Description:
- Cells are complex, autonomous machines that integrate many environmental cues to execute a desired response. Though this property makes cells versatile, it presents significant design challenges when, to treat diseases, we must alter cellular responses. To understand changes to the complex regulatory pathways that cause diseases, studies often investigate the...
- Keyword:
- systems biology, machine learning, dynamics, regulation, and differential gene expression
- Subject:
- Bioinformatics and Biology
- Creator:
- Finkle, Justin
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/12/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:14568 and etdadmin_upload_656753
-
- Description:
- Understanding the complex genome-phenome associations behind human complex traits will be a primary focus for the practice of precision medicine in the future. Identifying the genetic variants that contribute to the inter- and intra- phenotypic variations of individuals, elucidating pleiotropic architecture of common complex traits, and demonstrating how personal biomedical...
- Keyword:
- Electronic Health Records, Genome-wide association studies, Bioinformatics, Biomedical Informatics, Precision medicine, and Phenome-wide association studies
- Subject:
- Bioinformatics, Genetics, and Medicine
- Creator:
- Joo, Yoonjung Yoonie
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 04/28/2020
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- etdadmin_upload_719309 and http://dissertations.umi.com/northwestern:15009
-
- Description:
- Over 6 million adults in the United States have heart failure, a serious public health problem. Differences in the progression of heart failure are in part due to variability in sex, age, and genetic variation background including ancestry. Medical biobanks provide a resource to study this variability as they include...
- Subject:
- Bioinformatics and Genetics
- Creator:
- Pottinger, Tess D
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 01/21/2021
- Date Created:
- 2020-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- etdadmin_upload_742461 and http://dissertations.umi.com/northwestern:15091
-
- Description:
- The advent of sequencing technologies has generated a large amount of biological and medical data. These data such as genetic sequencing data and lab experimental evidence data can help understand critical biomedical problems. This dissertation makes contribution in three different but related applications in biomedical research. In Chapter 2, we...
- Keyword:
- Normalization, Metagenomics, Graph neural network, Clustering, and Differential abundance test
- Subject:
- Biostatistics, Statistics, and Bioinformatics
- Creator:
- Ma, Yuanjing
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 01/21/2021
- Date Created:
- 2020-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:15057 and etdadmin_upload_736532
-
- Description:
- Transcriptome profiling including whole genome bulk and single cell RNA sequencing (RNA-seq) enables the quantitative study of transcript changes at either tissue or single cell level. With the advancement in next generation sequencing technology, it is now part of routine lab practice. More than other high-throughput technologies, computational algorithms are...
- Keyword:
- single cell RNA-seq, RNA-seq, and Clustering algorithm
- Subject:
- Bioinformatics
- Creator:
- Ren, Ziyou
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 01/21/2021
- Date Created:
- 2020-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:15101 and etdadmin_upload_742881
-
- Description:
- Uterine leiomyomas (fibroids) are a major source of gynaecologic morbidity in reproductive age women and are characterised by the excessive deposition of a disorganised extracellular matrix, resulting in rigid benign tumours. Clinically, leiomyoma patients usually present with pelvic pain, urinary incontinence, as well as heavy cyclic and non-cyclic bleeding. Curative...
- Subject:
- Molecular biology, Bioinformatics, and Biology
- Creator:
- Moyo, Mthabisi Bongani
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 01/21/2021
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- etdadmin_upload_723828 and http://dissertations.umi.com/northwestern:15028
-
- Description:
- In the short amount of time that genetic manipulation has been possible through CRISPR technology, myriad applications have been developed. Results from one of the most promising applications of this technology, pooled screens, have shown that single guide RNAs (sgRNAs), RNA sequences used to target specific regions of the genome,...
- Keyword:
- sgRNA design, CRISPR efficiency, and Machine learning
- Subject:
- Biostatistics, Statistics, and Bioinformatics
- Creator:
- Zarate, Oscar Alberto
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/01/2021
- Date Created:
- 2020-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:15353 and etdadmin_upload_773909
-
- Description:
- Current genetic studies are largely biased towards European populations, leaving the discovery of genomics biomarkers and causative genetic variants unexplored in minority populations, such as African Americans. Meanwhile, African Americans are disproportionately affected by a variety of complex diseases and respond differently to many drug treatments. The disparity is due...
- Keyword:
- gene expression, pharmacogenomics, African American, and eQTL mapping
- Subject:
- Bioinformatics and Genetics
- Creator:
- Zhong, Yizhen
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/01/2021
- Date Created:
- 2020-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- http://dissertations.umi.com/northwestern:15303 and etdadmin_upload_765355
-
- Description:
- Uterine leiomyomas (fibroids) are a major source of gynaecologic morbidity in reproductive age women and are characterised by the excessive deposition of a disorganised extracellular matrix, resulting in rigid benign tumours. Clinically, leiomyoma patients usually present with pelvic pain, urinary incontinence, as well as heavy cyclic and non-cyclic bleeding. Curative...
- Subject:
- Molecular biology, Bioinformatics, and Biology
- Creator:
- Moyo, Mthabisi Bongani
- Owner:
- Scholarly Digital Publishing
- Language:
- en
- Date Uploaded:
- 02/01/2021
- Date Created:
- 2019-01-01
- Resource Type:
- Dissertation
- Alternate Identifier:
- etdadmin_upload_723828 and http://dissertations.umi.com/northwestern:15028