Digital Commons Network^™

A Quick Guide For Building A Successful Bioinformatics Community., Aidan Budd, Manuel Corpas, Michelle D Brazas, Jonathan C Fuller, Jeremy Goecks, Nicola J Mulder, Magali Michaut, B F Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg

Computational Biology Institute

"Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding …

Vivien Thomas: Master Craftsman, Gifted Teacher, And Unsung Hero., Alisha Joyner, B.S., Charles J. Yeo, Md, Pinckney J. Maxwell, Iv, Md

Department of Surgery Gibbon Society Historical Profiles

The field of pediatric cardiovascular surgery gained international recognition in 1944 with the first successful correction of a tetralogy of Fallot congenital anomaly in a 15-month-old patient. Dr. Helen Taussig (1898 to 1986), a pediatrician at Johns Hopkins Hospital, recognized the need for the procedure. Dr. Alfred Blalock (1899 to 1964), Chief of Surgery at Johns Hopkins Hospital, is credited with performing the surgery. However, there is an unsung hero who for many years did not receive a single mention in the medical literature. Vivien Thomas (1910 to 1985) was Dr. Blalock’s research assistant who is said to have stood …

Lifelong Physical Exercise Delays Age-Associated Skeletal Muscle Decline., S Zampieri, L Pietrangelo, S Loefler, H Fruhmann, M Vogelauer, S Burggraf, A Pond, M Grim-Stieger, J Cvecka, M Sedliak, V Tirpáková, W Mayr, N Sarabon, K Rossini, L Barberi, M De Rossi, V Romanello, S Boncompagni, A Musarò, M Sandri, F Protasi, U Carraro, H Kern

Publications

Aging is usually accompanied by a significant reduction in muscle mass and force. To determine the relative contribution of inactivity and aging per se to this decay, we compared muscle function and structure in (a) male participants belonging to a group of well-trained seniors (average of 70 years) who exercised regularly in their previous 30 years and (b) age-matched healthy sedentary seniors with (c) active young men (average of 27 years). The results collected show that relative to their sedentary cohorts, muscle from senior sportsmen have: (a) greater maximal isometric force and function, (b) better preserved fiber morphology and ultrastructure …

Validation Of In Vivo 2d Displacements From Spiral Cine Dense At 3t, Gregory J. Wehner, Jonathan D. Suever, Christopher M. Haggerty, Linyuan Jing, David K. Powell, Sean M. Hamlet, Jonathan D. Grabau, Walter Dimitri Mojsejenko, Xiaodong Zhong, Frederick H. Epstein, Brandon K. Fornwalt

Saha Cardiovascular Research Center Faculty Publications

BACKGROUND: Displacement Encoding with Stimulated Echoes (DENSE) encodes displacement into the phase of the magnetic resonance signal. Due to the stimulated echo, the signal is inherently low and fades through the cardiac cycle. To compensate, a spiral acquisition has been used at 1.5T. This spiral sequence has not been validated at 3T, where the increased signal would be valuable, but field inhomogeneities may result in measurement errors. We hypothesized that spiral cine DENSE is valid at 3T and tested this hypothesis by measuring displacement errors at both 1.5T and 3T in vivo.

METHODS: Two-dimensional spiral cine DENSE and tagged …

Mapping The Pareto Optimal Design Space For A Functionally Deimmunized Biotherapeutic Candidate, Regina S. Salvat, Andrew S. Parker, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold

Dartmouth Scholarship

The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the …

Trail-Based High Throughput Screening Reveals A Link Between Trail-Mediated Apoptosis And Glutathione Reductase, A Key Component Of Oxidative Stress Response., Dmitri Rozanov, Anton Cheltsov, Eduard Sergienko, Stefan Vasile, Vladislav Golubkov, Alexander E Aleshin, Trevor Levin, Elie Traer, Byron Hann, Julia Freimuth, Nikita Alexeev, Max A Alekseyev, Sergey P Budko, Hans Peter Bächinger, Paul Spellman

Computational Biology Institute

A high throughput screen for compounds that induce TRAIL-mediated apoptosis identified ML100 as an active chemical probe, which potentiated TRAIL activity in prostate carcinoma PPC-1 and melanoma MDA-MB-435 cells. Follow-up in silico modeling and profiling in cell-based assays allowed us to identify NSC130362, pharmacophore analog of ML100 that induced 65-95% cytotoxicity in cancer cells and did not affect the viability of human primary hepatocytes. In agreement with the activation of the apoptotic pathway, both ML100 and NSC130362 synergistically with TRAIL induced caspase-3/7 activity in MDA-MB-435 cells. Subsequent affinity chromatography and inhibition studies convincingly demonstrated that glutathione reductase (GSR), a key …

Atrial Fibrillation: Biophysics, Molecular Mechanisms, And Novel Therapies., Alexey V. Glukhov, Leonid V. Rosenshtraukh, Anamika Bhargava, Michele Miragoli, Bas J. D. Boukens

Anatomy and Regenerative Biology Faculty Publications

No abstract provided.

Mllt1 Yeats Domain Mutations In Clinically Distinctive Favourable Histology Wilms Tumours., Elizabeth J Perlman, Samantha Gadd, Stefan T Arold, Anand Radhakrishnan, Daniela S Gerhard, Jeffrey S. Dome, +19 Additional Authors

Pediatrics Faculty Publications

Wilms tumour is an embryonal tumour of childhood that closely resembles the developing kidney. Genomic changes responsible for the development of the majority of Wilms tumours remain largely unknown. Here we identify recurrent mutations within Wilms tumours that involve the highly conserved YEATS domain of MLLT1 (ENL), a gene known to be involved in transcriptional elongation during early development. The mutant MLLT1 protein shows altered binding to acetylated histone tails. Moreover, MLLT1-mutant tumours show an increase in MYC gene expression and HOX dysregulation. Patients with MLLT1-mutant tumours present at a younger age and have a high prevalence of precursor intralobar …

Effect Of Cold Plasma On Glial Cell Morphology Studied By Atomic Force Microscopy., Nina Recek, Xiaoqian Cheng, Michael Keidar, Uros Cvelbar, Alenka Vesel, Miran Mozetic, Jonathan Sherman

Neurological Surgery Faculty Publications

The atomic force microscope (AFM) is broadly used to study the morphology of cells. The morphological characteristics and differences of the cell membrane between normal human astrocytes and glial tumor cells are not well explored. Following treatment with cold atmospheric plasma, evaluation of the selective effect of plasma on cell viability of tumor cells is poorly understood and requires further evaluation. Using AFM we imaged morphology of glial cells before and after cold atmospheric plasma treatment. To look more closely at the effect of plasma on cell membrane, high resolution imaging was used. We report the differences between normal human …

Magnetic Resonance Imaging And Histology Correlation In The Neocortex In Temporal Lobe Epilepsy., Maged Goubran, Robert R Hammond, Sandrine De Ribaupierre, Jorge G Burneo, Seyed Mirsattari, David A Steven, Andrew G Parrent, Terry M Peters, Ali R Khan

Robarts Imaging Publications

OBJECTIVE: To investigate the histopathological correlates of quantitative relaxometry and diffusion tensor imaging (DTI) and to determine their efficacy in epileptogenic lesion detection for preoperative evaluation of focal epilepsy.

METHODS: We correlated quantitative relaxometry and DTI with histological features of neuronal density and morphology in 55 regions of the temporal lobe neocortex, selected from 13 patients who underwent epilepsy surgery. We made use of a validated nonrigid image registration protocol to obtain accurate correspondences between in vivo magnetic resonance imaging and histology images.

RESULTS: We found T1 to be a predictor of neuronal density in the neocortical gray matter (GM) …

Automatic Segmentation Of The Hippocampus For Preterm Neonates From Early-In-Life To Term-Equivalent Age., Ting Guo, Julie L Winterburn, Jon Pipitone, Emma G Duerden, Min Tae M Park, Vann Chau, Kenneth J Poskitt, Ruth E Grunau, Anne Synnes, Steven P Miller, M Mallar Chakravarty

Brain and Mind Institute Researchers' Publications

INTRODUCTION: The hippocampus, a medial temporal lobe structure central to learning and memory, is particularly vulnerable in preterm-born neonates. To date, segmentation of the hippocampus for preterm-born neonates has not yet been performed early-in-life (shortly after birth when clinically stable). The present study focuses on the development and validation of an automatic segmentation protocol that is based on the MAGeT-Brain (Multiple Automatically Generated Templates) algorithm to delineate the hippocampi of preterm neonates on their brain MRIs acquired at not only term-equivalent age but also early-in-life.

METHODS: First, we present a three-step manual segmentation protocol to delineate the hippocampus for preterm …

Fusion Analysis Of First Episode Depression: Where Brain Shape Deformations Meet Local Composition Of Tissue., Mahdi Ramezani, Purang Abolmaesumi, Amir Tahmasebi, Rachael Bosma, Ryan Tong, Tom Hollenstein, Kate Harkness, Ingrid Johnsrude

Brain and Mind Institute Researchers' Publications

Computational neuroanatomical techniques that are used to evaluate the structural correlates of disorders in the brain typically measure regional differences in gray matter or white matter, or measure regional differences in the deformation fields required to warp individual datasets to a standard space. Our aim in this study was to combine measurements of regional tissue composition and of deformations in order to characterize a particular brain disorder (here, major depressive disorder). We use structural Magnetic Resonance Imaging (MRI) data from young adults in a first episode of depression, and from an age- and sex-matched group of non-depressed individuals, and create …

Interface Stress In Socket/Residual Limb With Transtibial Prosthetic Suspension Systems During Locomotion On Slopes And Stairs, A. Eshraghi, Noor Azuan Abu Osman, H. Gholizadeh, S. Ali, Wan Abu Bakar Wan Abas

Research Publications (2011 to 2015)

OBJECTIVE: This study aimed to compare the effects of different suspension methods on the interface stress inside the prosthetic sockets of transtibial amputees when negotiating ramps and stairs. DESIGN: Three transtibial prostheses, with a pin/lock system, a Seal-In system, and a magnetic suspension system, were created for the participants in a prospective study. Interface stress was measured as the peak pressure by using the F-socket transducers during stairs and ramp negotiation. RESULTS: Twelve individuals with transtibial amputation managed to complete the experiments. During the stair ascent and descent, the greatest peak pressure was observed in the prosthesis with the Seal-In …

The Development And Application Of An Oncology Therapy-Related Symptom Checklist For Adults (Trsc) And Children (Trsc-C) And E-Health Applications., Arthur R Williams, David D Williams, Phoebe D Williams, Farrokh Alemi, Hosai Hesham, Blaine Donley, Raya Kheirbek

Medicine Faculty Publications

BACKGROUND: Studies found that treatment symptoms of concern to oncology/hematology patients were greatly under-identified in medical records. On average, 11.0 symptoms were reported of concern to patients compared to 1.5 symptoms identified in their medical records. A solution to this problem is use of an electronic symptom checklist that can be easily accessed by patients prior to clinical consultations.

PURPOSE: Describe the oncology Therapy-Related Symptom Checklists for Adults (TRSC) and Children (TRSC-C), which are validated bases for e-Health symptom documentation and management. The TRSC has 25 items/symptoms; the TRSC-C has 30 items/symptoms. These items capture up to 80% of the …

Discrimination Of Mild Cognitive Impairment And Alzheimer's Disease Using Transfer Entropy Measures Of Scalp Eeg, Joseph Mcbride, Xiaopeng Zhao, Nancy Munro, Gregory Jicha, Charles Smith, Yang Jiang

Sanders-Brown Center on Aging Faculty Publications

Mild cognitive impairment (MCI) is a neurological condition related to early stages of dementia including Alzheimer's disease (AD). This study investigates the potential of measures of transfer entropy in scalp EEG for effectively discriminating between normal aging, MCI, and AD participants. Resting EEG records from 48 age-matched participants (mean age 75.7 years)-15 normal controls, 16 MCI, and 17 early AD-are examined. The mean temporal delays corresponding to peaks in inter-regional transfer entropy are computed and used as features to discriminate between the three groups of participants. Three-way classification schemes based on binary support vector machine models demonstrate overall discrimination accuracies …

Evidence For Distinct Coastal And Offshore Communities Of Bottlenose Dolphins In The North East Atlantic., Machiel G. Oudejans, Fleur Visser, Anneli Englund, Emer Rogan, Simon N. Ingram

School of Biological and Marine Sciences

Bottlenose dolphin stock structure in the northeast Atlantic remains poorly understood. However, fine scale photo-id data have shown that populations can comprise multiple overlapping social communities. These social communities form structural elements of bottlenose dolphin (Tursiops truncatus) [corrected] populations, reflecting specific ecological and behavioural adaptations to local habitats. We investigated the social structure of bottlenose dolphins in the waters of northwest Ireland and present evidence for distinct inshore and offshore social communities. Individuals of the inshore community had a coastal distribution restricted to waters within 3 km from shore. These animals exhibited a cohesive, fission-fusion social organisation, with repeated resightings …

Fret Detection Of Lymphocyte Function-Associated Antigen-1 Conformational Extension, Alexandre Chigaev, Yelena Smagley, Mark K. Haynes, Oleg Ursu, Cristian G. Bologa, Liliana Halip, Tudor Oprea, Anna Waller, Mark B. Carter, Yinan Zhang, Wei Wang, Tione Buranda, Larry A. Sklar

Pharmaceutical Sciences Faculty Publications

Lymphocyte function-associated antigen 1 (LFA-1, CD11a/CD18, αLβ2-integrin) and its ligands are essential for adhesion between T-cells and antigen-presenting cells, formation of the immunological synapse, and other immune cell interactions. LFA-1 function is regulated through conformational changes that include the modulation of ligand binding affinity and molecular extension. However, the relationship between molecular conformation and function is unclear. Here fluorescence resonance energy transfer (FRET) with new LFA-1-specific fluorescent probes showed that triggering of the pathway used for T-cell activation induced rapid unquenching of the FRET signal consistent with extension of the molecule. Analysis of the FRET quenching at rest revealed an …

Multi-Parametric Mri And Texture Analysis To Visualize Spatial Histologic Heterogeneity And Tumor Extent In Glioblastoma., Leland S Hu, Shuluo Ning, Jennifer M Eschbacher, Nathan Gaw, Amylou C Dueck, Kris A Smith, Peter Nakaji, Jonathan Plasencia, Sara Ranjbar, Stephen J Price, Nhan Tran, Joseph Loftus, Robert Jenkins, Brian P O'Neill, William Elmquist, Leslie C Baxter, Fei Gao, David Frakes, John P Karis, Christine Zwart, Kristin R Swanson, Jann Sarkaria, Teresa Wu, J Ross Mitchell, Jing Li

Neurosurgery

BACKGROUND: Genetic profiling represents the future of neuro-oncology but suffers from inadequate biopsies in heterogeneous tumors like Glioblastoma (GBM). Contrast-enhanced MRI (CE-MRI) targets enhancing core (ENH) but yields adequate tumor in only ~60% of cases. Further, CE-MRI poorly localizes infiltrative tumor within surrounding non-enhancing parenchyma, or brain-around-tumor (BAT), despite the importance of characterizing this tumor segment, which universally recurs. In this study, we use multiple texture analysis and machine learning (ML) algorithms to analyze multi-parametric MRI, and produce new images indicating tumor-rich targets in GBM.

METHODS: We recruited primary GBM patients undergoing image-guided biopsies and acquired pre-operative MRI: CE-MRI, Dynamic-Susceptibility-weighted-Contrast-enhanced-MRI, …

Companion Diagnostics At The Intersection Of Personalized Medicine And Healthcare Delivery., Scott A Waldman, Andre Terzic

Department of Pharmacology and Experimental Therapeutics Faculty Papers

This article has been peer reviewed. It is the authors' final version prior to publication in Biomarkers in Medicine, Volume 9, Issue 1, January 2015, Pages 1-3.

The published version is available at DOI: 10.2217/bmm.14.99. Copyright © Future Medicine

Mcl1 Enhances The Survival Of Cd8+ Memory T Cells After Viral Infection, Jingang Gui, Zhuting Hu, Ching-Yi Tsai, Tian Ma, Yan Song, Amanda Morales, Li-Hao Huang, Ethan Dmitrovsky, Ruth Craig, Edward Usherwood

Dartmouth Scholarship

Viral infection results in the generation of massive numbers of activated effector CD8+ T cells that recognize viral components. Most of these are short-lived effector T cells (SLECs) that die after clearance of the virus. However, a small proportion of this population survives and forms antigen-specific memory precursor effector cells (MPECs), which ultimately develop into memory cells. These can participate in a recall response upon reexposure to antigen even at protracted times postinfection. Here, antiapoptotic myeloid cell leukemia 1 (MCL1) was found to prolong survival upon T cell stimulation, and mice expressing human MCL1 as a transgene exhibited a skewing …

Sox9 Inhibits -Trcp-Mediated Protein Degradation To Promote Nuclear Gli1 Expression And Cancer Stem Cell Properties, W. Deng, D. B. Vanderbilt, C.-C. Lin, K. H. Martin, K. M. Brundage, J. M. Ruppert

Faculty & Staff Scholarship

No abstract provided.

A Review Of Locomotion Systems For Capsule Endoscopy, Lejie Liu,, Shahrzad Towfighian, Amine Hila

Mechanical Engineering Faculty Scholarship

Wireless capsule endoscopy for gastrointestinal (GI) tract is a modern technology that has the potential to replace conventional endoscopy techniques. Capsule endoscopy is a pill-shaped device embedded with a camera, a coin battery, and a data transfer. Without a locomotion system, this capsule endoscopy can only passively travel inside the GI tract via natural peristalsis, thus causing several disadvantages such as inability to control and stop, and risk of capsule retention. Therefore, a locomotion system needs to be added to optimize the current capsule endoscopy. This review summarizes the state-of-the-art locomotion methods along with the desired locomotion features such as …

A Multidimensional Data Warehouse For Community Health Centers., Kislaya Kunjan, Tammy Toscos Phd, Ayten Turkcan, Brad N Doebbeling

Mirro Center Articles

Community health centers (CHCs) play a pivotal role in healthcare delivery to vulnerable populations, but have not yet benefited from a data warehouse that can support improvements in clinical and financial outcomes across the practice. We have developed a multidimensional clinic data warehouse (CDW) by working with 7 CHCs across the state of Indiana and integrating their operational, financial and electronic patient records to support ongoing delivery of care. We describe in detail the rationale for the project, the data architecture employed, the content of the data warehouse, along with a description of the challenges experienced and strategies used in …

Dna Methylation In Humans And Dogs: Evaluating The Impact Of Nutritional And Particulate Exposures, Luke Benjamin Montrose

Graduate Student Theses, Dissertations, & Professional Papers

Asthma is among the most common chronic diseases in children, among the leading causes of hospitalization for children, and one of the leading causes of school absenteeism. Discovery of preventable factors and the underlying mechanisms that exacerbate asthma among prevalent cases is important for mitigating the health burden of this childhood disease. Environmental factors such as exposure to particulate matter (PM) or nutritional deficiencies can lead to poor respiratory health among susceptible children. Recent animal studies suggest that PM exposures and dietary nutrients may influence asthma pathways through epigenetic mechanisms. Epigenetic modifications are heritable changes that can regulate gene activity …

Posture Affects How Robots And Infants Map Words To Objects., Af Morse, Vl Benitez, T Belpaeme, A Cangelosi, Lb Smith

School of Engineering, Computing and Mathematics

For infants, the first problem in learning a word is to map the word to its referent; a second problem is to remember that mapping when the word and/or referent are again encountered. Recent infant studies suggest that spatial location plays a key role in how infants solve both problems. Here we provide a new theoretical model and new empirical evidence on how the body - and its momentary posture - may be central to these processes. The present study uses a name-object mapping task in which names are either encountered in the absence of their target (experiments 1-3, 6 …

Molecular Characterization Of A Multidrug Resistance Incf Plasmid From The Globally Disseminated Escherichia Coli St131 Clone., Minh Duy Phan, Brian M. Forde, Kate M. Peters, Sohinee Sarkar, Steven Hancock, Mitchell Stanton-Cook, Zakour Nl Ben, Mathew Upton, Scott A. Beatson, Mark A. Schembri

School of Biomedical Sciences

Escherichia coli sequence type 131 (E. coli ST131) is a recently emerged and globally disseminated multidrug resistant clone associated with urinary tract and bloodstream infections. Plasmids represent a major vehicle for the carriage of antibiotic resistance genes in E. coli ST131. In this study, we determined the complete sequence and performed a comprehensive annotation of pEC958, an IncF plasmid from the E. coli ST131 reference strain EC958. Plasmid pEC958 is 135.6 kb in size, harbours two replicons (RepFIA and RepFII) and contains 12 antibiotic resistance genes (including the blaCTX-M-15 gene). We also carried out hyper-saturated transposon mutagenesis and multiplexed transposon …

Interfacial Polymerization For Colorimetric Labeling Of Protein Expression In Cells, Jacob L. Lilly, Phillip R. Sheldon, Liv J. Hoversten, Gabriela Romero, Vivek Balasubramaniam, Brad J. Berron

Chemical and Materials Engineering Faculty Publications

Determining the location of rare proteins in cells typically requires the use of on-sample amplification. Antibody based recognition and enzymatic amplification is used to produce large amounts of visible label at the site of protein expression, but these techniques suffer from the presence of nonspecific reactivity in the biological sample and from poor spatial control over the label. Polymerization based amplification is a recently developed alternative means of creating an on-sample amplification for fluorescence applications, while not suffering from endogenous labels or loss of signal localization. This manuscript builds upon polymerization based amplification by developing a stable, archivable, and colorimetric …

Sugihara Causality Analysis Of Scalp Eeg For Detection Of Early Alzheimer's Disease, Joseph C. Mcbride, Xiaopeng Zhao, Nancy B. Munro, Greg A. Jicha, Frederick A. Schmitt, Richard J. Kryscio, Charles D. Smith, Yang Jiang

Sanders-Brown Center on Aging Faculty Publications

Recently, Sugihara proposed an innovative causality concept, which, in contrast to statistical predictability in Granger sense, characterizes underlying deterministic causation of the system. This work exploits Sugihara causality analysis to develop novel EEG biomarkers for discriminating normal aging from mild cognitive impairment (MCI) and early Alzheimer's disease (AD). The hypothesis of this work is that scalp EEG based causality measurements have different distributions for different cognitive groups and hence the causality measurements can be used to distinguish between NC, MCI, and AD participants. The current results are based on 30-channel resting EEG records from 48 age-matched participants (mean age 75.7 …

Kallikrein Family Proteases Klk6 And Klk7 Are Potential Early Detection And Diagnostic Biomarkers For Serous And Papillary Serous Ovarian Cancer Subtypes., Ayala Tamir, Ushma Jag, Sreeja Sarojini, Craig Schindewolf, Takemi Tanaka, Rajendra Gharbaran, Hiren Patel, Anil Sood, Wei Hu, Ruzeen Patwa, Patrick Blake, Polina Chirina, Jin Oh Jeong, Heejin Lim, Andre Goy, Andrew Pecora, K Stephen Suh

Department of Medicine Faculty Papers

BACKGROUND: Early detection of ovarian cancer remains a challenge due to widespread metastases and a lack of biomarkers for early-stage disease. This study was conducted to identify relevant biomarkers for both laparoscopic and serum diagnostics in ovarian cancer.

METHODS: Bioinformatics analysis and expression screening in ovarian cancer cell lines were employed. Selected biomarkers were further validated in bio-specimens of diverse cancer types and ovarian cancer subtypes. For non-invasive detection, biomarker proteins were evaluated in serum samples from ovarian cancer patients.

RESULTS: Two kallikrein (KLK) serine protease family members (KLK6 and KLK7) were found to be significantly overexpressed relative to normal …

Dprp: A Database Of Phenotype-Specific Regulatory Programs Derived From Transcription Factor Binding Data, David T. W. Tzeng, Yu-Ting Tseng, Matthew Ung, I-En Liao, Chun-Chi Liu, Chao Cheng

Dartmouth Scholarship

Gene expression profiling has been extensively used in the past decades, resulting in an enormous amount of expression data available in public databases. These data sets are informative in elucidating transcriptional regulation of genes underlying various biological and clinical conditions. However, it is usually difficult to identify transcription factors (TFs) responsible for gene expression changes directly from their own expression, as TF activity is often regulated at the posttranscriptional level. In recent years, technical advances have made it possible to systematically determine the target genes of TFs by ChIP-seq experiments. To identify the regulatory programs underlying gene expression profiles, we …