UW madison
UW School of Medicine and Public Health
Carbone Cancer Center

Cancer Biology Training Grant (Predoctoral) T32-CA009135

The goal of this Training Grant, Training in Cancer Biology, is to limit cancer maximally as a disease by educating the next generation of cancer researchers to be as committed and competent as humanly possible. We shall build on our past success by evolving this program to lead training in cancer research optimally into the future. We are particularly proud of this grant because it has allowed us to innovate in our training by developing cutting-edge courses, addressing newly recognized needs of our trainees for their career development, training a more diverse group of students, and all along doing more productive cancer research.

TRAINEES

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

TRAINERS

Bill Sugden, Ph.D., Professor (Oncology); Mechanisms of the immortalization of human B-lymphocytes by Epstein-Barr virus.

Beth A. Weaver, Ph.D., Associate Professor (Cell and Regenerative Biology); Regulation of chromosome segregation during mitosis.

Paul G. Ahlquist, Ph.D., Professor (Oncology; Institute for Molecular Virology; Plant Pathology); RNA virus replication and gene expression; host factors in viral replication and pathogenesis.

Caroline Alexander, Ph.D., Professor (Oncology); Mammary stem cells; mouse mammary tumor models; Wnt signaling; syndecan-1.

Fotis Asimakopoulos, M.D., Ph.D., Assistant Professor (Hematology/Oncology); Myeloma research and phase I experimental therapeutics.

Jon Audhya, Ph.D., Associate Professor (Biomolecular Chemistry); Regulation of membrane dynamics and transport in disease.

David J. Beebe, Ph.D, Professor (Biomedical Engineering); Microfluidics; cell and cancer biology.

Christopher A. Bradfield, Ph.D., Professor (Oncology); Molecular biology of the PAS family of proteins.

Emery H. Bresnick, Ph.D., Professor (Cell and Regenerative Biology); Stem cell biology, epigenetics, molecular hematology, and vascular biology: from fundamental mechanisms to translational medicine.

Vincent Cryns, M.D., Professor (Endocrinology, Diabetes, and Metabolism); Molecular origins of cancer and obesity, molecular profiling and nanotechnology.

David T. Evans, Ph.D., Professor (Pathology and Laboratory Medicine); Host-pathogen interactions for human and simian immunodeficiency viruses.

Andreas Friedl, M.D., Professor (Pathology and Laboratory Medicine); Tumor-stroma interactions; heparan sulfate proteoglycans as modulators of growth factors in human disease; tumor angiogenesis.

Richard B. Halberg, Ph.D., Associate Professor (Gastroenterology and Hepatology); Tumor formation and progression in the gut: new concepts and novel targets for therapeutic intervention.

Anna Huttenlocher, M.D., Professor (Pediatrics and Medical Microbiology and Immunology); Understanding the basic molecular and adhesive mechanisms that regulate breast cancer invasion and metastasis.

David J. Jarrard, M.D., Professor (Urology); Genetic and epigenetic alterations in prostate cancer.

Eric C. Johannsen, M.D., Associate Professor (Infectious Disease); The role of Epstein-Barr virus (EBV) nuclear proteins in human disease and EBV biology; proteomics; bioinformatics.

Robert F. Kalejta, Ph.D., Professor (Oncology; Institute for Molecular Virology); Very early events in lytic and latent human cytomegalovirus infectious cycles.

Shannon C. Kenney, M.D., Professor (Oncology; Medicine); Molecular pathogenesis of Epstein-Barr virus.

Paul F. Lambert, Ph.D., Professor (Oncology); Molecular genetics of papillomaviruses; the role of papillomaviruses in human cancer.

Joshua M. Lang, M.D., Assistant Professor (Hematology/Oncology);

Daniel D. Loeb, Ph.D., Professor (Oncology); DNA replication of hepadnaviruses.

Paul C. Marker, Ph.D., Associate Professor (Pharmaceutical Sciences); Fgfr2 during prostatic development and cancer progression.

Douglas G. McNeel, M.D., Ph.D., Professor (Hematology/Oncology); Immunology of prostate cancer. 

Shigeki Miyamoto, Ph.D., Professor (Oncology); Regulation of the transcription factor NF-kB as a model system to study cancer.

Alan C. Rapraeger,  Ph.D., Professor (Human Oncology); Examining the mechanisms by which the syndecan family of cell surface receptors regulate cell growth, adhesion, and migration.

William Ricke, Ph.D., Associate Professor (Urology);  Prostate cancer, stromal-epithelial interactions, hormone action, endocrine disrupting chemicals, benign urology, translational research.

Lixin Rui, Ph.D., Assistant Professor (Hematology/Oncology); Elucidating molecular mechanisms of JAK-STAT signaling in lymphoma.

Linda A. Schuler, Ph.D., V.M.D., Professor (Comparative Biosciences); The role of prolactin in mammary cancer; prolactin receptors, signaling, and processing; prolactin actions on fetal and maternal tissues during pregnancy.

Nathan M. Sherer, Ph.D., Associate Professor (Molecular Virology  and Oncology); HIV-1 assembly and spread; host-pathogen interactions; retroviral gene regulation; virus trafficking; cell-cell communication; live cell imaging.

Deric Wheeler, Ph.D., Assistant Professor (Human Oncology); Resistance to molecular targeting agents.

Yongna Xing, Ph.D., Associate Professor (Oncology); Cell signaling pathways related to cancer; structural biology; biochemistry; proteomics.

Wei Xu, Ph.D.,  Professor (Oncology); Epigenetic transcriptional control in breast cancer.

Jing Zhang, Ph.D., Professor (Oncology); Hematopoietic and leukemic stem cells; mouse models for hematopoietic malignancies; cytokine signaling.

COURSES

Oncology 675: BioInformatics for Cancer Biologist

PREREQUISTE: 2nd (+) Year Graduate Student and enrollment in the Biophysics Graduate Program; Cancer Biology Graduate Program; the Cellular & Molecular Biology Graduate Program; Cellular Molecular Pathology Graduate Program; Integrated Program in Biochemistry; Molecular & Cellular Pharmacology Graduate Program; Molecular & Environmental Toxicology MD Graduate Program; or the Physiology Graduate Program.

DESCRIPTION: Course goal is threefold: First, to familiarize students with bioinformatics theory and principles; second, to provide students with real-world experience that they can apply to their own work; and third, to use the first two goals to provide a foundation of knowledge that the students can use critically to evaluate existing bioinformatics tools that they can use in their work - and in the absence of an appropriate tool, identify the analyses that demand the development of novel tools.

FORMAT: This course will meet on T/TH for 75 minutes from 1:00-2:15 PM; with 6 hours of outside of class preparation weekly, including readings, problem-sets, and projects. Class sessions involve traditional lecture interspersed with class discussion.   Students will be assess on the following: class participation (20 points), homework (140 points), and their final project (40 points).

LECTURE TOPICS:  Introduction to Bioinformatics, Statistics, Algorithms; Nucleic Acid Alignment; NextGen Sequencing Analysis; Proteomic Analysis; and Motif Search. 

LECTURE SCHEDULE:

WK1:                          Introduction to Bioinformatics/Statistics/Algorithms

WK2-3:                      Nucleic Acid Alignment

WK4-6:                      NextGen Sequencing Analysis

WK7-10:                   Proteomic Analysis

WK13-15:                 Motif Search

WK16:                       Final student projects due

SUPPORTING LECTURE MATERIALS (Available Online): 

1. An Introduction to Bioinformatics Algorithms (N. C. Jones and P.A. Pevzner), ANE Books, Cambridge, MA (2004).   https://ebookcentral.proquest.com/lib/wisc/detail.action?docID=3338847

Oncology 715: Ethics of Science

Description: The objective of this course is to teach graduate students and postdoctoral fellows about ethical issues in science and how to go about trying to resolve them.  The course is mostly organized around short lectures followed by small group, roundtable discussions of specific case studies in which issues commonly faced by scientists are considered.  Topics will include: assignment of credit and authorship, privileged communications, appropriate recording and treatment of data, scientific misconduct, dual-use research, intellectual property, use of animals and humans in research, conflicts of interest, and issues related to gender and minority equity.  Students prepare written assignments for each case study prior to its discussion in class.  Faculty provide introductory lectures on each issue and, in some cases, experts on particular subjects will present guest lectures. Student-led roundtable discussions are designed to allow each group to develop well-reasoned, morally-based solutions to the ethical dilemmas being discussed.

Class Format:  This course will meet on TH from 3:00-5:00 PM, in Rm. 6571 WIMR II. After an introduction by faculty to the topics of focus for the afternoon, you will break out into assigned small groups in which you will compare how each of you might deal with the issues raised by the case studies.  For each session, one of the students in each group will be assigned the role of 'facilitator' for each case to be discussed; that person's role is to ensure that the discussion keeps on track, that all aspects of the issues are fully discussed, and that all members of the group are provided ample opportunities to express their views.  Another group member will serve as “note taker”; s/he will be responsible for briefly summarizing the findings from the group.  These roles will rotate from week to week among the group members so that everyone has an opportunity to serve as a facilitator or note taker.  The faculty will contribute to the discussion with the goal of priming discussion of other viewpoints, providing additional factual information related to the topics, and bringing up related issues that might arise during discussion of the cases.

Course Grade will be S/U.  You are expected to attend all classes, sign the attendance sheet for yourself and no one else at the beginning of class, turn in all written assignments, and actively participate in the discussions to receive an S grade.  Written assignments consisting of a few lines of text without substantive content are unacceptable.  If you are unable to attend a class because of illness or a significant scheduling conflict (e.g., attendance at a scientific conference), please email the course director with your reason for absence and your written responses to the homework assignment.  Classroom discussions are an important component of this course.  Thus, one should try to avoid having to miss class.  If you already know that you will likely need to miss class more than once, you should probably arrange to take a different ethics course or wait until spring 2019 to take this one given it only meets seven times.

LECTURE SCHEDULE

February 1                   Focus: Ethical Reasoning; Authorship (Discussion Leader: Janet Mertz)

February 8                   Focus: Conflicts of Interest; Biosafety and Dual-Use Research of Concern (Discussion Leaders: Michael Gould and Janet Mertz)

February 15                 Focus: Data Analysis; Scientific Misconduct (Discussion Leader: Michael Gould)

February 22                 Focus: Patents and Material Transfer Agreements (Guest Speaker: Pilar Ossario, Ph.D., J.D.)

March 1                       Focus: Discrimination; Interpersonal Relationships (Discussion Leader: Janet Mertz)

March 8                       Focus: Animal and Human Subject Research (Discussion Leader: Michael Gould)

March 15                     Focus: “The Wisconsin Cystic Fibrosis Newborn Screening Study" (Guest Speaker: Norman Fost, M.D., M.P.H)

Oncology 725: Readings in Cancer Biology

Prerequisite: Cancer Biology Graduate Program, graduate student, or permission of instructor.  This course fulfills an important facet in the development of independent scientists by teaching them to critically read and review the current literature. This course is required for Cancer Biology PhD students and for students appointed to the NIH training grants in Cancer Biology and Virology.

Description:  A review and discussion of the current literature on topics related to Cancer Biology. The emphasis is on the development of skills in data analysis, interpretation, and writing.  The goal of this course is to prepare students to critically review and discuss the current scientific literature on topics related to cancer biology. The emphasis is on the development of skills in data analysis and interpretation and communication of research. Skills learned in this course are critical to the development of an independent scientist. This course is an essential component in the training of PhD students in data analysis and interpretation of research in the literature, as well as written and oral communication of their science.

Method of Instruction: Weekly lecture and discussion will be led weekly by instructor.   Critical discussion and examination of weekly readings and subjects. 

Class Format:  This course will meet on TH from 9:00-11:00 AM, in Rm. 6571 WIMR II. "Readings in Cancer Biology" is designed to help students become familiar with current literature in cancer research, to read articles critically, and to discuss them constructively.  Approximately 40 papers are read during the semester; students are asked to submit one question on each paper read for each class; and then asked to lead a critical discussion of that paper on the basis of the question they submitted. The instructor reads the questions and selects ones to ensure that the papers are considered thoroughly and that all students have the opportunity to lead a discussion each class. The instructor provides expertise in all the topics covered and oversees the discussion to insure scientific rigor and to optimize participation of all students. 

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