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STMC-relevant Courses (UNM)

Fall 2017:

BIOM 615: Signal Transduction and Cell Adhesion Seminar

The seminar is held every Wednesday in CRF 104 from 12:30-1 PM. Participants present three current papers on each topic. We also have Methods presentations that focus on state-of-the-art methods associated with the topic. We also have Hot Topics in STAT presentations where participants prepare a single summary slide of new papers of interest and discuss each paper for about 5 minutes. All are welcome to attend.

The schedule is as follows:

STAT Journal Club

Topic 1: Effects of the Microbiome on Host Cells

September 13th
September 20th
September 27th
Methods: October 4th

Hot Topics in STAT: October 11th

Topic 2: Epithelial to Mesenchymal Transition and Attachment

October 18th
October 25th
November 1st
Methods: November 8th

Hot Topics in STAT: November 15th

Topic 3: ER Stress and the Unfolded Protein Response

November 22th
November 29th
December 6th
Methods: December 13th

480/581: Biological Physics

Instructor: Keith Lidke, PhD

Room 1140, Physics and Astronomy
Email: klidke@unm.edu
Phone: 505-277-0302

Course website: http://panda3.phys.unm.edu/~klidke/BioPhysFall2017/

This course is designed to provide a flexible biophysics curriculum for undergraduate and graduate students from a range of majors and degree programs including Physics and Astronomy, Optics, Engineering and Biomedical Science. This is not a lecture based course, it is instead organized around a selection of guided study modules that cover a wide range of topics in biophysics, microscopy and spectroscopy. Many modules have a significant laboratory component. The course can be taken for 1 to 3 credits where each credit requires three modules (9 modules required for 3 credits). The class may be taken twice for up to a total of 6 credits.

BIOS 101: Principles of Biostatistics and Data Science for Cancer Researchers

University of New Mexico Comprehensive Cancer Center

Thursdays | 9 weeks | Beginning September 21

4:00 to 5:00 PM, UNMCCC Boardroom

Coordinator: Ji-Hyun Lee, Professor and Director, Biostatistics Shared Resource, UNM CCC
Email: JihyunLee@salud.unm.edu

Tel: 272-3718

Administrative Coordinator: Faith Brandit
Email: faithann@salud.unm.edu

Back by popular demand! Registration is now open for the 2017 Biostatistics for Cancer Researchers course. The goal of this course is to introduce the basic statistical concepts and methods for cancer research and is open to clinicians, fellows, cancer researchers, and cancer biology students.

The 9-week class series will occur every Thursday, beginning September 21 from 4:00 - 5:00 PM in the UNMCCC Educational Wing Boardroom. *Please note that some students may want to take only selective lectures, and this will be acceptable with prior registration.

Over 100 individuals participated in the course over the past three years and overwhelmingly found the methods and concepts learned to be extremely beneficial to their research. We look forward to another successful course!

Fall 2016:

NIH Required Training in Rigor and Reproducibility

October 18, Domenici Center West, Room 3010

STMC trainees are encouraged to complete instruction in research rigor, reproducibility and transparency. Once completed, you will have fulfilled new NIH requirements and recommendations, even if you are not funded by F,D,K and T mechanisms. Following this session, the Office of Research will certify the names of those trainees completing to Preaward office for inclusion on any grants submitted as PI, co-PI or as a trainee. In advance of the session you are required to view NIH Module #1 at this URL: https://grants.nih.gov/reproducibility/module_1/presentation_html5.html. In addition, please view the 4 NIH videos found at this URL: https://www.nih.gov/research-training/rigor-reproducibility/training.

The program will begin at 1:30 PM with the following agenda:

1:30 – 3:30: HSC faculty and mentors will lead interactive discussions on the 4 themes in the videos above. The topic areas include:

  • Lack of transparency
  • Blinding and randomization
  • Biological and technical replicates
  • Sample size outliers and exclusion criteria

3:30 – 4:00: Quiz for certifying attendance and completion

BIOS 101: Principles of Biostatistics and Data Science for Cancer Researchers

Ji-Hyun Lee, Professor and Director Biostatistics Shared Resource

The goal of this course is to introduce the basic statistical concepts and methods for cancer research and is open to clinicians, fellows, cancer researchers, and cancer biology students.

The 9-week class* series will occur in the UNMCCC Educational Rooms.
*Please note that some students may want to take only selective lectures, and this is allowable with prior registration.

Thursdays beginning October 6, 2016
4:00 - 5:00 PM
University of New Mexico Comprehensive Cancer Center
1201 Camino de Salud NE, Albuquerque

Please email us at HSC-UNMCC-Events@salud.unm.edu for more information.

Course Announcement 480 001 & 581 002

Biophysics
Kevin Cahill

This three-credit course discusses the physics and molecular biology of the cell. The main textbooks are my online notes Physical Biology (http://quantum.phys.unm.edu/biophysics-16/phbi.pdf) and Physical Biology of the Cell by Phillips and others (Garland Science, pdf available from bookzz.org).

The course meets on Tuesdays and Thursdays in room 5 from 5:30 to 6:45.

Email: cahill@unm.edu
Phone: 505-205-5448

Immunopathogenesis & Immunity in Infectious Disease

BIOM 505-013, ST: Immunopathogenesis, CRN: 58464, 2 cr hr
Fall 2016; Tue/Thu, 1:30-3:30PM, Starting Oct 4th
Course Director: Aaron Neumann (akneumann@salud.unm.edu)

This course is designed for students who have a graduate level understanding of basic immunology, cell and molecular biology. The course will follow the following topical emphases: Regional Immunity, Viral Pathogens, Bacterial Pathogens, Eukaryotic Pathogens. We will integrate a study of infectious disease pathogenesis and immunity in a series of lectures by content experts coupled with interactive journal club sessions. The course will also use agent-based computational modeling as an experimental tool to address questions relevant to infection and immune response dynamics. If you have questions, please contact the course director.

Fall 2015:

BIOSTATISTICS 101 for Cancer Researchers

What you always wanted to know about Biostatistics and were too afraid to ask

The University of New Mexico Comprehensive Cancer Center

8 weeks / Wednesdays / 4:00-5:00 PM / UNMCCC Boardroom

Coordinator: Ji-Hyun Lee, Professor and Director, Biostatistics Shared Resource
Email: JihyunLee@salud.unm.edu
Tel: 272-3718

Administrative Coordinator: Faith Brandit
Email: faithann@salud.unm.edu

Spring 2015:

BIOM 514. Immunobiology. (3)

This is a comprehensive, fundamentals-based immunology course for graduate students in the biomedical sciences or related fields. The course will have a problem-based component that will introduce students to experimental design in immunological research.
Prerequisite: graduate status.

BIOM 515. Cancer Biology. (3)

Fundamental elements of cancer development and progression will be the focus of this course. Basic biochemical and genetic mechanisms of tumorigenesis, including genomic instability, principles of tumor cell invasion and growth dysregulation will be emphasized.
Hu, Thompson, Wandinger-Ness

BIOM 615. Signal Transduction and Cell Adhesion Seminar. (1, no limit Δ)

Weekly presentation of current topics in signal transduction and cell adhesion research.

BIOM 555. Problem-Based Research Bioethics. (1)

This is a problem-based discussion course on topics in bioethics such as publication credits and authorships; conflict of interest and fraud, scientific misconduct, human genomics and other relevant issues.
Lidke and Bearer

BIOL 547 (4) Advanced techniques in Light Microscopy

Theory and practical methods of modern light microscopy (e.g., photomicroscopy, DIC optics, immunofluorescence microscopy, video microscopy, image processing, confocal microscopy, microinjection). One lecture, 1 lab.
Stricker

BIOL 456 / 556. Immunology. (3)

Immunoglobulin structure, antigen-antibody reactions, immunity and hypersensitivity; experimental approach will be emphasized. Three lectures. (PH)
Prerequisite: 203 and 203L and 204 and 204L.
Cunningham, Hofkin, Miller

BIOL 470 / 570. Biology: Discovery and Innovation. (4)

Critical-thinking, research-based, survey of a biological area. Primarily for students interested in research. 2.5 hour class, 1 hour of discussion. (ID)
Prerequisite: 203 and 203L and 204 and 204L.
Restriction: permission of instructor.
Werner-Washburne

BIOL 592 / 492. Introductory Mathematical Biology. (3)

Application of mathematics to models of biological systems, from genes to communities. Emphasis placed on broadly-applicable concepts and qualitative solution techniques. Laboratory exercises introduce students to MATLAB programming.
Prerequisite: (MATH 180 and 181) or (MATH 162 and 163)
Toolson

PHYS 554. Advanced Optics II. (3)

(Also offered as ECE 554)
Diffractions theory, coherence theory, coherent objects, and incoherent imaging, and polarization.
Prerequisite: 463.

CS 422 / 522. Digital Image Processing. (3)

Introduction to fundamentals of digital image processing. Specific topics include grey level histograms, geometric/grey level transformations, linear systems theory, Fourier transforms, frequency domain filtering, wavelet transforms, image compression, edge detection, color vision, and binary image morphology.
Prerequisite: MATH 314 or MATH 321.

CS 365. Introduction to Scientific Modeling. (3)

Symbolic computation applied to scientific problem solving, modeling, simulation and analysis.
Prerequisite: 151L or 152L.

Fall 2015:

CHEM 446 / 546. Laboratory Methods in Molecular Biology. (4)

Principles of DNA and RNA purification, enzymatic manipulation of nucleic acids, molecular cloning, gel electrophoresis, hybridization procedures and nucleotide sequencing. Two hours lecture, 5 hours lab. (CM)
Restriction: permission of instructor.
Adema, Cripps, Hanson, Natvig, Vesbach

BIOC 563 / 463 and 564/464. Biochemistry of Disease I. (1-3)

Five three-week topics, each designed to develop some basic concepts of biochemistry, cell and molecular biology in the context of disease states.
Prerequisite: 423 or 545.

CHEM 512. Characterization Methods for Nanostructures. (3)

(Also offered as CHNE, NSMS 512)
Nanostructure characterization methods. Examine principles underlying techniques and limitations, and how to interpret data from each method: electron beam, scanning probe, x-ray, neutron scattering, optical and near field optical. Lab demonstrations and projects provide experience.

MATH 540. Stochastic Processes with Applications. (3)

(Also offered as STAT 565)
Markov chains and processes with applications. Classification of states. Decompositions. Stationary distributions. Probability of absorption, the gambler's ruin and mean time problems. Queuing and branching processes. Introduction to continuous time Markov processes. Jump processes and Brownian motion.
Prerequisite: STAT 527.

PHYS 463. Advanced Optics I. (3)

(Also offered as ECE 463)
Electromagnetic theory of geometrical optics, Gaussian ray tracing and matrix methods, finite ray tracing, aberrations, interference.

Courses Offered for Summer 2014

Introduction to Matlab for Scientist and Engineers

Instructors:

Mark Olah (mjo@cs.unm.edu)
Keith Lidke (klidke@unm.edu)

Course Description:

Matlab is an interpreted programming language with a GUI interface and powerful libraries for manipulating arrays and matrices, plotting, graphical rendering, curve fitting and other core scientific programming tasks.

This course will be an 8-lecture tutorial in Matlab programming for scientists and engineers that will cover topics ranging from the introductory level manipulation of array data and plotting to more advanced topics on data structures, functional programming, object-oriented programming and use of the Matlab debugger and profiler to write efficient scientific programs.

No previous Matlab experience is required although those already familiar with Matlab will gain a deeper understanding of the internals of Matlab and the more advanced features it provides. The course will combine lectures with hands-on Matlab programming and there will be several assignments which will reinforce topics covered in lecture.

Official course registration information:

Registration deadline is June 3.

Date: Wed (1:00 - 2:20 PM). Starting June 4th, and proceeding for 8 weeks.
Location: DSH 143

Course numbers:

Undergraduates should register for 1 credit of: 14891 PHYC 451 Problems, section 010.

Graduate students should register for 1 credit of: 14895 PHYC 551 Problems, section 010.

Courses Offered for Spring 2014

Clinical Cancer Perspectives

Led by Ashwani Rajput, MD, Chief of Surgical Oncology

BIOM 505-002, CRN 42794

Clinical Cancer Perspectives is an interactive short course on the clinical challenges faced daily by cancer patients and physicians. The course is sponsored by the Cancer Nanotechnology Training Center (cntc.unm.edu) but is open to all trainees and faculty in the biomedical and physical sciences and engineering. The main goal of the course is increase interaction between the basic and clinical sciences in order to guide nanoscience research towards key problems that directly impact clinical care. The lecturers are all prominent physicians and physician-investigators with expertise in particular human cancers. They will provide their various perspectives on the biggest roadblocks in clinical cancer care, emphasizing areas where applications of micro- and nano-technologies could overcome these roadblocks. The students will be encouraged to share their ideas or technology solutions to real-world clinical problems.

Place: CRF 204 (except the last session, to be held in the Gross Anatomy Lab)
Time: Wednesdays from 4 to 5:30
Dates: The course will begin Wednesday March 26, 2014 and will run for 8 weeks until Wednesday May 14.
Lecturers: The order of presentations will be announced shortly. This is a one-credit course. Grades will be based on in-class participation.

Advanced Techniques in Light Microscopy

This course covers light microscopy from the its basic principles to the newest techniques of super-resolution imaging, single particle tracking, laser dissection and ion imaging. Instructors for this interdisciplinary, cross-campus course are from the Departments of Biology, Physics, Pathology and Neuroscience and from the NSMS graduate program. Class size is limited in order to provide every student with adequate "hands-on" training. The course is particularly important for students entering STMC labs dedicated to the spatial organization of signaling pathways.

Immunobiology (BIOM 514)

A comprehensive, fundamentals-based immunology course that includes a problem-based component. STMC graduate students working in any area of Immunology Systems Biology are encouraged to take this course in the Spring of their first year.

Cancer Biology (BIOM 515)

This course focuses on fundamental elements of cancer development and progression. Covers biochemical and genetic mechanisms of tumorigenesis, including genomic instability, principles of tumor cell invasion and growth dysregulation. STMC graduate students working on Cancer-related Systems Biology projects should take this course in the Spring of their first year.

Courses Offered for Fall 2013

Career Development Workshop (my IDP)

Instructor: Dr. Elaine Bearer

Time: Monday, September 09, 2013, 4:30 - 6:30 PM

Location: CRF G25

Pizza and drinks will be provided.

More information: myidp.sciencecareers.org

Download course flyer pdf icon

Topics in Interdisciplinary Biological and Biomedical Sciences (TiBBs)

Time: Mondays, 3:00 - 5:30 PM

Location: PiBBs Suite in the Biology Bldg

This interdisciplinary course is offered in the UNM Biology Dept. It presents and discusses recent work in biological science that bridges scientific disciplines, integrates different approaches, and demonstrates the effectiveness of collaborative research. Units are taught by individuals from biology, computer science and information technology. For more info, go to http://biology.unm.edu/pibbs/tibbs.html

UNIT 1: Introduction to Molecular Computing and Nanotechnology, August 19 to September 16

Dr. Darko Stefanovic will lecture on recent developments in molecular computing, as well as DNA nanotechnology. Students will also read, present and discuss current research papers.

UNIT 2: Topics in Bioinformatics, September 23 to October 14

Students and professors can feel overwhelmed with the amount of data that is being generated, and struggle with how to deal with it. This module focuses on the ethics of good data keeping, what file formats and tools are available, and will encourage students to generate an example data plan document.

Courses Offered for Fall 2012

Topics in Interdisciplinary Biology and Biological Sciences (TiBBs). UNIT 2: Biomedical Modeling

Instructor: Dr. Melanie Moses, with contributions from Computer Science and Pathology

Time: October 1 to October 29

Students will learn how different modeling platforms and approaches have been used to answer practical biomedical problems. This unit will include several case studies of successful biomedical modeling by interdisciplinary teams that include a computer scientist and faculty from the SpatioTemporal Modeling Center in the UNM Medical school. Discussions will focus on what kinds of biomedical questions are amenable to modeling, what is required for successful interdisciplinary collaboration, and how tight integration between modelers and laboratory scientists leads to new insights into biomedical problems.

Courses Offered for Summer 2012

Modeling of Intracellular Calcium Dynamics

Instructor: Dr. Bradford E. Peercy

Time: Tuesdays and Thursdays, 9:30am-11am, from June 4-June 22
Place: CRF G25

Calcium transmits external stimuli to internal targets. Calcium signals often initiate by production of inositol-1,4,5-trisphosphate (IP3) and IP3 binding to a calcium channel in the endoplasmic reticulum (ER) membrane. Calcium, so released from the ER, can propagate, oscillate, and trigger events from secretion to genetic upregulation. Mathematical modeling has been monumental in capturing such dynamic behaviors of calcium and predicting others. In this short course, we will describe and apply many modeling tools used to describe calcium handling within a cell and use computational tools to analyze and simulate calcium signals. Students are encouraged to bring a laptop onto which we can install a copy of the (freely available) dynamical systems software, XPPAUT, which we will use for most computational exploration.

Courses Offered for Spring 2012

Professional Development Workshop I: The Essential Toolbox

Instructor: Dr. Laurie Hudson

Time: Wednesdays 4:00 - 6:00 PM for 8 weeks beginning March 21st

STMC Graduate and Postdoctoral Fellows are strongly encouraged to register for semester one of a two-semester seminar designed to enhance their development into independent scientists working across disciplines to improve the understanding and treatment of human disease. The first 8 weeks will focus on the skills needed to lay the foundation for a successful career. The second 8 weeks (in Spring 2012) will apply these skills towards successful grant planning, writing and submission.

Intro to Computational Biomedicine (Physical Oncology Focus)

Instructors: Drs. V Cristini, A Chauviere, + guests

Tuesdays 1:00 ‐ 3:00 PM
Place: CRF 204

In this course, students are engaged in novel peer-reviewed research at the interface of medicine and the engineering and physical sciences, e.g., knowledge of literature relevant to a specific study and understanding of the corresponding biological background, soundness of the mathematical formulation of equations modeling the biological problem, insight into novel biology obtained from model investigations. The course consists of 3 3-week long modules - a general one covering tools for computational biomedicine; one focused on modeling tumor spread (with guest cell biologist, Prof. Bridget Wilson); and one devoted to modeling intracellular transport (with guest cell biologist Prof. Elaine Bearer). One class meeting/week includes both a lecture and assessment of progress to provide feedback/help.

Advanced Techniques in Light Microscopy

Time: Tuesdays 8:30 AM – 11:50 PM
Lecture - Castetter Hall, Rm258; Lab - Rm 256/257

Advanced Techniques in Light Microscopy covers light microscopy from the its basic principles to the newest techniques of super-resolution imaging, single particle tracking, laser dissection and ion imaging. Instructors for this interdisciplinary , cross-campus course are from the Departments of Biology, Physics, Pathology and Neuroscience and from the Nanoscience and Microsystems graduate program. Class size is limited in order to provide every student with adequate "hands-on" training. The course is particularly important for students entering STMC labs dedicated to the spatial organization of signaling pathways.

Courses Offered for Fall 2011

Statistical Methods for Analyzing Gene Expression Microarray Data

Instructor: Huining Kang, PhD

Meets every Wed. for eight weeks, 1:00 - 3:30 PM

Dr. Huining Kang will be teaching "Statistical Methods for Analyzing Gene Expression Microarray Data." This eight-week course meets every Wednesday beginning on October 19. It is designed for people from diverse backgrounds.

Courses Offered for Summer 2011

Image processing and data analysis using MATLAB

Course Leader: Keith Lidke

Dates: Daily from July 01 to July 15 (no class July 04)
Time: 9:00 - 10:00 AM
Place: CRF 104, CRF 204.

This short course will start at a very basic level, assuming little or no background with programming in MATLAB, and progress to more advanced topics. It is expected that not all participants will be interested in the later lectures. Students are free to attend any portion of the course. Analysis required for single particle tracking will used as an example throughout the course. Students are encouraged to bring a laptop with an installation of MATLAB to class, although this is not required.

Courses Offered for Spring 2011

Special Topics in Computational Biology

Organizers:

Stanly Steinberg, Professor of Mathematics and Statistics

Elaine Bearer, Professor of Pathology

First day: January 18, 2011
Last day: May 12, 2011
Thursdays @ 5-6:30 pm

The course will consist of lectures and discussion by faculty and students of the Center for Spatiotemporal Modeling of Cell Signaling (STMC), an interdisciplinary center with members and collaborators in the Health Sciences Center, The College of Arts and Sciences, the School of Engineering and the Sandia and Los Alamos National Labs.

The first lecture and discussion block will cover the biology, data analysis, and modeling of cell signaling with an emphasis on the role of membrane organization in the regulation of signaling. The second block will cover the biology and modeling of cancer, including tumor, cell, and molecular behavior, as well as quantitative image analysis for experimental verification. The remaining block will depend on the interests of the students.

You may attend without registering. However registered students will receive one credit for participating in the course.

There will be 15 lectures:

January 20: B. Wilson, signaling

January 27: A. Halasz, modeling

February 03: D. Lidke, signaling
"Caught in the act: quantifying protein behaviour in living cells"

February 10: F. Espinoza, data

February 17: A. Chauviere
"Cell migration modeling and application to cancer"

February 24: D. Marsh, cancer

March 03: H. Hatzikirou, cancer
"Discrete spatio-temporal modeling of glioma"

March 10: V. Cristini
"Multiscale breast cancer modeling and development"

March 17: Spring Break

March 24: Angela Wandinger-Ness & Joe Song

March 31: S. Posse, MR Spectroscopy

April 07: E. Bearer, image analysis
"Reward circuitry is perturbed in the absence of the serotonin transporter"

April 14: W.D. Wadsworth, statistics

April 21: J. Edwards, modeling

April 28: M. Moses, modeling
"Scale Invariance of Immune System Response Rates and Times: Perspectives on Immune System Architecture and Implications for Artificial Immune Systems"

Colloidal Nanocrystals for Biomedical Applications

Course Director: Marek Osinski, Ph.D.

ECE 581-001/BIOM 581-001/NSMS 581-001 (3 credit hours)

This is a graduate level interdisciplinary course intended for students who plan a professional career combining aspects of engineering, materials science, and biomedical sciences. The course will be literature based, with five most recent volumes of SPIE Proceedings containing papers from "Colloidal Quantum Dots for Biomedical Applications" conferences provided for students' use during the semester. Class sessions will alternate between presentations by invited experts and student-led discussion of a particular topic based on selected literature. For each topic, a problem will be assigned and one week each month will be devoted to solving the problem and giving team presentations. As a pre-professional course, the expectations for students by the instructors will be high. In general, students should be prepared to spend several hours outside of class for each class session to read the assignments and prepare for the discussions, presentations, or problem solving sessions.