SoM Course Catalog Data Report - Stanford University School of ...

raviolirookeryBiotechnology

Oct 2, 2013 (3 years and 10 months ago)

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S
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C
OURSE
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ATALOG
D
ATA
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EPORT

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UN
:

T
UESD
AY
,

A
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24
,

20
12



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ANES

HRP

ORTHO

BIOC

IMMUNOL

OTOHNS

BIOMEDIN

INDE

PATH

BIOPHYS

MCP

PEDS

CBIO

MED

PSYC

COMPMED

MI

RAD

CSB

NBIO

RADO

CTS

NENS

SBIO

DBIO

NEPR

SOMGEN

DERM

NSUR

STEMREM

FAMMED

OBGYN

SURG

GENE

OP
H
T

UROL



Subject:

ANES


ANES 70Q


Short (transcript) title:

RAMFICATIONS OF CRITICL ILNESS

Course ID:

208896

Career:

UG

Effective Date:

01
-
Aug
-
12

Other Offering:



Title:

The Psychosocial and Economic Ramifications of Critical Illness

Description:

Preference to sophomores. The impact of critical illness on a patient and family members;
difficulties involved in the decision making pro
cess for the patient, family, and healthcare
professionals. Topics include: conventional views of death and dying, epidemiology of critical
illness, grief, coping skills, cultural variations, euthanasia and withdrawal of care, palliative
care and hospice,
advanced directive and legal aspects of medical catastrophe, psychosocial
dynamics of family meetings, and emotional ramifications of medical decisions.




Units:

3
--

3






Grading Basis:

RSN
-

Satisfactory/No Credit

Components:

ISS




Quarters Offered:


OTH
-

not given this year


Repeatable For Credit:
N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Ludwig Lin









ANES 80Q


Short (transcript) title:

RESEARCHING STRANGE THINGS

Course ID:

212087

Career:

UG

Effective Date:

01
-
A
ug
-
12

Other Offering:



Title:

Researching Strange Things

Description:

Devising and implementing strong scientific research designs to better understand complex and
mysterious phenomena. Parapsychology topics include remote viewing, telekin
esis,
precognition, telepathic communication, and other forms of extrasensory perception. History of
parapsychology research, including how science has debunked popular claims of supernatural
feats; therapeutic approaches still used today but often discred
ited (such as homeopathy and
crystal healing), as well as commonly
-
supported but controversial techniques such as hypnosis,
acupuncture, and naturopathy. Emphasis on distinguishing between scientific and
pseudoscientific research methods and how to properl
y design experiments regardless of the
subject matter. Course format includes lectures, discussion, group projects, and research
experimentation.


Units:

3
--

3






Grading Basis:

ROP
-

Letter or Credit/No Credit

Components:

ISS




Quarters Offered:


OTH
-

not given this

Instructor(s):

Jarred Younger







ANES 113Q


Short (transcript) title:

DISEASE
-
ORIENTED HUMAN PHYSIOL

Course ID:

202536

Career:

UG

Effective Date:

01
-
Aug
-
12

Other Offering:



Title:

Disease
-
Oriented Appro
ach to Human Physiology

Description:

Describes the role of physiology of major organ systems in a healthy person and how it is
altered in disease. Presents therapeutic approaches to normalizing the pathophysiologic state
including current therapies and t
hose under investigation. Organ systems and diseases
discussed include cardiovascular (myocardial infarction, trauma and infection leading to shock),
central nervous (stroke, concussion, cerebral hemorrhage, spinal
-
cord trauma, meningitis),
pulmonary (pne
umonia, asthma, emphysema), renal (kidney failure), and hepatic (cirrhosis,
hepatitis). Field trips to operating rooms at Stanford Medical Center are offered.





Units:

3
--

3






Grading Basis:

ROP
-

Letter or Credit/No Credit

Components:

ISS



Quarter
s Offered:


OTH
-

not given this year


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Myer Rosenthal









ANES 199


Short (transcript) title:

UNDERGRADUATE RESEARCH

Course ID:

127649

Career:

UG

Effective Dat
e:

01
-
Sep
-
06

Other Offering:



Title:

Undergraduate Research

Description:

Allows for qualified students to undertake investigations sponsored by individual faculty
members. Prerequisite: consent of instructor.


Units:

1
--

18






Grading
Basis:

ROP
-

Letter or Credit/No Credit

Components:

INS




Quarters Offered:

AUT WIN SPR SUM


Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Alex Macario, Andrew Patterson, Anita Honkanen, Anthony Doufas, Audrey

Shafer, Brenda Golianu, Brendan Carvalho, Chandra Ramamoorthy, Christina Mora
-
Mangano,
Clifford Schmiesing, David Clark, David Drover, David Gaba, David Yeomans, Diana
McGregor, Edward Bertaccini, Edward Mariano, Edward Riley, Elliot Krane, Emily Ratner,
Fiona Clements, Frank Sarnquist, Frederick Mihm, Gary Peltz, Geoffrey Lighthall, Glyn
Williams, Gregory Hammer, Hendrikus Lemmens, Ian Carroll, James Trudell, Jarred Younger,
Jay Brodsky, John Brock
-
Utne, John Pollard, Juliana Barr, Julie Good, Kevin Malot
t, Lawrence
Chu, Lawrence Saidman, Leland Hanowell, Linda Foppiano, Lindsey Vokach
-
Brodsky, Lisa
Wise
-
Faberowski, M MacIver, M. Boltz, Martin Angst, Max Kanevsky, Michael Chen, Myer
Rosenthal, Pedro Tanaka, Pieter van der Starre, Richard Jaffe, Rona Giffar
d, Ronald Pearl,
Sean Mackey, Sheila Cohen, Stephen Fischer, Steven Howard, Steven Lipman, Timothy
Angelotti, Vivekanand Kulkarni, Vladimir Nekhendzy, William Feaster








ANES 202


Short (transcript) title:

ANES/PTHPHYS IMPS PERIOP PTNTS

Course ID:

2066
38

Career:

MED

Effective Date:

01
-
Aug
-
09

Other Offering:



Title:

Anesthesiology and Pathophysiologic Implications for the Perioperative Patient

Description:

Provides participants a patient
-
care
-
related review of organ physiology and an in
-

depth
discussion of the pathophysiologic mechanisms at work in the perioperative period that
influence outcome in the surgical patient and their management. Organ systems addressed
include cardiovascular, respiratory, renal, hematologic, and cerebral. Sub
ject matter including
airway management, ventilatory support, transfusion practices and the acute management of
shock provides useful information for all students currently or in the future involved in acute
care of the critically ill patient. Additional t
opics specific to anesthesia, including anesthetic
pharmacology. Lecturers are Stanford anesthesia faculty and visiting guest faculty. Prerequisite:
completion of first year curriculum is strongly encouraged.




:

Units:

1
--

1






Grading Basis:

MED
-

Me
dical School MD Grades

Components:

LEC




Quarters Offered:


WIN


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Myer Rosenthal










ANES 207


Short (transcript) title:

MEDICAL ACUPUNCTURE

Course ID:

127654

Career:

MED

Effective Date:

01
-
Aug
-
09

Other Offering:



Title:

Medical Acupuncture

Description:

Acupuncture is part of a comprehensive system of traditional Chinese Medicine developed over
the past two millennia. This course reviews the
history and theoretical basis of acupuncture for
the treatment of various diseases as well as for the alleviation of pain. Issues related to the
incorporation of acupuncture into the current health care system and the efficacy of acupuncture
in treating v
arious diseases are addressed. Includes practical, hands
-
on sections.



Units:

2
--

2






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

SEM




Quarters Offered:


SPR


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat At
tempts:


Instructor(s):

Brenda Golianu









ANES 215


Short (transcript) title:

JRNL CLB NEUR,BEH,COG SCH CONC

Course ID:

205903

Career:

MED

Effective Date:

01
-
Aug
-
09

Other Offering:



Title:

Journal Club for Neuroscience, Behavior and C
ognition Scholarly Concentration

Description:

Review of current literature in both basic and clinical neuroscience in a seminar format
consisting of both faculty and student presentations.


Units:

1
--

1






Grading Basis:

MED
-

Medical School MD Grades

C
omponents:

SEM




Quarters Offered:


WIN SPR


Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

David Yeomans









ANES 243


Short (transcript) title:

INTRO INTEGRATIVE MEDICINE

Course ID:

205965

Career:

MED

Effective Date:

01
-
Aug
-
11

Other Offering:

FAMMED 243 MED

Title:

Introduction to Integrative Medicine

Description:

Presentations by local, national, and international experts in various modalities of integrative
medicine commonly used by pat
ients in the US, including mind
-
body medicine (biofeedback,
clinical hypnosis, meditation, yoga); traditional whole systems of medicine (traditional Chinese
medicine, Ayurveda); biological therapies (botanical medicine, supplements, herbal medicine);
manip
ulative therapies (chiropractic, massage); and acupuncture. Lectures focus on evidence
supporting the potential value of various treatment modalities and explanations of both the
traditional and proposed scientific mechanisms of actions. Most classes inclu
de an experiential
portion.


Units:

1
--

1






Grading Basis:

MED
-

Medical School MD Grades

Components:

SEM




Quarters Offered:


OTH
-

given next year


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Sakti S
rivastava, Tracy Rydel









ANES 280


Short (transcript) title:

EARLY CLINICAL EXPERIENCE

Course ID:

127657

Career:

MED

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

Early Clinical Experience in Anesthesia

Description:

Provides an
observational experience as determined by the instructor and student. Prerequisite:
consent of instructor.


Units:

1
--

2






Grading Basis:

MED
-

Medical School MD Grades

Components:

INS




Quarters Offered:

AUT WIN SPR SUM



Repeatable For
Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Alex Macario, Alice Edler, Andrew Patterson, Anita Honkanen, Anthony
Doufas, Audrey Shafer, Brenda Golianu, Brendan Carvalho, Chandra Ramamoorthy, Christina
Mora
-
Mangano, Clifford Schmiesin
g, David Clark, David Drover, David Gaba, David
Yeomans, Diana McGregor, Edward Bertaccini, Edward Mariano, Edward Riley, Elliot Krane,
Emily Ratner, Fiona Clements, Frank Sarnquist, Frederick Mihm, Gary Peltz, Geoffrey
Lighthall, Gerald Goresky, Glyn Will
iams, Gregory Hammer, Hendrikus Lemmens, Ian
Carroll, James Trudell, Jarred Younger, Jay Brodsky, John Brock
-
Utne, John Pollard, Juliana
Barr, Julie Good, Kevin Malott, Lawrence Chu, Lawrence Saidman, Leland Hanowell, Linda
Foppiano, Lindsey Vokach
-
Brodsky
, Lisa Wise
-
Faberowski, Ludwig Lin, M MacIver, M.
Boltz, Martin Angst, Max Kanevsky, Michael Chen, Myer Rosenthal, Pedro Tanaka, Pieter van
der Starre, Raymond Gaeta, Richard Jaffe, Rona Giffard, Ronald Pearl, Sean Mackey, Sheila
Cohen, Stephen Fischer, St
even Howard, Steven Lipman, Timothy Angelotti, Vivekanand
Kulkarni, Vladimir Nekhendzy, William Feaster






Y



ANES 299


Short (transcript) title:

DIRECTED READING

Course ID:

127658

Career:

MED

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

Directed Reading in Anesthesiology

Description:

Prerequisite: consent of instructor.





Units:

1
--

18






Grading Basis:

MED
-

Medical School MD Grades

Components:

INS




Quarters Offered:

AUT WIN SPR SUM

Repeatable For Credit:

Y

Max Re
peat Units:


Max Repeat Attempts:



Instructor(s):

Alex Macario, Alice Edler, Andrew Patterson, Anita Honkanen, Anthony
Doufas, Audrey Shafer, Brenda Golianu, Brendan Carvalho, Chandra Ramamoorthy, Christina
Mora
-
Mangano, Clifford Schmiesing, David Clark,
David Drover, David Gaba, David
Yeomans, Diana McGregor, Edward Bertaccini, Edward Mariano, Edward Riley, Elliot Krane,
Emily Ratner, Fiona Clements, Frank Sarnquist, Frederick Mihm, Gary Peltz, Geoffrey
Lighthall, Gerald Goresky, Glyn Williams, Gregory Ha
mmer, Hendrikus Lemmens, Ian
Carroll, James Trudell, Jarred Younger, Jay Brodsky, John Brock
-
Utne, John Pollard, Juliana
Barr, Julie Good, Kevin Malott, Lawrence Chu, Lawrence Saidman, Leland Hanowell, Linda
Foppiano, Lindsey Vokach
-
Brodsky, Lisa Wise
-
Fabe
rowski, Ludwig Lin, M MacIver, M.
Boltz, Martin Angst, Max Kanevsky, Michael Chen, Myer Rosenthal, Pedro Tanaka, Pieter van
der Starre, Raymond Gaeta, Richard Jaffe, Rona Giffard, Ronald Pearl, Sean Mackey, Sheila
Cohen, Stephen Fischer, Steven Howard, Ste
ven Lipman, Timothy Angelotti, Vivekanand
Kulkarni, Vladimir Nekhendzy, William Feaster






Y




ANES 370


Short (transcript) title:

MEDICAL SCHOLARS RESEARCH

Course ID:

204809

Career:

MED

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

Medical Scholars Research

Description:

Provides an opportunity for student and faculty interaction, as well as academic credit and
financial support, to medical students who undertake original research. Enrollment is limited to
students with approved
projects.




:

Units:

4
--

18






Grading Basis:

MED
-

Medical School MD Grades

Components:

INS




Quarters Offered:

AUT WIN SPR SUM



Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Alex Macario, Alice Edler, A
ndrew Patterson, Anita Honkanen, Anthony
Doufas, Audrey Shafer, Brenda Golianu, Brendan Carvalho, Chandra Ramamoorthy, Christina
Mora
-
Mangano, Clifford Schmiesing, David Clark, David Drover, David Gaba, David
Yeomans, Diana McGregor, Edward Bertaccini, Edw
ard Mariano, Edward Riley, Elliot Krane,
Emily Ratner, Fiona Clements, Frank Sarnquist, Frederick Mihm, Gary Peltz, Geoffrey
Lighthall, Gerald Goresky, Glyn Williams, Gregory Hammer, Hendrikus Lemmens, Ian
Carroll, James Trudell, Jarred Younger, Jay Brodsk
y, John Brock
-
Utne, John Pollard, Juliana
Barr, Julie Good, Kevin Malott, Lawrence Chu, Lawrence Saidman, Leland Hanowell, Linda
Foppiano, Lindsey Vokach
-
Brodsky, Lisa Wise
-
Faberowski, Ludwig Lin, M MacIver, M.
Boltz, Martin Angst, Max Kanevsky, Michael Ch
en, Myer Rosenthal, Pedro Tanaka, Pieter van
der Starre, Raymond Gaeta, Richard Jaffe, Rona Giffard, Ronald Pearl, Sean Mackey, Sheila
Cohen, Stephen Fischer, Steven Howard, Steven Lipman, Timothy Angelotti, Vivekanand
Kulkarni, Vladimir Nekhendzy, William

Feaster






N




ANES 399


Short (transcript) title:

GRADUATE RESEARCH

Course ID:

127686

Career:

GR

Effective Date:

01
-
Sep
-
08

Other Offering:



Title:

Graduate Research

Description:

Students undertake investigations sponsored by individua
l faculty members. Problems related
to metabolism, toxicity, and mechanisms of anesthesia; pharmacologic studies involving pain
management; the genetic and molecular basis of hemodynamic insufficiency. Animal studies
may be included. Interested students
should contact Drs. Trudell, MacIver, Clark, Giffard,
Patterson, Angelotti, Drover, Chu, or Angst.




:

Units:

1
--

18






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

INS




Quarters Offered:

AUT WIN SPR SUM



Repeatable For
Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Alex Macario, Alice Edler, Andrew Patterson, Anita Honkanen, Anthony
Doufas, Audrey Shafer, Brenda Golianu, Brendan Carvalho, Chandra Ramamoorthy, Christina
Mora
-
Mangano, Clifford Schmiesin
g, David Clark, David Drover, David Gaba, David
Yeomans, Diana McGregor, Edward Bertaccini, Edward Mariano, Edward Riley, Elliot Krane,
Emily Ratner, Fiona Clements, Frank Sarnquist, Frederick Mihm, Gary Peltz, Geoffrey
Lighthall, Gerald Goresky, Glyn Will
iams, Gregory Hammer, Hendrikus Lemmens, Ian
Carroll, James Trudell, Jarred Younger, Jay Brodsky, John Brock
-
Utne, John Pollard, Juliana
Barr, Julie Good, Kevin Malott, Lawrence Chu, Lawrence Saidman, Leland Hanowell, Linda
Foppiano, Lindsey Vokach
-
Brodsky
, Lisa Wise
-
Faberowski, Ludwig Lin, M MacIver, M.
Boltz, Martin Angst, Max Kanevsky, Michael Chen, Myer Rosenthal, Pedro Tanaka, Pieter van
der Starre, Raymond Gaeta, Richard Jaffe, Rona Giffard, Ronald Pearl, Sean Mackey, Sheila
Cohen, Stephen Fischer, St
even Howard, Steven Lipman, Timothy Angelotti, Vivekanand
Kulkarni, Vladimir Nekhendzy, William Feaster









Subject:

BIOC


BIOC 118Q


Short (transcript) title:

GENOMICS AND MEDICINE

Course ID:

127304

Career:

UG

Effective Date:

01
-
Aug
-
12

Other Offering:



Title:

Genomics and Medicine

Description:

Preference to sophomores. Knowledge gained from sequencing human genomes and
implications for medicine and biomedical research. Novel diagnoses and treatment of diseases,
including stem cells, ge
ne therapy and rational drug design. Personal genomics and how it is
used to improve health and well being. Social and ethical implications of genetic information
such as privacy, discrimination and insurability. Course Webpage:
http://biochem118.stanford
.edu/.


GER:

DB
-
EngrAppSci


:

Units:

3
--

3






Grading Basis:

ROP
-

Letter or Credit/No Credit

Components:

ISS


Quarters Offered:

AUT


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Douglas Brutlag









B
IOC 158


Short (transcript) title:

GENOMICS, BIOIN AND MEDICINE

Course ID:

212157

Career:

UG

Effective Date:

01
-
Aug
-
11

Other Offering:

BIOC 258 GR HUMBIO 158G UG

Title:

Genomics, Bioinformatics and Medicine

Description:

Molecular basis of
inherited human disease. Diagnostics approaches: simple Mendelian
diseases and complex, multifactorial diseases. Genomics: functional genomics, epigenetics,
gene expression, SNPs, copy number and other structural genomic variations involved in
disease.
Novel therapeutic methods: stem cell therapy, gene therapy and drug developments
that depend on the knowledge of genomics. Personal genomics, pharmacogenomics, clinical
genomics and their role in the future of preventive medicine. Prerequisites: BIO 41 or

HUMBIO 2A or consent of instructor. Those with credit in BIOC 118 not eligible to enroll.
Course webpage: http://biochem158.stanford.edu/


GER:


DB
-
NatSci


:

Units:

4
--

4






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Qua
rters Offered:

AUT WIN SPR


Repeatable For Credit:
Y

Max Repeat Units:

8

Max Repeat Attempts:

2

Instructor(s):

Douglas Brutlag







BIOC 199


Short (transcript) title:

UNDERGRADUATE RESEARCH

Course ID:

201475

Career:

UG

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

Undergraduate Research

Description:

Students undertake investigations sponsored by individual faculty members. Prerequisite:
consent of instructor.




:

Units:

1
--

18






Grading Basis:

ROP
-

Letter or Credit/No
Credit

Components:

INS




Quarters Offered:

AUT WIN SPR SUM



Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Aaron Straight, Daniel Herschlag, Douglas Brutlag, James Chen, James
Spudich, Julie Theriot, Mark Kras
now, Patrick Brown, Pehr Harbury, Philip Beachy, Rajat
Rohatgi, Rhiju Das, Ronald Davis, Suzanne Pfeffer










BIOC 200


Short (transcript) title:

APPLIED BIOCHEMISTRY

Course ID:

210251

Career:

MED

Effective Date:

01
-
Aug
-
09

Other Offering:



Title:

Applied Biochemistry

Description:

Enrollment limited to MD candidates. Fundamental concepts of biochemistry as applied to
clinical medicine. Topics include thermodynamics, enzyme kinetics, vitamins and cofactors,
metabolism of carb
ohydrates, lipids, amino acids and nucleotides, and the integration of
metabolic pathways. Clinical case studies discussed in small
-
group, problem
-
based learning
sessions.





Units:

1
--

1






Grading Basis:

MED
-

Medical School MD Grades

Components:

LE
C




Quarters Offered:

AUT



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Julie Theriot, Pehr Harbury, Tina Cowan







BIOC 201


Short (transcript) title:

ADVANCED MOLECULAR BIOLOGY

Course ID:

127308

Career
:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:



Title:

Advanced Molecular Biology

Description:

Literature
-
based lectures and discussion on rapidly developing frontiers in chromosome
structure and function and modern insights into the contr
ol of gene expression. Emphasis is on
experimental approaches and insights. Topics include chromosome organization, novel modes
of transcriptional control, RNA
-
based mechanisms for controlling gene expression and
emerging translational regulatory mechanism
s. Prerequisite: undergraduate molecular biology.





Units:

5
--

5






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

DIS

LEC



Quarters Offered:


OTH
-

not given this year



Repeatable For Credit:

N

Max Repeat Units:


Max
Repeat Attempts:




Instructor(s):

Aaron Straight, Mark Krasnow











BIOC 202


Short (transcript) title:

BIOCHEMISTRY BOOTCAMP

Course ID:

212148

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:



Title:

Biochemistry Bootcamp

Descri
ption:

Open to first year Biochemistry students or consent of instructor. Hands
-
on, five
-
day
immersion in biochemical methods and practice, theory and application of light microscopy,
and computational approaches to modern biological problems.





Units:

1
--

1






Grading Basis:

RSN
-

Satisfactory/No Credit

Components:

LEC




Quarters Offered:

AUT



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:




Instructor(s):

Aaron Straight







BIOC 205


Short (transcript) title:

MOL
ECULAR FOUNDATIONS

Course ID:

203354

Career:

MED

Effective Date:

01
-
Aug
-
11

Other Offering:



Title:

Molecular Foundations of Medicine

Description:

For medical students. Topics include DNA structure, replication, repair, and recombination;
gene expression, including mechanisms for regulating transcription and translation;
chromosome structure and function; gene cloning, protein engineering, and genomics. Patient
presentations and journal clubs illustrate how molecular biology affects the pra
ctice of
medicine.




:

Units:

3
--

3






Grading Basis:

MED
-

Medical School MD Grades

Components:

LEC




Quarters Offered:

AUT



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:




Instructor(s):

Gilbert Chu, Mark Krasnow











BIOC 210


Short (transcript) title:

ADVNCD TOPICS MEMBRNE TRAFKING

Course ID:

127317

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:



Title:

Advanced Topics in Membrane Trafficking

Description:

The structure, function, and bio
synthesis of cellular membranes and organelles. Current
literature. Prerequisite: consent of instructor.





Units:

3
--

3






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


SUM



Repeatable For
Credit:

N

Max Repeat Units:


Max Repeat Attempts:




Instructor(s):

Suzanne Pfeffer








BIOC 215


Short (transcript) title:

FRONTIERS IN BIOLOGIC RESEARCH

Course ID:

127322

Career:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:

DBIO 215 GR GENE 215 GR


Title:

Frontiers in Biological Research

Description:

Literature discussion in conjunction with the Frontiers in Biological Research seminar series in
which investigators present current work. Students and faculty meet beforehand to discuss
paper
s from the speaker¿s primary research literature. Students meet with the speaker after the
seminar to discuss their research and future direction, commonly used techniques to study
problems in biology, and comparison between the genetic and biochemical app
roaches in
biological research.





Units:

1
--

1






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

DIS

SEM



Quarters Offered:

AUT WIN



Repeatable For Credit:

Y

Max Repeat Units:

3

Max Repeat Attempts:

3



Instructor(s):

An
ne Villeneuve, Michele Calos, Pehr Harbury








BIOC 218


Short (transcript) title:

COMPUTATIONAL MOLEC BIOLOGY

Course ID:

127325

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

BIOMEDIN 231 GR

Title:

Computational Molecular Biology

Description:

Practical, hands
-
on approach to field of computational molecular biology. Recommended for
molecular biologists and computer scientists desiring to understand the major issues concerning
analysis of genomes, sequences and structures. Various ex
isting methods critically described
and strengths and limitations of each. Practical assignments utilizing tools described. All
homework and coursework submitted electronically. Course webpage:
http://biochem218.stanford.edu/.


Units:

3
--

3






Grading
Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:

AUT WIN SPR


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Douglas Brutlag








BIOC 220


Short (transcript) title:

CHMSTRY OF

BIOLOGICAL PROCESS

Course ID:

204501

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

CSB 220 GR

Title:

Chemistry of Biological Processes

Description:

The principles of organic and physical chemistry as applied to biomolecules. Goal is

a working
knowledge of chemical principles that underlie biological processes, and chemical tools used to
study and manipulate biological systems. Prerequisites: organic chemistry and biochemistry, or
consent of instructor.





Units:

4
--

4






Grading
Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


OTH
-

not given this year, alt years


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Thomas Wandless









BIOC 221


Short
(transcript) title:

TEACHING OF BIOCHEMISTRY

Course ID:

127328

Career:

GR

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

The Teaching of Biochemistry

Description:

Required for teaching assistants in Biochemistry. Practical experience i
n teaching on a one
-
to
-
one basis, and problem set design and analysis. Familiarization with current lecture and text
materials; evaluations of class papers and examinations. Prerequisite: enrollment in the
Biochemistry Ph.D. program or consent of instructo
r.


Units:

3
--

3






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

INS




Quarters Offered:

AUT WIN SPR SUM


Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Aaron Straight, Daniel Herschlag, D
ouglas Brutlag, James Chen, James
Spudich, Julie Theriot, Mark Krasnow, Patrick Brown, Pehr Harbury, Philip Beachy, Rajat
Rohatgi, Rhiju Das, Ronald Davis, Suzanne Pfeffer












BIOC 224


Short (transcript) title:

ADVANCED CELL BIOLOGY

Course ID:

1275
79

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

BIO 214 GR MCP 221 GR

Title:

Advanced Cell Biology

Description:

For Ph.D. students. Current research on cell structure, function, and dynamics. Topics include
complex cell phenomena such

as cell division, apoptosis, compartmentalization, transport and
trafficking, motility and adhesion, differentiation, and multicellularity. Current papers from the
primary literature. Prerequisite for advanced undergraduates: BIO 129A,B, and consent of
in
structor.




Units:

2
--

5






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


WIN


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Aaron Straight, Julie Theriot,
Maxence Nachury, Ron Kopito, Suzanne Pfeffer








BIOC 226


Short (transcript) title:

INTERDISCIP TRANSLATIONAL RSCH

Course ID:

211067

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:



Title:

Interdisciplinary Approaches to Biochemis
try: Single Molecule Biophysics to Clinical
Outcomes

Description:

Interdisciplinary analyses from basic biochemistry and biophysics to clinical outcomes of
disease states and potential therapeutic interventions (translational research). Focus on cardiac
sy
stem. Cardiomyopathies arise from missense mutations in cardiac muscle proteins, including
the cardiac myosin motor. Single molecule biophysics and classical enzyme kinetics and use of
induced pluripotent stem cells (iPS cells) and single cell studies la
y foundation for discussions
of effects of cardiomyopathy mutations on heart function. Potential therapeutic approaches
discussed, including genetic analysis, DNA cloning, reconstitution of functional assemblies, x
-
ray diffraction and 3D reconstruction of

electron microscope images, spectroscopic methods,
computational approaches, single molecule biophysics, use of induced pluripotent stem cells in
research, and other interdisciplinary approaches. Current papers examined. Prerequisites: basic
biochemistry.


Units:

3
--

3






Grading Basis:

ROP
-

Letter or Credit/No Credit

Components:

LEC




Quarters Offered:


OTH
-

not given this year

Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

James Spudich, Kathleen Ruppe
l







BIOC 230


Short (transcript) title:

MOLECULAR INTERVENTIONS

Course ID:

203431

Career:

GR

Effective Date:

01
-
Aug
-
09

Other Offering:



Title:

Molecular Interventions in Human Disease

Description:

For M.D. students who intend to declar
e a concentration in molecular basis of medicine, MSTP
students, and Ph.D. students. Advanced medical biochemistry focusing on cases where
molecular
-
level research has led to new medical treatments or changes in the understanding of
important diseases. Dif
ferent topics each week explore the underlying molecular basis of a
variety of diseases and the reasons for success and failure in molecular approaches to treatment.
Student
-
led discussions dissect papers from the primary medical and scientific research
li
terature.


Units:

2
--

3






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

LEC




Quarters Offered:


OTH
-

not given this year


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Julie Theriot,
Pehr Harbury










BIOC 236


Short (transcript) title:

BIOLOGY BY THE NUMBERS

Course ID:

208892

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

APPPHYS 236 GR

Title:

Biology by the Numbers: Evolution

Description:

Topics in biology f
rom a quantitative perspective. Subjects vary. 2011
-
12 focus: evolution,
from basic principles of evolutionary dynamics to fundamental quantitative questions that are
far from being answered; from early life, metabolic processes, and molding of earth by
mi
crobes to spread of human epidemics; from analysis of genomes and molecular phylogenies
to aspects of multi
-
cellular development. Prerequisites: Familiarity with ordinary differential
equations and probability. Biology background not required.




:

Units:

3
--

3






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


OTH
-

not given this year


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Daniel Fisher, Julie Theriot








BIOC 241


Short (transcript) title:

BIOLOGICAL MACROMOLECULES

Course ID:

127288

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

BIOPHYS 241 GR SBIO 241 GR

Title:

Biological Macromolecules

Description:

The physical and chemical basis of

macromolecular function. Forces that stabilize biopolymers
with three
-
dimensional structures and their functional implications. Thermodynamics,
molecular forces, structure and kinetics of enzymatic and diffusional processes, and relationship
to their prac
tical application in experimental design and interpretation. Biological function and
the level of individual molecular interactions and at the level of complex processes. Case
studies in lecture and discussion of classic and current literature. Enrollment
limited to 30.
Prerequisites: None; background in biochemistry and physical chemistry preferred but material
available for those with deficiency; undergraduates with consent of instructor only.




:

Units:

3
--

5






Grading Basis:

MOP
-

Medical Option (M
ed
-
Ltr
-
CR/NC)

Components:

DIS

LEC



Quarters Offered:

AUT



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Daniel Herschlag, Pehr Harbury, Rhiju Das, William Weis









BIOC 257


Short (transcript) title:

CU
RRENTS IN BIOCHEMISTRY

Course ID:

203383

Career:

GR

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

Currents in Biochemistry

Description:

Seminars by Biochemistry faculty on their ongoing research. Background, current advances and
retrea
ts, general significance, and tactical and strategic research directions.





Units:

1
--

1






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

SEM




Quarters Offered:

AUT



Repeatable For Credit:

N

Max Repeat Units:


Max
Repeat Attempts:


Instructor(s):

James Spudich









BIOC 258


Short (transcript) title:

GENOMICS, BIOIN AND MEDICINE

Course ID:

212157

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

BIOC 158 UG HUMBIO 158G UG

Title:

Genomics, Bioinfo
rmatics and Medicine

Description:

Molecular basis of inherited human disease. Diagnostics approaches: simple Mendelian
diseases and complex, multifactorial diseases. Genomics: functional genomics, epigenetics,
gene expression, SNPs, copy number and other

structural genomic variations involved in
disease. Novel therapeutic methods: stem cell therapy, gene therapy and drug developments
that depend on the knowledge of genomics. Personal genomics, pharmacogenomics, clinical
genomics and their role in the fut
ure of preventive medicine. Prerequisites: BIO 41 or
HUMBIO 2A or consent of instructor. Those with credit in BIOC 118 not eligible to enroll.
Course webpage: http://biochem158.stanford.edu/


Units:

4
--

4






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:

AUT WIN SPR


Repeat
able For Credit:
Y

Max Repeat Units:

8

Max Repeat Attempts:

2


Instructor(s):

Douglas Brutlag










BIOC 298


Short (transcript) title:

BIOCHEMISTRY CONSLTNG SERVICE

Course I
D:

208872

Career:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:



Title:

Biochemistry Consulting Service

Description:

Students are presented with requests for advice from faculty and students in the biological
sciences and Medical School enc
ountering experimental and analytical problems in their
research. Students work with the instructor and other biochemistry faculty to propose solutions.
May be repeated for credit.




:

Units:

3
--

3






Grading Basis:

MOP
-

Medical Option
(Med
-
Ltr
-
CR/NC)

Components:

PRC




Quarters Offered:


OTH
-

not given this year


Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Patrick Brown









BIOC 299


Short (transcript) title:

DIRECTED READING

Course

ID:

127339

Career:

GR

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

Directed Reading in Biochemistry

Description:

Prerequisite: consent of instructor. (Staff)


Units:

1
--

18






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Co
mponents:

INS




Quarters Offered:

AUT WIN SPR SUM



Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Aaron Straight, Daniel Herschlag, Douglas Brutlag, James Chen, James
Spudich, Julie Theriot, Mark Krasnow, Patr
ick Brown, Pehr Harbury, Philip Beachy, Rajat
Rohatgi, Rhiju Das, Ronald Davis, Suzanne Pfeffer






Y




BIOC 370


Short (transcript) title:

MEDICAL SCHOLARS RESEARCH

Course ID:

205566

Career:

MED

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

Medical Scholars Research

Description:

Provides an opportunity for student and faculty interaction, as well as academic credit and
financial support, to medical students who undertake original research. Enrollment is limited to
stu
dents with approved projects.




Units:

4
--

18






Grading Basis:

MED
-

Medical School MD Grades

Components:

INS




Quarters Offered:

AUT WIN SPR SUM



Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Aaron Stra
ight, Daniel Herschlag, Douglas Brutlag, James Chen, James
Spudich, Julie Theriot, Mark Krasnow, Patrick Brown, Pehr Harbury, Philip Beachy, Rajat
Rohatgi, Rhiju Das, Ronald Davis, Suzanne Pfeffer










BIOC 399


Short (transcript) title:

RESEARCH & SPE
CIAL ADV WORK

Course ID:

127341

Career:

GR

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

Graduate Research and Special Advanced Work

Description:

Allows for qualified students to undertake investigations sponsored by individual faculty

members.


Units:

1
--

18






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

INS




Quarters Offered:

AUT WIN SPR SUM


Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Aaron Straight, Daniel
Herschlag, Douglas Brutlag, James Chen, James
Spudich, Julie Theriot, Mark Krasnow, Patrick Brown, Pehr Harbury, Philip Beachy, Rajat
Rohatgi, Rhiju Das, Ronald Davis, Suzanne Pfeffer






Y




BIOC 459


Short (transcript) title:

FRONTIERS INTERDSCP BIOSCN
CS

Course ID:

103400

Career:

GR

Effective Date:

01
-
Aug
-
12

Other Offering:

BIO 459 GR BIOE 459 GR CHEMENG 459 GR CHEM 459 GR
PSYCH 459 GR

Title:

Frontiers in Interdisciplinary Biosciences

Description:

Students register through their affiliated depar
tment; otherwise register for CHEMENG 459.
For specialists and non
-
specialists. Sponsored by the Stanford BioX Program. Three seminars
per quarter address scientific and technical themes related to interdisciplinary approaches in
bioengineering, medicine,
and the chemical, physical, and biological sciences. Leading
investigators from Stanford and the world present breakthroughs and endeavors that cut across
core disciplines. Pre
-
seminars introduce basic concepts and background for non
-
experts.
Registered st
udents attend all pre
-
seminars; others welcome. See
http://biox.stanford.edu/courses/459.html. Recommended: basic mathematics, biology,
chemistry, and physics.





Units:

1
--

1






Grading Basis:

RSN
-

Satisfactory/No Credit

Components:

LEC




Quarters
Offered:

AUT WIN SPR


Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Channing Robertson







BIOC 801


Short (transcript) title:

TGR PROJECT

Course ID:

204449

Career:

GR

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

TGR Project

Description:


Units:

0
--

0






Grading Basis:

RTG
-

TGR

Components:

T/D




Quarters Offered:

AUT WIN SPR SUM



Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Aaron
Straight, Daniel Herschlag, Douglas Brutlag, James Chen, James
Spudich, Julie Theriot, Mark Krasnow, Patrick Brown, Pehr Harbury, Philip Beachy, Rajat
Rohatgi, Rhiju Das, Ronald Davis, Suzanne Pfeffer









BIOC 802


Short (transcript) title:

TGR DISSERT
ATION

Course ID:

127344

Career:

GR

Effective Date:

01
-
Sep
-
06

Other Offering:



Title:

TGR Dissertation

Description:


Units:

0
--

0






Grading Basis:

RTG
-

TGR

Components:

T/D




Quarters Offered:

AUT WIN SPR SUM


Repeatable For
Credit:

Y

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Aaron Straight, Daniel Herschlag, Douglas Brutlag, James Chen, James
Spudich, Julie Theriot, Mark Krasnow, Patrick Brown, Pehr Harbury, Philip Beachy, Rajat
Rohatgi, Rhiju Das, Ronald Davis
, Suzanne Pfeffer

















Subject:

BIOMEDIN


BIOMEDIN 109Q


Short (transcript) title:

GENOMICS: TECH & CLTRL RVLTN

Course ID:

204696

Care
er:

UG

Effective Date:

01
-
Aug
-
12

Other Offering:

GENE 109Q UG

Title:

Genomics: A Technical and
Cultural Revolution

Description:

Preference to sophomores. Concepts of genomics, high
-
throughput methods of data collection,
and computational approaches to analysis of data. The social, ethical, and economic
implications of genomic science. Students may f
ocus on computational or social aspects of
genomics.



Units:

3
--

3



Writing 2




Grading Basis:

ROP
-

Letter or Credit/No Credit

Components:

ISS




Quarters Offered:


OTH
-

not given this year



Repeatable For Credit:

N

Max Repeat Units:


Ma
x Repeat Attempts:


Instructor(s):

Russ Altman










BIOMEDIN 156


Short (transcript) title:

ECON OF HEALTH & MEDICAL CARE

Course ID:

113357

Career:

UG

Effective Date:

01
-
Aug
-
11

Other Offering:

BIOMEDIN 256 GR ECON 126 UG HRP 256 GR

Title:

Economics of Health and Medical Care

Description:

Institutional, theoretical, and empirical analysis of the problems of health and medical care.
Topics: demand for medical care and medical insurance; institutions in the health sector;
economics of informat
ion applied to the market for health insurance and for health care;
measurement and valuation of health; socioeconomic status and epidemiology; economics of
obesity.Graduate students with research interests should take ECON 248. Prerequisites: ECON
50 and
ECON 102A or Stats 116 or the equivalent. Recommended: ECON 51.





Units:

5
--

5






Grading Basis:

ROP
-

Letter or Credit/No Credit

Components:

DIS

LEC



Quarters Offered:

AUT


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts
:


Instructor(s):

Jayanta Bhattacharya








BIOMEDIN 200


Short (transcript) title:

BIOMEDICAL INFORM COLLOQUIUM

Course ID:

127214

Career:

GR

Effective Date:

01
-
Aug
-
09

Other Offering:



Title:

Biomedical Informatics Colloquium

Description
:

Series of colloquia offered by program faculty, students, and occasional guest lecturers. May be
repeated three times for credit.





Units:

1
--

1






Grading Basis:

RSN
-

Satisfactory/No Credit

Components:

COL




Quarters Offered:

AUT WIN SPR




Repeatable For Credit:
Y

Max Repeat Units:

3

Max Repeat Attempts:

3


Instructor(s):

Mark Musen









BIOMEDIN 201


Short (transcript) title:

BIOMEDIC INFORM STUDENT SEM

Course ID:

127215

Career:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:



Title:

Biomedical Informatics Student Seminar

Description:

Participants report on recent articles from the Biomedical Informatics literature or their research
projects. Goals are to teach critical reading of scientific papers and presenta
tion skills. May be
repeated three times for credit.





Units:

1
--

1






Grading Basis:

RSN
-

Satisfactory/No Credit

Components:

SEM




Quarters Offered:

AUT WIN SPR SUM



Repeatable For Credit:
Y

Max Repeat Units:

3

Max Repeat Attempts:

3



I
nstructor(s):

Mark Musen












BIOMEDIN 205


Short (transcript) title:

BIOMED INFORMATCS FOR
MEDICINE

Course ID:

207818

Career:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:



Title:

Biomedical Informatics for Medicine

Description:

Primarily for M.D. students; open to other graduate students. Emphasis is on practical
applications of bioinformatics and medical informatics for medicine, health care, clinicians, and
biomedical research, focused on work at Stanford. Topics may include: m
ethods to analyze
genetic conditions, integrative methods for microarray, proteomic, and genomic data to
understand the etiology of disease, clinical information systems in local healthcare facilities,
cellular and radiology imaging, and pharmacogenomics.
Enrollment for 2 units includes weekly
assignments. Non
-
MD students may enroll for 1 unit. May be repeated for credit. Prerequisite:
background in biomedicine. Recommended: background in programming.





Units:

1
--

2






Grading Basis:

MSN
-

Medical Sati
sfactory/No Credit

Components:

LEC




Quarters Offered:

AUT SPR


Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Atul Butte






N



BIOMEDIN 206


Short (transcript) title:

INFORMATICS IN INDUSTRY

Course ID:

209
421

Career:

GR

Effective Date:

24
-
Nov
-
09

Other Offering:



Title:

Informatics in Industry

Description:

Effective management, modeling, acquisition, and mining of biomedical information in
healthcare and biotechnology companies and approache
s to information management adopted
by companies in this ecosystem. Guest speakers from pharmaceutical/biotechnology
companies, clinics/hospitals, health communities/portals, instrumentation/software vendors.
May be repeated for credit.




:

Units:

1
--

1






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

SEM




Quarters Offered:


SPR


Repeatable For Credit:

Y

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Nigam Shah, Nikesh Kotecha






BIOMEDIN 207


Short
(transcript) title:

DIGITAL MEDICINE

Course ID:

210090

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:



Title:

Smart Health through Digital Medicine

Description:

The widespread use of Health IT, such as Electronic Health Records, will

radically alter the
practice of medicine in the coming decades. Comprised of guest lectures, site visits and project
assignments, the goal of this course is to provide an understanding of which software and
technology designs can advance the delivery and
quality of healthcare. May be taken for 1 unit
(lectures only), 2 units (lectures and site visits), or 3 units (lectures, site visits, and project).





Units:

1
--

3






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

LEC




Quarters Off
ered:


WIN


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Amarendra Das










BIOMEDIN 210


Short (transcript) title:

MODELING BIOMEDICAL SYSTEMS

Course ID:

127217

Career:

GR

Effective Date:

04
-
Jan
-
12

Other

Offering:

CS 270 GR

Title:

Modeling Biomedical Systems: Ontology, Terminology, Problem Solving

Description:

Methods for modeling biomedical systems and for making those models explicit in the context
of building software systems. Emphasis
is on intelligent systems for decision support and
Semantic Web applications. Topics: knowledge representation, controlled terminologies,
ontologies, reusable problem solvers, and knowledge acquisition. Recommended: exposure to
object
-
oriented systems, bas
ic biology.





Units:

3
--

3






Grading Basis:

ROP
-

Letter or Credit/No Credit

Components:

DIS

LEC



Quarters Offered:


WIN



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Mark Musen









BIOMEDIN 211


Short (transcript) title:

HEALTH INFORMATICS DESIGN

Course ID:

127218

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

CS 271 GR

Title:

Smart Health through Effective Design

Description:

Methods of designing and engineering software sy
stems in complex clinical environments.
Case studies illustrate factors leading to success or failure of systems. Project assignments
involve focused team
-
based design work. Topics: user and organizational requirements, data
and knowledge modeling, compon
ent
-
based system design, system prototyping, and human
-
systems interaction. Prerequisite: BIOMEDIN 210 recommended, or database or object
-
oriented programming course.


Units:

3
--

3






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC


Quarters Offered:


WIN



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Amarendra Das










BIOMEDIN 212


Short (transcript) title:

INTR BIOMED INFMTICS RSCH METH

Course ID:

141029

Career:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:

BIOE 212 GR CS 272 GR GENE 212 GR

Title:

Introduction to Biomedical Informatics Research Methodology

Description:

Hands
-
on software building. Student teams conceive, design, specify, implement, evaluate, and
report on

a software project in the domain of biomedicine. Creating written proposals, peer
review, providing status reports, and preparing final reports. Guest lectures from professional
biomedical informatics systems builders on issues related to the process of p
roject management.
Software engineering basics. Prerequisites: BIOMEDIN 210, 211, 214, 217 or consent of
instructor.


Units:

3
--

3






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


SPR


Repeatable F
or Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Russ Altman, Teri Klein










BIOMEDIN 214


Short (transcript) title:

ALGORITHMS COMP MOLECULAR
BIO

Course ID:

141030

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

BIOE 214 GR

CS 274 GR GENE 214 GR

Title:

Representations and Algorithms for Computational Molecular Biology

Description:

Topics: introduction to bioinformatics and computational biology, algorithms for alignment of
biological sequences and structures, compu
ting with strings, phylogenetic tree construction,
hidden Markov models, Gibbs Sampling, basic structural computations on proteins, protein
structure prediction, protein threading techniques, homology modeling, molecular dynamics
and energy minimization, s
tatistical analysis of 3D biological data, integration of data sources,
knowledge representation and controlled terminologies for molecular biology, microarray
analysis, machine learning (clustering and classification), and natural language text processing
.
Prerequisites: programming skills; consent of instructor for 3 units.




Units:

3
--

4






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:

AUT


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat
Attempts:


Instructor(s):

Russ Altman









BIOMEDIN 215


Short (transcript) title:

DATA DRIVEN MEDICINE

Course ID:

212220

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:



Title:

Data Driven Medicine

Description:

With the spread of
electronic health records and increasingly low cost assays for patient
molecular data, powerful data repositories with tremendous potential for biomedical research,
clinical care and personalized medicine are being built. But these databases are large and
difficult for any one specialist to analyze. To find the hidden associations within the full set of
data, we introduce methods for data
-
mining at the internet scale, the handling of large
-
scale
electronic medical records data for machine learning, methods
in natural language processing
and text
-
mining applied to medical records, methods for using ontologies for the annotation and
indexing of unstructured content as well as semantic web technologies. Includes a
programming project. See also BIOMEDIN 225, wh
ich does not include the project.
Prerequisites: BIOMEDIN 210; CS 106A highly recommended; CS 345A recommended.





Units:

3
--

3






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:

AUT


Repeatable Fo
r Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Nigam Shah









BIOMEDIN 216


Short (transcript) title:

LECTURES
-

BIOMEDIN 214

Course ID:

141031

Career:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:



Title:

Represent
ations and Algorithms for Molecular Biology: Lectures

Description:

Lecture component of BIOMEDIN 214. One unit for medical and graduate students who attend
lectures only; may be taken for 2 units with participation in limited assignments and final
project.

Lectures also available via internet. Prerequisite: familiarity with biology
recommended.




Units:

1
--

2






Grading Basis:

MSN
-

Medical Satisfactory/No Credit

Components:

LEC




Quarters Offered:

AUT


Repeatable For Credit:

N

Max Repeat
Units:


Max Repeat Attempts:


Instructor(s):

Russ Altman









BIOMEDIN 217


Short (transcript) title:

TRANSLATIONAL BIOINFORMATICS

Course ID:

206403

Career:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:

CS 275 GR

Title:

Translational Bioi
nformatics

Description:

Analytic, storage, and interpretive methods to optimize the transformation of genetic, genomic,
and biological data into diagnostics and therapeutics for medicine. Topics: access and utility of
publicly available data sources; types

of genome
-
scale measurements in molecular biology and
genomic medicine; analysis of microarray data; analysis of polymorphisms, proteomics, and
protein interactions; linking genome
-
scale data to clinical data and phenotypes; and new
questions in biomedici
ne using bioinformatics. Case studies. Prerequisites: programming ability
at the level of CS 106A and familiarity with statistics and biology.





Units:

4
--

4






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


SPR

Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Atul Butte









BIOMEDIN 218


Short (transcript) title:

TRANSLATIONAL BIOINFORMATICS

Course ID:

207061

Career:

GR

Effective Date:

01
-
Aug
-
10

Other Offering:



Title:

Translational Bioinformatics Lectures

Description:

Same content as BIOMEDIN 217; for medical and graduate students who attend lectures and
participate in limited assignments and final project. Analytic, storage, and interpretive me
thods
to optimize the transformation of genetic, genomic, and biological data into diagnostics and
therapeutics for medicine. Topics: access and utility of publicly available data sources; types of
genome
-
scale measurements in molecular biology and genomic

medicine; analysis of
microarray data; analysis of polymorphisms, proteomics, and protein interactions; linking
genome
-
scale data to clinical data and phenotypes; and new questions in biomedicine using
bioinformatics. Case studies. Prerequisites: programm
ing at the level of CS 106A; familiarity
with statistics and biology.





Units:

2
--

2






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


SPR



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat
Attempts:


Instructor(s):

Atul Butte









BIOMEDIN 219


Short (transcript) title:

MATHMTCL MODELS & MED
DECISNS

Course ID:

209422

Career:

GR

Effective Date:

01
-
Aug
-
09

Other Offering:



Title:

Mathematical Models and Medical Decisions

Des
cription:

Analytic methods for determining the optimal diagnostic and therapeutic decisions for the care
of individual patients and for the design of policies affecting the care of patient populations.
Topics: utility theory and probability modeling, empir
ical methods for estimating disease
prevalence, probability models for periodic processes, binary decision
-
making techniques,
Markov models of dynamic disease state problems, utility assessment techniques, parametric
utility models, utility models for mult
idimensional outcomes, analysis of time
-
varying clinical
outcomes, and the design of cost
-
contstrained clinical policies. 2 units requires completion of a
case study project. Prerequisites: introduction to calculus and basic statistics.

Units:

1
--

2






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


WIN


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Mark Musen, Michael Higgins









BIOMEDIN 224


Short
(transcript) title:

PRINCIPLES OF
PHARMACOGENOMICS

Course ID:

212730

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:



Title:

Principles of Pharmacogenomics

Description:

Introduction to the relevant pharmacology, genomics, experimental

methods for high
-
throughput measurements (sequencing, expression, genotyping), analysis methods for GWAS,
chemoinformatics, and natural language processing. Review of key gene classes (cytochromes,
transporters, GPCRs), key drugs for which genetics is cri
tical (warfarin, clopidogrel, statins,
NSAIDs, neuropsychiatric drugs and cancer drugs). Also reviews resources for
pharmacogenomics (PharmGKB, Drugbank, CMAP, and others) as well as issues in doing
clinical implementation of pharmacogenomics testing. Read
ing of key papers, including student
presentations of this work.; problem sets; final project selected with approval of instructor.
Prerequisites: two of BIO 41, 42, 43, 44X, 44Y or consent of instructor.





Units:

3
--

3






Grading Basis:

MOP
-

Medical

Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:


WIN


Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Russ Altman, Teri Klein










BIOMEDIN 225


Short (transcript) title:

DATA DRIVEN MEDICINE L
ECTURES

Course ID:

212225

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:



Title:

Data Driven Medicine: Lectures

Description:

With the spread of electronic health records and increasingly low cost assays for patient
molecular data, po
werful data repositories with tremendous potential for biomedical research,
clinical care and personalized medicine are being built. But these databases are large and
difficult for any one specialist to analyze. To find the hidden associations within the f
ull set of
data, we introduce methods for data
-
mining at the internet scale, the handling of large
-
scale
electronic medical records data for machine learning, methods in natural language processing
and text
-
mining applied to medical records, methods for us
ing ontologies for the annotation and
indexing of unstructured content as well as semantic web technologies. The final project from
Biomedin 215 is not required. Prerequisites: Biomedin 210 highly recommended; CS 106A, CS
345A recommended.





Units:

2
--

2






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:

AUT



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:



Instructor(s):

Nigam Shah










BIOMEDIN 231


Short (transcript) title:

COMPUTATIONAL MOLEC BIOLOGY

Course ID:

127325

Career:

GR

Effective Date:

01
-
Aug
-
11

Other Offering:

BIOC 218 GR

Title:

Computational Molecular Biology

Description:

Practical, hands
-
on approach to field of computational molecular biology. Re
commended for
molecular biologists and computer scientists desiring to understand the major issues concerning
analysis of genomes, sequences and structures. Various existing methods critically described
and strengths and limitations of each. Practical assi
gnments utilizing tools described. All
homework and coursework submitted electronically. Course webpage:
http://biochem218.stanford.edu/.




Units:

3
--

3






Grading Basis:

MOP
-

Medical Option (Med
-
Ltr
-
CR/NC)

Components:

LEC




Quarters Offered:

AUT

WIN SPR



Repeatable For Credit:

N

Max Repeat Units:


Max Repeat Attempts:


Instructor(s):

Douglas Brutlag











BIOMEDIN 233


Short (transcript) title:

ANALYSIS OF DISCRETE DATA

Course ID:

125457

Career:

GR

Effective Date:

01
-
Aug
-
11

Other
Offering:

HRP 261 GR STATS 261 GR

Title:

Intermediate Biostatistics: Analysis of Discrete Data