Curriculum Vitae
Carol Friedman
Date of Preparation: 2/16/2015
Personal Data
Name: Carol Friedman
Birthplace: New York, NY
Citizenship: USA
Academic Training
1989 Ph.D. Computer Science, New
York University
1986. M.A. Computer Science, New York University
1962. B.S. Mathematics, City College CUNY, magna cum laude, elected to
Phi Beta Kappa
Academic Appointments
|
7/2012 |
-present |
Graduate Program Director & Professor, Department of
Biomedical Informatics, Columbia University |
|
7/2009 |
-6/2012 |
Vice Chair & Professor, Department of Biomedical
Informatics, Columbia University |
|
7/2002 |
-6/2009 |
Professor, Department of Biomedical Informatics, Columbia
University |
|
9/2000 |
- 6/2002 |
Senior Lecturer, Department of Medical Informatics, |
|
1/1999 |
- 6/2002 |
Professor, Computer Science, |
|
7/1998 |
- 8/2000 |
Associate Professor, Department of Medical Informatics, |
|
1/1996 |
-12/1998 |
Associate Professor, Computer Science, Queens College CUNY |
|
1/1995 |
- 6/1998 |
Assistant Professor, Department of Medical Informatics, |
|
9/1991 |
- 6/1996 |
Adjunct Assistant Professor, Department of Medical
Informatics, |
|
9/1990 |
-12/1995
|
Assistant Professor, Computer Science, |
|
4/1989 |
- 8/1990 |
Assistant Professor, Department of Medicine, |
Phi Beta Kappa, 1962
Graduated Magna Cum Laude, 1962
SCAMC 1995 Best Electronic Poster
Starren J, Friedman C, and Johnson S.
The
Columbia Integrated Speech Interpretation system CISIS. In Gardner RM,
editor,
Proceedings
of the 19th Annual Symposium on Computer Applications in Medical Care, 1995, pg 985.
Invited Speaker to the 1995 Spring Congress sponsored by AMIA
Fall 1996 AMIA Best paper on an Application
Jain NL, Knirsch
C, Friedman C, and Hripcsak G. Identification of suspected tuberculosis
patients
based on natural language processing of chest radiography reports. In Cimino
JJ, ed.
Proceeding
of the fall 1996 AMIA Conference, Hanley & Belfus,
Philadelphia, 1996:542-546.
Invited to present at International Medical Informatics Association WG6 1997
and 1999
Fall 1998 AMIA Best theoretical paper
Friedman C, Hripcsak G, Shablinsky I. An evaluation of natural language processing
methodologies.
In Chute CG, ed. Proceedings 1998 AMIA Annual Symposium.
Phil: Hanley &
Belfus, 1998; 855-859.
Fellow of the American College of Medical Informatics (ACMI), Fall 1998
Papers selected for Annual IMIA Yearbook of Medical Informatics: 1999, 2001
Patent US6055494
System and method for medical
language extraction and encoding, Issued 4/25/2000
Patent US6182029
System and method for language
extraction and encoding utilizing the parsing of text data in accordance with
domain parameters, Issued 1/30/2001
Invited Speaker to the European Bio-Sci
meeting, 6/2002
Invited speaker to the Association for Computational Linguistics, Workshop in
Biomedicine, 2003
Commissioned by the National Academies to write a report on Natural Language
Processing and the Prevention of Medical Errors, 2003
European Patents 0929870 and 236832
System and method for language
extraction and encoding, Issued 3/24/2004 and 5/19/2004
Invited speaker to Semantic Mining in Biomedicine Symposium, Wellcome Trust, UK, 2005
Fellow of the
AMIA Donald A. B. Lindberg Award for Innovation in Biomedical
Informatics, 2010
NIH
from NLM (R02LM010016), PI, 7/1/2013-6/31/2017
NIH
from NLM (R01LM06910), investigator (PI, Hripcsak), 9/30/2013–9/29/2018
NHGRI: U01 HG006380, investigator (PI,
Weng), 8/2011–7/2015
Previous Grant Support
NIH
from NLM (R01LM010016-01), PI, 7/1/2009-6/31/2013
NIH
from NLM (R01LM010016-01S1), PI, 9/1/2009-8/31/2011
NIH
from NLM (R01LM010016-01S2), PI, 9/1/2009-8/31/2011
NIH
from NLM (R01LM06910), investigator (PI, Hripcsak), 9/30/2009–9/29/2013
NIH
from NLM (R01LM009886), investigator (PI, Weng), 4/1/2009-3/31/2012
NIH
from NLM (R01LM10140), investigator (PI, Rabadan), 7/1/2009-6/30/2011
NIH
from NCI (R01CA141307), investigator(PI, Xu),
10/1/2009-7/31/2013
NIH from NLM (R01LM008635), PI, 7/1/05-6/30/10 ($2,190,693)
NIH from NLM (R21LM009638), PI, 09/30/07-09/29/09
NYC/DOHMH Center of Excellence in Public Health Informatics, investigator (PI,
Hripcsak), 06/01/07-07/01/09
NIH from NLM (R01LM007659), PI, 7/1/03-6/30/07 ($1,902,831)
NSF SEI+III(BIO), PI of Columbia subcontract, 9/1/04-8/31/07 ($249,000)
NIH U54 (GM072980), investigator (PI:Califano),
9/6/05-7/31/10 ($2,480,315,first yr)
NIH from NLM (R01GN01372), co-PI (PI:Rzhetsky), 7/1/01-6/30/08 ($250,000/yr)
NIH S2114-22/22, co-PI, (PI:Kukafka),
10/1/02-9/30/04 ($76,453/yr)
NIH from NLM, (R01LM07268), investigator (PI:Johnson),
7/01/2002-6/30/2005 ($346,376/yr)
NIH from NLM (R01LM0610), (PI:Hripcsak),
04/01/2000-03/31/2006 ($250,000/yr)
EIA from NSF (EIA-0312250), PI, 2/1/03-1/31/04 ($61,162)
NIH from NLM (R01LM06274), PI, 7/1/97-12/31/2003 ($250,000)
NSF ITR/IM+AP, co-PI, (PI:Rzhetsky), 9/1/01-8/31/03
($6,139)
AHRQ , investigator, (PI:Hripcsak), 09/01/2001
$223,030
DLI2 from NSF IIS 9817434, investigator, (PI:McKeown),
9/1/99-8/31/05 ($5,000,375)
PSC-CUNY Research Awards (6-64044, 6-61483), PI, 7/1/91-6/30/94 ($9,000)
NIH Grant from NLM (R29LM05627), PI, 1/1/92-6/31/97 ($549,271)
New York State Science and Technology Foundation, PI, 11/1/94-6/30/97
($210,000)
NIST ATP Subcontract with Sunquest Systems, PI,
11/1/96-10/30/98 ($220,000)
NIST ATP Subcontract with Kurzweil, PI, 12/1/97-11/30/99 ($561,988)
New York State Science and Technology Foundation, co-PI, 7/1/97-6/30/99
($298,474)
NIH Grant from NLM (R01LM06274), PI . 7/1/97-6/30/00 ($632,000 award)
New York State Science and Technology Foundation, co-PI, 1/1/98-6/30/99
($201,795)
New York State Science and Technology Foundation, PI, 4/1/01-6/30/01 ($30,000)
Departmental and University
Committees
Honors and Awards Committee, Queens College CUNY, 1991-2002
Curriculum Committee, Queens College CUNY, 1991-2002
Faculty Advisor, Queens College CUNY, 1991-2002
Library Committee, Queens College CUNY, 1992-1995
Howard Hughes Scientific Awards Committee, Queens College CUNY, 1994-1997
Chair, Departmental Search Committee, 1999
Data Structures Course Coordinator, Queens College, CUNY, 2002
Academic Appointments Committee, Biomedical Informatics, Columbia University,
2002-present
Ad-hoc Tenure Committee,
Training Committee, Biomedical Informatics, Columbia
University, 2007-present
Executive Committee, Biomedical Informatics, Columbia
University, 2007-present
Coordinating Admissions Committee, Graduate School of Arts
and Sciences, Columbia University, 2008-present
IT Committee, Biomedical Informatics, Columbia University,
2009-present
Chair, Search Committee, Biomedical Informatics, Columbia
University, 2009-present
Executive Training Committee, Biomedical Informatics,
Columbia University, 2013-present
Teaching Experience and
Advising
Database Management Systems
Programming Language Theory
Natural Language Programming
Data Structures
Software Design
Independent Study
Research Seminar
Text mining
Pharmacovigilance
Graduate Research Advisor - CUNY
Galit Blum, 194, 1995 Use of N-GRAMS for vocabulary
discovery
Leon Tat-Kim, 1996 Integrating a natural language parser into a working
Clinical Information System
Samer Salame, 2001 Use of
regular expression to recognize noun phrases
Hongfang Liu (Ph.D. advisor), 1999-2002 Corpus-based
ambiguity resolution of biomedical terms based on knowledge sources and machine
learning
Research
Advisor Columbia University
Nilesh Jain, 1996 Using NLP to detect patients suspicious for tuberulosis
Nilesh Jain, 1997 Using NLP to detect findings in mammogram reports
Irina Shablinsky, 1997 2000 Elliciting
information needs of physicians from
information in patient records
Qing Zeng, 1998 Training NLP system to interpret findings in
electrocardiogram reports
Donald Harrington, 1998, 1999 Summarizing findings in chest x-rays over time
Michael Krauthammer, 1998 Using BLAST to identify the names of genes and
proteins in text
Hong Yu, 1998, 1999 Identifying abbreviations in biomedical text and mapping
them to their full forms
Adam Wilcox, 2000 Natural language as a tool in the development of a controlled
vocabulary.
Rahul Bajaj, 2000-2001 Assessing natural language processing to detect
congestive heart failure from chest x-ray reports
Bhanu Bahl, 2002-2004 Using
NLP to structure and extracting chromosome analysis test and results in
pathology reports
Hua Xu, 2002-2008 Methods for improving NLP systems
Lifeng Chen, 2003-2005 Modeling relation between
phenotypic and genotypic information in journal articles
Olivia Tuason, 2003-2004 Developing a biomedical
terminological resource for natural language processing
Trevor Cohen, 2003-2004. Detecting psychiatric patients who
are dangerous using NLP
Karina Tulipano, 2004-2008. Triaging
MRI images to detect patients with stroke
Li Zhou, 2004-2008. NLP and analysis of time.
Ying Tao, 2004-2007. Knowledge discovery and visualization with NLP
Michael Bales, 2004 -2006.
Investigating feasibility of ICF coding of clinical
rehabilitation reports
Jung-Wei Fan, 2005-2010. Automated semantic
classification to improve UMLS.
Xiaoyan Wang, 2007-present. Pharmacovigilance using NLP, statistics, and the EHR.
Krystl Haerian, 2010-present.
Knowledge-based methods to reduce confounding and improve
pharmacovigilance.
Ying Li, 2010-present.
Acquiring drug-related knowledge using NLP.
Wei-wei
Wang, 2010-2013. Acquiring adverse event evidence from
journal articles.
Hojjat Salmasian, 2010-present.
Automated methods for detecting medication overuse.
Qinlang Chen, 2013-present. An accurate method to obtain and summarize adverse drug events from
the literature.
Kuo Lin, 2013-present. A
method to retrieve drug-herb interactions from the literature.
Sivan Kinberg, 2013-present.
Studying the adverse effects of medications in patients with
IBD using comprehensive information in the EHR.
Evelyn Rustia, 2013-present.
Integrating genomic and clinical information for pediatric
oncology patients.
Grant Reed, 2015-present. Transforming a
comprehensive database from clinical narrative reports to the standard form
described by OHSDI.
Thesis Committee member for
Justin Starren From Multimodal Sublanguages to Medical Data Presentations ,
1995-1997
Adam Wilcox Automated classification of medical text reports , 1997-2000
Hong Yu Acquiring synonyms and disambiguating homonyms in biomedical text ,
1998 2002
Jen-Hsiang Chuang Detecting medical errors via clinical databases , 2000-2002
Michael Krauthammer Data mining the literature and patient database
to discover genomic connections using patient data, 1998 2004
David Campbell Natural language processing, 1998-2005
Li Zhou, 2005-2007
Trevor Cohen, 2005-2007
Other Professional
Activities
AMIA Publications Committee – 1998-2004
Editorial Board Member for
Journal of American
Medical Informatics Association, 1999-present
Journal of Biomedical Informatics,
2001-present
Journal of
Biomedical Discovery and Collaboration, 2005-present
Journal of
Biomedical Semantics, 2009-present
Search Committee for Editor of Journal of American Medical
Informatics Association, 2002
Program Committee for Natural Language Workshop in Biomedicine, Association for
Computational Linguistics Conference, 2002, 2003
Program Committee for Pre-Trek Track Workshop in Bioinformatics, JDL
Conference, 2002
Co-chair for Natural Language Track, Pacific Symposium in Biocomputing, 2003
Program Committee for BIOLINK Workshop sponsored by NSF, 2003
Program Committee for 2nd International Symposium on Semantic Mining in
Biomedicine, 2006
Program Committee for HTL-NAACL 06 - Bio NLP, 2006
Program Committee for BioLink SIG - ISMB 06, 2006
Scientific Program Committee, AMIA 2007, AMIA 2009
Co-chair for BioNLP 2007
Manuscript reviewer for
International Journal of Medical
Informatics
Journal of American Medical
Informatics Association
Journal of Biomedical Informatics
Natural Language Engineering
American Medical Informatics
Association Fall Symposium
Methods of Information in Medicine
Artificial Intelligence in Medicine
Bioinformatics
Nature Reviews Genetics
BMC Bioinformatics
BMC Medical Decision Making
International
Journal of Clinical Pharmacology and Therapeutics
Guest editor for Special Sublanguage Issue of Journal of Biomedical
Informatics, 2003
Guest co-editor for Special Named Entity Recognition Issue of Journal of
Biomedical Informatics, 2004
Member
at Large, ACMI Executive Committee, 2005-2006
ACMI
Honors and Awards Committee, 2005-2007
Board
of Scientific Counselors,
Special
Emphasis Review Panel, National Library of Medicine, 2000, 2001
Ad Hoc Member of Genome Study Section, National Library of Medicine, 6/2001
Grant
reviewer for NSF, 2003,2006
Grant
reviewer for California Breast Cancer Research Program, 2002, 2003, 2004
Grant reviewer for Genome
Special
Emphasis Review Panel, National Library of Medicine,2006-2007
ACMI Scientific Affairs Committee, 2003-2004
Chair,
Board of Scientific Counselors,
Board
of Regents, National Library of Medicine, 2007-2011
Extramural
Committee, Board of Regents, National Library of Medicine, 2007-2011
National
Health Standards Working Group, National Library of Medicine, 2008-2010
Publications
Peer Reviewed Articles
Grishman
R, Sager N, (Friedman) Raze C, and Bookchin B. The linguistic string parser. In AFIPS Conference
Proceedings, AFIPS Press,
*(Friedman)~Raze C. A computational
treatment of coordinate conjunctions. American
Association of Computational Linguistics, 1976, 52.
Grishman R, Hirschman L, and Friedman C. Isolating
domain dependence in natural language interfaces. In
Proceedings of the Conference on Applied Natural Language Processing, Association
for Computational Linguistics, Menlo Park, CA, 1983, pp 46--53.
*Friedman C and Sager N et al. Computer structuring of free-text patient data.
In Dayhoff R, editor, Proceedings of the Seventh
Annual Symposium on Computer Applications in Medical Care (SCAMC7), pp
688--691.
Chi E, Friedman C, Sager N, and Lyman MS. Processing free-text input to obtain
a database of medical information. In Proceedings of the 8th Annual ACM-SIGIR
Conference on Research and Development in Information Retrieval, Association
for Computing Machinery, New York, 1985.
Marsh E and Friedman C. Transporting the linguistic string project system for a
medical to a navy domain. ACM Transactions on Office Automation Systems, 1985,
3(2):121--140.
Sager N, Chi E, Friedman C, and Lyman MS. Modeling natural language data for
automatic creation of a database from free-text input. Database Engineering,
1985, 8(3):45--55.
Chi E, Lyman MS, Friedman C, and Macleod C. A database
of computer-structured narrative: methods of computing complex relations. In
Ackerman MJ, editor, Proceedings of the 9th Annual Symposium on Computer
Applications in Medical Care (SCAMC9), IEEE Computer Society Press, Washington,
DC., 1985.
Lyman MS, Sager N, Friedman C, and Chi E. Computer-structured narrative in ambulatory
care: its use in longitudinal review of clinical data. In Ackerman MJ, editor,
Proceedings of the 9th Annual Symposium on Computer Applications in Medical
Care (SCAMC9), IEEE Computer Society Press,
Sager N, Friedman C, and Lyman MS et al. The analysis and processing of clinical narrative. In Salamon R, Blum M, and Jorgensen M, editors, Proceedings of
the Fifth World Congress on Medical Informatics (MEDINFO 86), North Holland,
1986, pp 1101--1105.
*Friedman C. A computational treatment of the comparative.
In Proc. of the 27th Annual Meeting of the Association for Computational
Linguistics, Association for Computational Linguistics, Morristown, New Jersey,
1989, pp 161--168.
*Friedman C, Hripcsak G, Johnson SB, Cimino JJ, and Clayton PD. A generalized relational schema for an integrated clinical patient
database. In Proceedings of the Fourteenth Annual
Symposium on Computer Applications in Medical Care, IEEE Computer Society
Press, Los Alamitos, CA, 1990, pp 335--339. PMCID: PMC2245527.
Cimino JJ, Hripcsak G, Johnson SB, Friedman C, Fink
DJ, and Clayton PD. UMLS as knowledge base - a rule-based expert system
approach to controlled medical vocabulary management. In
Proceedings of the Fourteenth Annual Symposium on Computer Applications in
Medical Care, IEEE Computer Society Press, Los Alamitos, CA, 1990, pp 175--179.
Johnson SB, Cimino JJ, Hripcsak G, Friedman C, and
Clayton PD. Using metadata to integrate medical knowledge in a clinical system.
In Proceedings of the Fourteenth Annual Symposium on Computer Applications in
Medical Care , IEEE Computer Society Press,
Sideli RV and Friedman C. Validating patient names in an
integrated clinical information
system. In PD Clayton, editor, Proceedings of the Fifteenth Annual
Symposium on Computer Applications in Medical Care, Washington, D.C., 1991, pp
588--592. PMCID: PMC2247599.
Johnson SB, Friedman C, Cimino JJ,
Clark AS, Hripcsak G, and Clayton PD. A
conceptual schema for a central patient database. In PD Clayton, editor,
Proceedings of the Fifteenth Annual Symposium on Computer Applications in
Medical Care, Washington, D.C., 1991, pp 381--385. PMCID: PMC2247559.
*Friedman C and Sideli RV. Tolerating spelling errors during patient
validation. Computers and Biomedical Research, October
1992, 25:486--509.
Cimino JJ, Johnson SB, Hripcsak G, Sideli R, Fink D, Friedman C, and Clayton
PD. One year's experience with the unified medical lanugage system (UMLS) in academia and patient care.
In Proceedings of the Seventh World Congress on Medical
Informatics, North-Holland, New York, 1992. pp
1501--1505.
*Friedman C. The UMLS coverage of clinical radiology.
In Frisse ME, editor, Proceedings of the Sixteenth
Annual Symposium on Computer Applications in Medical Care, McGraw Hill, New
York, 1993, pp 309--313. PMCID: PMC2248002.
*Friedman C, Cimino JJ, and Johnson SB. A
conceptual model for clinical radiology reports.
In Safran C, editor, Seventeenth Symposium for
Computer Applications in Medical Care, McGraw-Hill, New York, 1994, pp
829--833.
*Friedman C, Alderson P, Austin J, Cimino JJ, and Johnson SB. A general natural language text processor for clinical radiology.
Journal of American Medical Informatics Association, March 1994, 1(2):161--174.
*Friedman C, Cimino JJ, and Johnson SB. A schema for
representing medical language. Journal of American Medical Informatics
Association, May 1994, 1(3):233--248.
*Friedman C, Huff SM, Hersh WH, Gordon EP, and Cimino JJ. The Canon effort:
working toward a merged model. Journal of American Medical Informatics
Association, Jan 1995, 2(1):4--18. PMCID: PMC116233.
*Friedman C, Starren J, and Johnson S. Architectural requirements for a
multipurpose natural language processor in the clinical environment. In Gardner
RM, editor, Proceedings of the Nineteenth Annual Symposium on Computer
Applications in Medical Care, 1995, pp 347--351. PMCID: PMC2579112.
Hripcsak G, Friedman C, Alderson PO, DuMouchel W,
Johnson SB, and Clayton PD. Unlocking clinical data from narrative reports.
Annals of Internal Medicine, May 1995, 122(9):681--688.
*Friedman C, Hripcsak G, DuMouchel W, Johnson SB, and
Clayton PD. Natural language processing in an operational clinical information
system. Natural Language Engineering, 1995, 1(1):1--28, 1995.
Du Mouchel W, Friedman C, Hripcsak
G, Johnson SB, and Clayton PD. Two applications of
statistical modelling to natural language processing. In Fisher VD and
Lenz H, editors, AI and Statistics,Springer-Verlag,
NY, 1996:413-421.
Jain NL, Knirsch C, Friedman C, and
Hripcsak G. Identification of suspected tuberculosis patients based on natural
language processing of chest radiography reports. In Cimino JJ, ed.
Proceeding of the fall 1996 AMIA Conference, Hanley & Belfus,
Philadelphia, 1996:542-546. PMCID: PMC2233236.
Johnson SB and Friedman C. Integrating data from natural
language processing into a clinical information system. In Cimino JJ,
ed. Proceeding of the fall 1996 AMIA Conference, Hanley & Belfus, Philadelphia, 1996:577-541. PMCID: PMC2233157.
*Friedman C and Hripcsak G. Evaluating natural language processors in the
clinical domain. In Chute CG, ed. Proceedings of the Conference on Natural
Language and Medical Concept Representation (IMIA WG6),
*Friedman C. Towards a comprehensive medical language processing systems:
methods and issues. In Proceedings of the fall 1997 AMIA
Conference. In Masys DR, ed. Proceedings of
the fall 1997 AMIA Conference, Hanley & Belfus,
Philadelphia, 1997:595-599. PMCID: PMC2233560,
Jain NL and Friedman C. Identification of findings suspicious for breast cancer
based on natural language processing of mammogram reports. In Masys DR, ed. Proceedings of the fall 1997 AMIA Conference,
Hanley & Belfus, Philadelphia, 1997:829-833.
PMCID: PMC2233320.
Hripcsak G, Kuperman GJ, and Friedman C. Extracting
findings from narrative reports: software transferability and sources of
physician disagreement. Methods of Information in Medicine, 1998:37:1-7.
Knirsch CA, Jain NL, Pablos-Mendez
A, Friedman C, and Hripcsak G. Respiratory isolation of tuberculosis patients
using clinical guidelines and an automated clinical decision support system.
Infection Control and Hospital Epidemiology, 1998:19(2):94-100.
*Friedman, C. and Hripcsak, G. Evaluating natural language processors in the
clinical domain. Meth Inf in Med. 1998;37:334-344.
* Friedman C, Hripcsak G, Shablinsky I. An evaluation of natural language processing methodologies. In Chute CG, ed. Proceedings 1998 AMIA Annual Symposium.
Phil: Hanley & Belfus, 1998; 855-859. PMCID:
PMC2232366.
*Friedman, C., Hripcsak, G., Shagina, L., and Liu, Hongfang. Representing information in
patient reports using natural language processing and the extensible markup
language. J Am Med Inf Assoc. 1999;6:76-87. PMCID: PMC61346.
Hripcsak, G., Kuperman, GJ.,
Friedman, C., and Heitjan DF. A
reliability study for evaluating information extraction from radiology reports.
J Am Med Inf Assoc. 1999;6:143-150.
PMCID: PMC61353.
*Friedman C, Knirsch CA, Shagina
L, Hripcsak G. Automating a severity score guideline for community-acquired
pneumonia employing medical language processing of discharge summaries. In Lorenzi NM, ed. Proceedings of 1999
AMIA Fall Annual Symposium. Phila.: Hanley & Belfus,
1999;256-260. PMCID: PMC2232753.
*Friedman, C. and Hripcsak, G. Natural language processing and its future in
medicine. Academic Medicine. 1999;74(8):890-895.
Shablinsky I, Starren J, Friedman C. What do ER
physicians really want? A method for elucidating ER information needs. In Lorenzi NM, ed. Proceedings of 1999
AMIA Fall Annual Symposium. Phila.: Hanley & Belfus,
1999;390-394. PMCID: PMC2232515.
Yu H, Friedman C, Rhzetsky A, Kra
P. Representing genomic knowledge in the UMLS semantic network. In Lorenzi NM, ed. Proceedings of 1999
AMIA Fall Annual Symposium. Phila.: Hanley & Belfus,
1999;181-186.
Elkins JS, Friedman C, Boden-Albala B, Sacco RL,
Hripcsak G. Coding neuroradiology reports for the northern manhattan
stroke study: a comparison of natural language processing and manual review.Comput Biomed Res. 2000;33:1-10.
Barrows RC, Busuioc M, and Friedman C. Limited
parsing of notational text visit notes: ad-ho vs. NLP approaches. In Overhage M, ed.. Proc AMIA Symp 2000, Phila: Hanley & Belfus, 2000;51-55. PMCID: PMC2243829.
*Friedman C. A broad coverage natural language processing system. In Overhage M, ed. Proc AMIA Symp 2000, Phila: Hanley & Belfus, 2000;270-274. PMCID:
PMC2243979.
Liu H and Friedman, C. A method for vocabulary development
and visualization based on medical language processing and XML. In Overhage M, ed. Proc AMIA Symp 2000, Phila: Hanley & Belfus, 2000; 502-506. PMCID: PMC2243989.
Krauthammer M, Rzhetsky A, Morozov P, Friedman C. Using BLAST for identifying gene and
protein names in journal articles. GENE 2000;259:245-52.
Rzhetsky
A, Koike T, Kalachikov SM, Gomez M, Krauthammer SH,
Kaplan P, Kra P, Russo JJ, Friedman C. A knowledge model for analysis and simulation of regulatory
networks. Bioinformatics 2000;16(12):1120-28.
*Friedman C, Kra P, Krauthammer M, Yu H, Rzhetsky A. GENIES: a natural-language processing system
for the extraction of molecular pathways from journal articles. Bioinformatics
2001:suppl1:S74-82.
*Friedman C, Liu H, Shagina L, Johnson SB, Hripcsak
G. Evaluating the UMLS as a source of lexical knowledge for medical language
processing. Proc AMIA Symp
2001, Phila: Hanley & Belfus,
2001;189-193. PMCID: PMC2243298.
Liu H, Friedman C. A study of abbreviations in the UMLS.
Proc AMIA Symp 2001, Phila: Hanley & Belfus, 2001;393-397. PMCID: PMC2243414.
Lussier Y, Friedman C. Automating SNOMED coding using
medical language understanding: a feasibility study. Proc
AMIA Symp 2001, Phila:
Hanley & Belfus, 2001;418-422.
PMCID: PMC2243482.
Liu H, Lussier Y, Friedman C. Disambiguating
ambiguous biomedical terms in biomedical narrative text: an unsupervised
method. Journal of Biomedical Informatics 2001;34:249-261.
Yu H, Hripcsak G, Friedman C. Mapping abbreviations to full forms in biomedical
articles. J Am Med Inf Assoc
2002;9(3):262-272.
Yu H, Hatzivassiloglou, Friedman C,
Rzhetsky A, Wilbur J. Automatic extraction of gene
and protein synonyms from MEDLINE and journal articles. Proc
AMIA Symp 2002: 919-923. PMCID: PMC2244511.
Hripcsak G, Austin JHM, Alderson PO, Friedman C. A
database of 889,921 chest radiographic reports: use of natural language
processing to translate information. Radiology 2002;224(1):157-163.
PMCID: PMC344586.
Liu H, Johnson S, Friedman C. Automatic Construction of Sense-Tagged Corpora
Based on Conceptual Relations in the UMLS. J Am Med Inf
Assoc 2002;9(6):621-636.
Krauthammer M, Kra P, Iossifov
I, Gomez SM, Hripcsak G, Hatzivassiliglou V, Friedman
C, Rzhetsky A. Of truth and pathways: chasing bits of
information through myriads of articles. Bioinformatics 2002;18
Suppl 1:S249-S257.
Liu H, Lussier Y, Friedman C. Disambiguating
ambiguous biomedical terms in biomedical narrative text: an unsupervised
method. J Biomed Inform 2001 (published online Jan 22, 2002); 34:249-261.
Liu H, Johnson SB, Friedman C. Automatic resolution of
ambiguous terms based on machine learning and conceptual relations in the UMLS.
J Am Med Inf Assoc: 2002; 9(6):621-636. PMCID: PMC349379.
Liu H, Aronson AR, Friedman C. A study of abbreviations in
MEDLINE abstracts. 2002 AMIA Symp:2002:464-469 (paper
finalist). PMCID: PMC2244212.
Krauthammer M, Johnson SB, Hripcsak G, Campbell DA, Friedman
C. Representing nested semantic information in a linear string of text using
XML. 2002 AMIA Symp; 2002:405-409. PMCID: PMC2244450.
Chuang JC, Friedman C, Hripcsak G. A comparison of Charlson
comorbidities derived from medical language processing and administrative data.
2002 AMIA Symp; 2002:160-164 (paper finalist;
nominated for Homer award). PMCID: PMC2244199.
Yu H, Hatzivassiloglou V, Friedman F, Rzhetsky A, Wilbur J. Automatic Extraction of Gene and
Protein Synonyms from MEDLINE and Journal Articles. 2002 AMIA Symp; 2002:919-923.
*Friedman C, Kra P. Two biomedical sublanguages: a
description based on the theories of Zellig Harris. J
Biomed Inform: 2002 published online April 2003; 35(4):225-235.
Liu H, Friedman C. Mining terminological knowledge using parenthetical
expressions in large corpora. 2003
*Friedman C, Liu H, Shagina L. A
vocabulary development and visualization tool based on natural language processing
and the mining of textual patient reports. J Biomed Inform; 2003 Jun;36(3):189-201.
Chen L, Friedman C. Extracting phenotypic information from the literature via
natural language processing.Medinfo. 2004;11(Pt 2):758-62.
Tuason O, Chen L, Liu H, Blake JA, Friedman C.
Biological nomenclatures: a source of lexical knowledge and ambiguity. Pac Symp Biocomput.
2004;:238-49.
Liu H, Friedman C. CliniViewer: a tool for viewing
electronic medical records based on natural language processing and XML. Medinfo.
2004;11(Pt 1):639-43.
Xu H, Anderson K, Grann VR,
Friedman C. Facilitating cancer research using natural language processing of
pathology reports. Medinfo. 2004;11(Pt 1):565-72.
Bakken S, Hyun S, Friedman C, Johnson SB. A comparison of semantic categories
of the ISO reference terminology models for nursing and the MedLEE
natural language processing system. Medinfo. 2004;11(Pt 1):472-6.
*Friedman C, Shagina L, Lussier
YA, Hripcsak G. Automated encoding of clinical documents based on natural
language processing.J Am Med Inform Assoc. 2004
Sep-Oct;11(5):392-402. Epub 2004 Jun 7. PMCID:
PMC516246.
Iossifov
I, Krauthammmer M, Friedman C, Hatzivassiloglou
V, Bader JS, White KP, Rzhetsky A. Probabilistic
inference of molecular networks from noisy data sources. Bioinformatics. 2004 May 22;20(8):1205-13.
Epub 2004 Feb 10.
Liu H, Teller V, Friedman C. A multi-aspect comparison study
of supervised word sense disambiguation. J Am Med Inform Assoc. 2004
Jul-Aug;11(4):320-31. Epub
2004 Apr 2. PMCID:
PMC436083.
Rzhetsky A, Iossifov
I, Koike T, Krauthammer M, Kra P, Morris M, Yu H, Duboue PA, Weng W, Wilbur WJ, Hatzivassilogou
V, Friedman C. GeneWays: a system for extracting,
analyzing, visualizing, and integrating molecular pathway data. J Biomed
Inform. 2004 Feb;37(1):43-53.
Chen L, Liu H, Friedman C. Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics. 2005 Jan 15;21(2):248-56.
Epub 2004 Aug 27.
Tao,Y, Liu,Y,
Friedman,C. and Lussier,YA.
The use of information visualization techniques in
bioinformatics during the postgenomic era. Drug Discov. Today:BIOSILICO.
2004;2(6):237-245.
Tao Y, Friedman C, Lussier YA.
Visualizing information across multidimensional post-genomic
structured and textual databases.Bioinformatics.
2005 Apr 15;21(8):1659-67. Epub
2004 Dec 14.
Mendonca EA, Haas J, Shagina
L, Larson E, Friedman C. Extracting information on pneumonia in infants using
natural language processing of radiology reports. J Biomed Inform. 2005 Aug;38(4):314-21. Epub 2005 Mar 30.
Hass JP, Mendonca EA, Ross B, Friedman C, Larson E.
Use of computerized surveillance to detect nosocomial pneumonia in neonatal
intensive care unit patients. Am J Infect Control.
2005 Oct;33(8):439-43.
Zhou L, Tao Y, Cimino JJ, Chen ES, Liu H, Lussier YA,
Hripcsak G, Friedman C. Terminology model discovery using natural language
processing and visualization techniques. J Biomed Inf
(in press).
Bakken S, Hyun S, Friedman C, Johnson SB. ISO reference terminology models for
nursing: applicability for natural language processing of nursing narratives. Int J Med Inf. 2005;74:615-622.
Zhou L, Friedman C, Parsons S, Hripcsak G. System architecture for temporal
information extraction, representation, and reasoning in clinical narrative
reports.2005 AMIA Symp. 2005:869-874. PMCID:
PMC1560711.
Bales ME, Kukafka R, Burkhardt A, Friedman C. Qualitative
assessment of International Classification of Functioning, Disability, and
Health with respect to the desiderata for controlled medical vocabularies.
Int J Med Inform. 2005 Aug 22; Epub
Aug 22.
Lussier YA, Borlawski T,
Rappaport D, Liu Y, Friedman C. PhenoGO:
assigning phenotypic context to Gene Ontology annotations with natural language
processing. Pac Symp Bio.
2006:64-75.
Tulipano P.K., Tao Y, Millar WS, Zanzonico P, Kolbert K, Xu H, Yu
H, Chen L, Lussier YA, Friedman C. Natural language
processing and visualization in the molecular imaging domain. J.Biomed.Inform. 2006 Sep 26. (DOI:http://dx.doi.org/10.1016/j.jbi.2006.08.002).
PMCID:
PMC1560602.
Friedman C, Borlawsky T, Shagina L, Xing HR, Lussier YA. Bio-Ontology and
text: bridging the modeling gap. Bioinformatics. 2006
Oct 1;22(19):2421-9.
Liu
H, Hu ZZ, Torii M, Wu C, Friedman C. Quantitative assessment of
dictionary-based protein named entity tagging. J.Am.Med.Inform.Assoc.
2006 Sep;13(5):497-507. PMCID: PMC1561801.
Kukafka R, Bales
ME, Burkhardt A, Friedman C. Human and automated coding of rehabilitation
discharge summaries according to the International Classification of
Functioning, Disability, and Health. J.Am.Med.Inform.Assoc.
2006 Sep;13(5):508-15. PMCID: PMC1561799.
Zhou L, Tao Y,
Cimino JJ, Chen ES, Liu H, Lussier YA, Hripcsak G,
Friedman C. Terminology model discovery using natural language processing and
visualization techniques. J.Biomed.Inform. 2006 Dec;39(6):626-36.
Chen ES, Hripcsak
G, Friedman C. Disseminating natural language processed clinical narratives. In Proc 2006 AMIA Symp;
2006. p. 126-30. PMCID: PMC1839529.
Borlawsky T, Friedman C, Lussier Y. Generating executable knowledge for
evidence-based medicine using natural language and semantic processing. In Proc. AMIA 2006 Symp; 2006. p.
56-60. PMCID:
PMC1839756.
Hristovski D,
Friedman C, Rindflesch T, Peterson BJ. Exploiting semantic
relations for literature-based discovery. In Proc AMIA 2006 Symp; 2006.
p. 349-53. PMCID:
PMC1839258.
Xu H, Markatou M, Dimova R, Liu H,
Friedman C. Machine learning and word sense disambiguation in the biomedical
domain: design and evaluation issues. BMC Bioinformatics.
2006;7:334.
Sam L, Liu Y, Li Jianrong, Friedman C, Lussier YA. Discovery of protein interaction networks shared by diseases.
Pac Symp Bio.
2007:76-87.
Xu H, Fan JW, Hripcsak G, Mendonca EA, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics. 2007 Apr 15;23(8):1015-22. PMID:17314123.
Tao
Y, Sam L, Li J, Friedman C, Lussier YA.
Information theory applied to the sparse gene ontology annotation network to
predict novel gene function. Bioinformatics. 2007 Jul
1;23(13):i529-38.
Hristovski
D, Friedman C, Rindflesch T. Implementing a
literature-based discovery system using semantic relations. Medinfo 2007.
Xu H, Fan JW,
Hripcsak G, Mendonca EA, Markatou
M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics. 2007 Apr 15;23(8):1015-22.
Epub 2007 Feb 21.