Curriculum
Vitae
Carol
Friedman
Date of Preparation: 8/31/2007
Personal
Data
Name:
Carol Friedman
Birthplace:
Citizenship:
Academic
Training
1989 Ph.D. Computer Science,
1986. M.A.
Computer Science,
1962. B.S. Mathematics, City College CUNY, magna cum laude, elected to
Phi Beta Kappa
Academic
Appointments
|
7/2002 |
-present |
Professor, Department of
Biomedical Informatics, |
|
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
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,
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
NIH from NLM (R01LM008635),
PI, 7/1/05-6/30/09 ($2,179,256)
NIH from NLM (R01LM007659), PI, 7/1/03-6/30/08 ($1,650,889)
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 ($18,547,875
first year)
Previous
Grant Support
NIH from
NLM (R01GN01372), co-PI (PI:Rzhetsky),
7/1/01-6/30/03 ($1,207,500)
NIH
S2114-22/22, co-PI, (PI:Kukafka), 10/1/02-9/30/04
($159,984)
NIH from NLM, (R01LM07268), investigator (PI:Johnson),
7/01/2002-6/30/2005 ($1,193,058)
NIH from NLM (R01LM0610), (PI:Hripcsak),
04/01/2000-03/31/2006 ($2,423,532)
EIA from NSF (EIA-0312250), PI, 2/1/03-1/31/04 ($100,000)
NIH from NLM (R01LM06274), PI, 7/1/97-12/31/2003 ($1,573,467)
NSF ITR/IM+AP, co-PI, (PI:Rzhetsky), 9/1/01-8/31/03
($1,000,000)
AHRQ R18 HS11806 , investigator, (PI:Hripcsak),
10/01/01-9/30/04 ($1,085,608)
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 Lernout and Hauspie, 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)
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, Medical Informatics, Columbia University,
2002-present
Ad-hoc
Tenure Committee,
Training
Committee, Columbia University, 2007-present
Executive
Committee, Columbia University, 2007-present
Teaching
Experience and Advising
Database
Management Systems
Programming Language Theory
Natural Language Programming
Data Structures
Software Design
Independent Study
Research
Seminar
Text
mining
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-present
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-present. Triaging MRI images to detect patients with stroke
Li Zhou, 2004-present. NLP and analysis of time.
Ying Tao, 2004-present. Knowledge discovery and
visualization with NLP
Michael
Bales, 2004 - Investigating feasibility of ICF coding of clinical
rehabilitation reports
Jung-Wei Fan, 2005-present. Automated semantic classification to improve UMLS
Xiaoyan Wang, 2007-present.
Finding associations between biomedical entities using NLP
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
Michael
Bales, 2005-present
Li Zhou, 2005-2007
Trevor Cohen, 2005-2007
Karina Tulipano, 2004-present. Triaging MRI images to detect patients with stroke
Other
Professional Activities
AMIA
Publications Committee – 1998-2004
Editorial Board of Journal of American Medical Informatics Association,
1999-present
Editorial Board of Journal of Biomedical Informatics, 2001-present
Editorial Board of Journal of Biomedcal Discovery and
Collaboration, 2005-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
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
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-present
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,
*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,
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,
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.
Johnson SB, Friedman C, Cimino JJ,
*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,
*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.
*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.
*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.
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,
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.
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.
*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.
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.
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.
*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.
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.
*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
*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
Yu H, Friedman C, Rhzetsky A, Kra
P. Representing genomic knowledge in the UMLS semantic network. In
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.
*Friedman C. A broad coverage natural language processing
system. In Overhage M, ed. Proc AMIA Symp 2000, Phila: Hanley & Belfus, 2000;270-274
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.
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-langauge
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.
Liu H, Friedman C. A study of abbreviations in the UMLS.
Proc AMIA Symp 2001, Phila:
Hanley & Belfus, 2001;393-397.
Lussier Y, Friedman C. Automating SNOMED coding using
medical language understanding: a feasibility study. Proc AMIA Symp 2001, Phila: Hanley & Belfus, 2001;418-422.
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.
Hripcsak
G,
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.
Liu H, Aronson AR, Friedman C. A study of abbreviations in MEDLINE abstracts.
2002 AMIA Symp:2002:464-469 (paper finalist).
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..
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).
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.
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.
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.
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)
*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.
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.
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.
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.
Hristovski D, Friedman C, Rindflesch
T, Peterson BJ. Exploiting semantic relations for
literature-based discovery. In Proc AMIA 2006 Symp; 2006. p. 349-53.
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 shoared 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. Epub 2007 Feb 21.
Fan JW, Xu H, Friedman C. Using
distributional analysis to semantically classify UMLS concepts. Medinfo 2007 (in press).
Hristovski
D, Friedman C, Rindflesch T. Implementing
a literature-based discovery system using semantic relations. Medinfo 2007 (in
press).
Xu H, Fan
JW, Friedman C. Combining multiple evidence for gene
symbol disambiguation. In Proc BioNLP
Workshop 2007 (in press).
Fan
JW, Friedman C. Classification of biomedical concepts using distributional
similarity. J.Am.Med.Inform.Assoc. 2007 Jul-Aug;14(4):467-77. Epub 2007 Apr 25.
Fan JW, Xu
H, Friedman, C. Using contextual and lexical features
to restructure and validate the classification of biomedical concepts. BMC Bioinformatics. 2007 Jul 24;8(1):264
[Epub ahead of print]
Reviews,
Books, Chapters, Articles
*(Friedman)
Raze C. The Parsing and Transformational Expansion of
Coordinate Conjunction Strings}. String Program
Reports 11, Linguistic String Project,
Sager N, Gordon D, Marsh E, Hirschman L, and Friedman C et
al. Computer-Based Investigation into the Structure of Information. String Program Reports 15, Linguistic String Project,
Sager N, Tick LJ, Story G, Friedman C, and Christenson C. Data model for
natural language information. ACM-SIGART Newsletter, (86),
1983.
Sager N, Johnson S, Macleod C, Kosaka
M, Friedman C, and Chi E. Computable Models of Time and Quantity in Natural
Language Data. String Project Reports 16, Linguistic
String Project,
*Friedman C. Sublanguage text processing -- application to medical narrative.
In Grishman R and Kittredge R, editors, Analyzing
Language in Restricted Domains, Lawrence Erlbaum, Hillsdale, NJ, 1986, pp
85--102.
Sager N, Friedman C, and Lyman MS et al. Medical Language Processing: Computer
Management of Narrative Data. Addison-Wesley,
*Friedman C. Editorial, Journal of Biomedical Informatics:2002;35:213-214
(published online April 2003).
Chun H, Fuller SS, Friedman C, Hersh W, eds.
Knowledge Management and Data Mining in Biomedicine. Springer,
NY, 2005.
*Friedman C. Semantic text parsing for patient records. In Chun H, Fuller SS,
Friedman C, Hersh W, eds. Knowledge Management and
Data Mining in Biomedicine. Springer, NY, 2005.
Rzhetsky A, Iossifov I,
Koike T, Krauthammer M, Kra P, Morris M, Yu H, Dubhoue PA, Eng W, Wilbur JW, Hatzivassiloglou
V, Friedman C. GeneWays: a system for extracting,
analyzing, visualizing, and integrating molecular pathway data. In Koslow SH, Subramaniam
S, eds. Databasing the Brain. Wiley & Sons:2005;241-250.
*Friedman
C, Johnson SB. Natural language and text processing in biomedicine. In Shortliffe EH, Cimino JJ, eds. Biomedical
Informatics: Computer Applications in Health Care and Biomedicine. Springer, NY, 2006.
Abstracts
Starren J,
Friedman C, and Johnson S. Design and development of the
Starren J, Friedman C, and Johnson S. The
*Friedman C, Shagina L, Socratous
SA, and Zeng X. A WEB-based version of MedLEE: A medical language extraction and encoding system ,
In Cimino JJ, ed. Proceeding of the fall 1996 AMIA
Conference, Hanley & Belfus, Philadelphia,
1996:938.
Wilcox A, Friedman C, Hripcsak G.
Natural language as a tool in the development of a controlled vocabulary.
In Chute, CG, ed. Proceedings 1998 AMIA Annual Symposium.
Phil: Hanley & Belfus, 1998; 1098.
Rosenthal D, and Friedman C. Theater-style
demonstration: continuous-speech structured reporting. In
Chute, CG, ed. Proceedings 1998 AMIA Annual Symposium. Phil: Hanley
& Belfus, 1998:1116.
Rzhetsky A, Koike T, Kalachikov
S, Kra P, Friedman C. A knowledge
model for analysis and simulation of regulatory network based on information in
electronic publications. In
Lussier YA, Friedman C, Shagina
L, Eng P. Automating ICD-9-CM encoding using medical language processing: a
feasibility study. Proc AMIA Symp 2000:1072.
Shablinsky I, Starren J,
Friedman C. Knowledge-driven highlighting of clinical texts: does it help or
distract. Proc AMIA Symp 2000:1134.
Krauthammer M, Rzhetsky A, Morozov
P, Friedman C. Using BLAST, a DNA and protein sequence comparison tool for
finding gene and protein names in journal articles. Proc AMIA Symp 2000:1052.
Xu H,
Friedman C. Facilitating Research in Pathology using Natural Language
Processing. Proc AMIA Symp: 2003;:1057.
Hyun S, Bakken S, Friedman C, Johnson SB. Natural
Language Processing Challenges in HIV/AIDS Clinic Notes. Proc
AMIA Symp. 2003;:872.
Johnson SB,
Bales ME, Kukafka R, Burkhardt A, Friedman C. Extending a medical language
processing system to the functional status domain. AMIA Annu Symp
Proc. 2005;:888.
Xu
H, Krupke D., Blake J., Friedman C. A natural
language processing (nlp) tool to assist in the curation of laboratory mouse tumor biology database. In Proc 2006 AMIA Symp; 2006. p. 1150.