Acknowledgements:

This Human Brain Project/Neuroinformatics research is funded jointly by the National Library of Medicine and the National Institute of Mental Health. This site utilizes a modified version of the Entrez/PubMed search interface to Medline. The Medline database and the MMTx program (a Java implementation of the MetaMap algorithm) were graciously provided by the National Library of Medicine. The NeuroNames 2002 CD was provided by Prof. Douglas M. Bowden of the University of Washington. The Gene and Protein Name database was provided by Lorraine Tanabe and W. John Wilbur of the National Center for Biotechnology Information. Thanks to Matt Janicak for designing the website logo.

References

• Arrowsmith and other text mining references
• Others who have reviewed, replicated or assessed our tools
• The process of scientific discovery
• MicroRNA and bioinformatics studies
• Other publications

Arrowsmith and other text mining references:

Smalheiser NR. (2017) Rediscovering Don Swanson:The Past, Present and Future of Literature-based Discovery. Journal of Data and Information Science.

Peng, Y., Bonifield, G. and Smalheiser, N. R. (2017) Gaps within Biomedical Literatures: Strategies for Discovery. Frontiers in Research Metrics & Analytics.

Kehoe, A., Torvik, V., Ross, M. and Smalheiser, N. Predicting MeSH beyond MEDLINE. Workshop on Scholarly Web Mining '17. February 10, 2017, Cambridge, UK. DOI 10.1145/3057148.3057155.

De Groote, S. L., Schulz, M., and Smalheiser, N. R. (2015) Examining the impact of the National Institutes of Health Public Access Policy on the citation rates of journal articles. PLoS ONE 10(10): e0139951. Won the 2016 Ida and George Eliot Prize of the Medical Library Association. doi: 10.1371/journal.pone.0139951

D'Souza, J.L. and Smalheiser, N.R. (2014) Three journal metrics and their application to biomedical journals. PLoS ONE 9(12): e115681.

Smalheiser NR. Literature-based discovery: beyond the ABCs. J. Am. Information Sci. Technol. 2011. 63: 218-224.

Smalheiser NR, Zhou W, Torvik VI. Distribution of "Characteristic" Terms in MEDLINE Literatures. Information 2011; 2(2):266-276.

Swanson DR. Literature-based Resurrection of Neglected Medical Discoveries. J Biomed Discov Collab. 2011 Apr 20;6:34-47. doi: 10.5210/disco.v6i0.3515.

Torvik VI, Smalheiser NR. Author name disambiguation in MEDLINE. ACM Transactions on Knowledge Discovery from Data 2009, 3(3):11.

Smalheiser NR, Torvik VI, Zhou W. Arrowsmith two-node search interface: A tutorial on finding meaningful links between two disparate sets of articles in MEDLINE. Comput Meth Program Biomed. 2009; 94(2): 190-197.
A preprint version of this paper is available here

Smalheiser NR, Torvik VI. Author name disambiguation. In Annual Review of Information Science and Technology (B. Cronin, Ed.), Vol. 43 (2009), pp. 287-313.
A preprint version of this chapter is available here, and the final print version is available from the publisher Information Today, Inc.

Smalheiser NR, Torvik VI. The place of literature-based discovery in contemporary scientific practice. In: Literature-based discovery (M. Weeber, P. Bruza, Eds.), Springer, 2008. pp 13-22.
A preprint version of this chapter is available here.

Swanson DR. Running, esophageal acid reflux, and atrial fibrillation: A chain of events linked by evidence from separate medical literatures. Med Hypotheses. 2008. Epub May 2.

Smalheiser NR, Zhou W, Torvik, VI. Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results. J Biomed Discov Collab. 2008; 3:2. Epub Feb 15.

Torvik VI, Smalheiser NR. A quantitative model for linking two disparate sets of articles in Medline. Bioinformatics 2007; 23(13): 1658-1665. Supplementary figures and tables.

Zhou W, Yu C, Smalheiser N, Torvik V, Hong J. Knowledge-intensive conceptual retrieval and passage extraction of biomedical literature. Proc. 30th Ann. Intl. ACM SIGIR Conf. on Research & Development on Information Retrieval, in press (this conference was peer-reviewed and had overall 18% acceptance rate).

Zhou W, Torvik VI, Smalheiser NR. ADAM: another database of abbreviations in Medline. Bioinformatics 2006; 22(22): 2813-2818.

Torvik VI, Smalheiser NR. Author name disambiguation in MEDLINE. Presented at Workshop for Scholarly Databases & Data Integration, Indiana University, Bloomington, IN. August 31, 2006.

Smalheiser NR, Torvik VI, Bischoff-Grethe A, Burhans LB, Gabriel M, Homayouni R, Kashef A, Martone ME, Perkins GA, Price DL, Talk AC, West R. Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators. J Biomed Discov Collab. 2006 Jul 3;1(1):8.

Smalheiser NR. Aiding biomedical researchers with tools to assist discovery. AMIA Spring Congress 2006.

Swanson DR, Smalheiser NR, Torvik VI. Ranking indirect connections in literature-based discovery: The role of Medical Subject Headings (MeSH). JASIST 2006;57(11):1427-1439.

Swanson DR. Atrial fibrillation in athletes: Implicit literature-based connections suggest that overtraining and subsequent inflammation may be a contributory mechanism. Med Hypotheses. 2006;66(6):1085-92.

Zhang W, Yu C, Smalheiser NR, Torvik VI. Segmentation of publication records of authors from the web. Proceedings of the 22nd IEEE International Conference on Data Engineering (ICDE'06). Atlanta, GA. April, 2006. Download the datasets and Java programs used in the experiments (130 MB).

Smalheiser, NR. The Arrowsmith Project: 2005 Status Report. Invited address at the 8th International Conference on Discovery Science and the 16th International Conference on Algorithmic Learning Theory, October 8-11, 2005, Singapore. Lecture Notes in Artificial Intelligence (A. Hoffman, H. Motoda, and T. Scheffer, Editors) 3735:26-43. Lecture Notes in Computer Science Series. Copyright Springer-Verlag.

Smalheiser NR, Perkins GA, Jones S. Guidelines for negotiating scientific collaborations. Formally endorsed by the AMIA Working Group on Ethical, Legal and Social Issues. PLoS Biology 2005; 3(6): e217.

Torvik VI, Weeber M, Swanson DR, Smalheiser NR. A probabilistic similarity metric for Medline records:a model for author name disambiguation. JASIST 2005; 56(2): 140-158.

Brown GG, Pieper S, Martone M, Aucoin N, Joyner A, Bischoff-Grethe A, Torvik V. The Query Atlas: A brain referenced knowledge discovery tool. Society for Neuroscience Annual Meeting, 2004.

Smalheiser NR. Knowledge Discovery in Medline and Other Databases. In: "The Bioinformatics of Brains: From Genes and Proteins to Behaviors." (Williams RW, ed.) pp. 9-16. Washington, DC: Society for Neuroscience 2003. Powerpoint slides

Smalheiser NR. Linking investigators. A centralized linking facility for data sharing and coordination of samples in tissue banks. EMBO Reports 2003; 4: 108-110. Link to EMBO Reports.

Swanson DR. An introduction to Medline searching. Presented at the Arrowsmith Project short course, UIC Psychiatric Institute, September 3-5, 2003.

Smalheiser NR, Swanson DR, Torvik VI, Palmer C, Cragin M, Hogan T, West R, Bischoff-Grethe A, Yu C. (presenters) Informatics tools for scientific discovery and collaboration. Arrowsmith Project short course, UIC Psychiatric Institute, September 3-5, 2003.

Smalheiser NR, Yu C, Torvik VI, Wu Z, Raghavan V, Qian H, Meng W. SE-Album: A SELEGO Application in Integrated Retrieval From Multiple Online Bio-Informatics Search Systems Poster presented at the 2003 BISTI Symposium "Digital Biology: The Emerging Paradigm".

Smalheiser NR. What every Psychiatric Researcher should know about Informatics, presented at the International Congress on Schizophrenia Research, March 29 - April 2, 2003.

Gardner D, Toga AW, Ascoli GA, Beatty JT, Brinkley JF, Dale AM, Fox PT, Gardner EP, George JS, Goddard N, Harris KM, Herskovits EH, Hines ML, Jacobs GA, Jacobs RE, Jones EG, Kennedy DN, Kimberg DY, Mazziotta JC, Miller PL, Mori S, Mountain DC, Reiss AL, Rosen GD, Rottenberg DA, Shepherd GM, Smalheiser NR, Smith KP, Strachan T, Van Essen DC, Williams RW, Wong ST. Towards effective and rewarding data sharing. Neuroinformatics. 2003;1(3):289-95.

Smalheiser NR. Informatics and hypothesis-driven research. EMBO Reports 2002; 3: 702. Link to EMBO Reports.

Smalheiser NR, Torvik VI, Weeber M, Swanson DR. The Arrowsmith Project: New Tools to assist Biomedical Discovery and Collaboration, presented at the Beckman Institute, University of Illinois at Urbana-Champaign, October 1, 2002.

Torvik VI, Weeber M, Smalheiser NR, Swanson DR. Identifying Authors that Link Disparate Literatures, poster presented at the Human Brain Project annual meeting, Bethesda, MD, May 6-7, 2002.

Swanson DR, Smalheiser NR, Bookstein A. Information discovery from complementary literatures: categorizing viruses as potential weapons. JASIST 2001; 52: 797-812.

Smalheiser NR. Predicting emerging technologies with the aid of text-based data mining: a micro approach. Technovation 2001; 21: 689-693.

Smalheiser NR. Arrowsmith Data Mining Techniques in Neuro-Informatics. National Institutes of Health R01 proposal, 2000.

Swanson DR, Smalheiser NR. Implicit text linkages between Medline records: using Arrowsmith as an aid to scientific discovery. Library Trends 1999; 48: 48-59.

Smalheiser NR, Swanson DR. Calcium-independent phospholipase A2 and schizophrenia. Arch. Gen. Psychiat. 1998; 55: 752-753.

Smalheiser NR, Swanson DR. Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. Computer Methods and Programs in Biomedicine 1998; 57: 149-153.

Swanson DR, Smalheiser NR. An interactive system for finding complementary literatures: a stimulus to scientific discovery. Artificial Intelligence 1997; 91: 183-203.

Smalheiser NR, Swanson DR. Indomethacin and Alzheimer s Disease. Neurology 1996; 46: 583.

Smalheiser NR, Swanson DR. Linking estrogen to Alzheimer's Disease: an informatics approach. Neurology 1996; 47: 809-810.

Smalheiser NR, Swanson DR. Assessing a gap in the biomedical literature: magnesium deficiency and neurologic disease. Neurosci. Res. Commun. 1994; 15: 1-9.

Swanson DR. Intervening in the life cycles of scientific knowledge. Library Trends 1993; 41: 606-631.

Swanson DR. Complementary structures in disjoint science literatures. in Bookstein, A., Chiaramella, Y., Salton, G. & Raghavan, V. V., eds., SIGIR 1991 Proceedings of the Fourteenth Annual International ACM/SIGIR Conference on Research and Development in Information Retrieval, Chicago, (ACM Press, NY). 280-289.

Swanson DR. Somatomedin C and arginine; implicit connections between mutually-isolated literatures, Perspect. Biol. Med. 1990; 33: 157-186.

Swanson DR. The absence of co-citation as a clue to undiscovered causal connections. in Borgman, C. L., ed. Scholarly Communication and Bibliometrics (Sage Publ., Newbury Park, CA). 1990; 129-137.

Swanson DR. Medical literature as a potential source of new knowledge. Bull. Med. Libr. Assoc. 1990; 78: 29-37.

Swanson DR. Online search for logically-related noninteractive medical literatures: A systematic trial-and-error strategy. JASIS 1989; 40: 356-358.

Swanson DR. Migraine and magnesium: eleven neglected connections. Perspect. Biol. Med. 1988; 31: 526-557.

Swanson DR. Two medical literatures that are logically but not bibliographically connected. JASIS 1987; 38: 228-233.

Swanson DR. Undiscovered public knowledge. Library Quarterly 1986; 56: 103-118.

Swanson DR. Fish oil, Raynaud's Syndrome, and undiscovered public knowledge. Perspect. Biol. Med. 1986; 30: 7-18.

Swanson DR. New Horizons in psychoanalysis: Treatment of necrosistic personality disorders. Perspectives in Biology and Medicine, 29, Summer 1986, pp. 493-498.

Others who have reviewed, replicated or assessed our tools:

Engwall, K. D. (2017). Anne O'Tate. Journal of the Medical Library Association: JMLA, 105(2), 200-202. http://doi.org/10.5195/jmla.2017.92

Lerchenmueller MJ, Sorenson O. Author Disambiguation in PubMed: Evidence on the Precision and Recall of Author-ity among NIH-Funded Scientists. PLoS One. 2016 Jul 1;11(7):e0158731. doi: 10.1371/journal.pone.0158731.

Liu W, Islamaj Dogan R, Kim S, Comeau DC, Kim W, Yeganova L, Lu Z, Wilbur WJ. Author Name Disambiguation for PubMed. J Assoc Inf Sci Technol. 2014 Apr;65(4):765-781. doi: 10.1002/asi.23063.

Bramer, W. M., Holland, L., Mollema, J., Hannon, T., & Bekhuis, T. (2014). Removing duplicates in retrieval sets from electronic databases: comparing the efficiency and accuracy of the Bramer-method with other methods and software packages. In Proceedings of the 14th European Association for Health Information and Libraries (EAHIL) Conference (pp. 57-9).

Lu, Z. (2011). PubMed and beyond: a survey of web tools for searching biomedical literature. Database, 2011. https://doi.org/10.1093/database/baq036.

Cohen T, Schvaneveldt R, Widdows D. Reflective Random Indexing and indirect inference: A scalable method for discovery of implicit connections. J Biomed Inform. 2009 Sep 15. [Epub ahead of print]

Yetisgen-Yildiz M, Pratt W. A new evaluation methodology for literature-based discovery systems. J Biomed Inform. 2009 Aug;42(4):633-43.

Bruza P, Weeber M. (Eds.) Literature-based discovery. Information Science and Knowledge Managemen Series, Vol. 15., Springer, 2008. This book has eleven chapters contributed by the leading researchers in the LBD field.

Kostoff RN. Literature-Related Discovery (LRD): Introduction and background. Technological Forecasting and Social Change 2008; 75(2): 165-185.

Kostoff RN, Briggs MB, Solka JL, Rushenberg RL. Literature-related discovery (LRD): Methodology. Technological Forecasting and Social Change 2008; 75(2): 185-202.

Kostoff RN, Block JA, Stump JA, Johnson D. Literature-related discovery (LRD): Potential treatments for Raynaud's Phenomenon. Technological Forecasting and Social Change 2008; 75(2): 203-214.

Kostoff RN. Literature-related discovery (LRD): Potential treatments for cataracts. Technological Forecasting and Social Change 2008; 75(2): 215-225.

Kostoff RN, Briggs MB. Literature-Related Discovery (LRD): Potential treatments for Parkinson's Disease. Technological Forecasting and Social Change 2008; 75(2): 226-238.

Kostoff RN, Briggs MB, Lyons TJ. Literature-related discovery (LRD): Potential treatments for Multiple Sclerosis. Technological Forecasting and Social Change 2008; 75(2): 239-255.

Kostoff RN, Solka JL, Rushenberg RL, Wyatt JA. Literature-related discovery (LRD): Water purification. Technological Forecasting and Social Change 2008; 75(2): 256-275.

Kostoff RN, Block JA, Solka JL, Briggs MB, Rushenberg RL, Stump JA, Johnson D, Lyons TJ, Wyatt JR. Literature-related discovery (LRD): Lessons learned, and future research directions. Technological Forecasting and Social Change 2008; 75(2): 276-299.

Ahlers C, Hristovski D, Kilicoglu H, Rindflesch TC. Using the Literature-Based Discovery Paradigm to Investigate Drug Mechanisms. AMIA Annu Symp Proc 2007: 6-10.

Weeber, M. Drug Discovery as an Example of Literature-Based Discovery. In Computational Discovery of Scientific Knowledge, Lecture Notes in Computer Science, Springer. 2007: 290-306.

Yetisgen-Yildiz M, Pratt W. Using statistical and knowledge-based approaches for literature-based discovery. J Biomed Inform. 2006 Dec;39(6):600-11.

Hristovski D, Friedman C, Rindflesch TC, Peterlin B. Exploiting semantic relations for literature-based discovery. AMIA Annu Symp Proc 2006: 349-53.

Kostoff RN. Systematic acceleration of radical discovery and innovation in science and technology. Technological Forecasting and Social Change 2006; 73(8): 923-936.

Bekhuis T. Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy. Biomedical Digital Libraries 2006, 3:2.

Hunter L, Cohen KB. Biomedical language processing: what's beyond PubMed? Mol Cell. 2006 Mar 3;21(5):589-94.

Jensen LJ, Saric J, Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet. 2006 Feb;7(2):119-29.

Weeber M, Kors JA, Mons B. Online tools to support literature-based discovery in the life sciences. Brief Bioinform. 2005 Sep;6(3):277-86.

Jelier R, Jenster G, Dorssers LC, van der Eijk CC, van Mulligen EM, Mons B, Kors JA. Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes. Bioinformatics. 2005 May 1;21(9):2049-58.

Hristovski D, Peterlin B, Mitchell JA, Humphrey SM. Using literature-based discovery to identify disease candidate genes. Int J Med Inform. 2005 Mar;74(2-4):289-98.

Skeels MM, Henning K, Yetisgen-Yildiz M, Pratt W. Interaction Design for Literature-Based Discovery. Proceedings of the ACM International Conference on Human Factors in Computing Systems (CHI 2005). Portland, OR. April 2005.

Palmer CL, Cragin MH, Hogan TP. Information at the Intersections of Discovery: Case Studies in Neuroscience. Proc. ASIST annual meeting. 2004 Nov; 448-455.

Wren JD. Extending the mutual information measure to rank inferred literature relationships. BMC Bioinformatics. 2004 Oct 7;5(1):145.

Das Neves, FA. Stepping Stones and Pathways:Improving Retrieval by Chains of Relationships between Documents. PhD Dissertation, Virginia Polytechnic Institute and State University. September, 2004.

Srinivasan P, Libbus B. Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics. 2004 Aug 4;20 Suppl 1:I290-I296.

Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR. Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics. 2004 Feb 12;20(3):389-98.

Wren JD, Garner HR. Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. Bioinformatics. 2004 Jan 22;20(2):191-8.

Srinivasan P Text Mining: Generating Hypotheses from MEDLINE JASIST 2004; 55(5): 396-413.

Pratt W, Yetisgen-Yildiz M. LitLinker: Capturing Connections across the Biomedical Literature. Proceedings of the International Conference on Knowledge Capture (K-Cap'03). p. 105-112. Florida, October 2003.

Stegmann J, Grohmann G.Hypothesis generation guided by co-word clustering. Scientometrics 2003; 56(1): 111-135.

Weeber M, Vos R, Klein H, De Jong-Van Den Berg LT, Aronson AR, Molema G. Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomide.JAMIA 2003; 10: 252-9.

Hristovski D, Peterlin B, Mitchell JA, Humphrey SM. Improving literature based discovery support by genetic knowledge integration. Stud Health Technol Inform 2003; 95: 68-73.

Gordon MD, Lindsay RK, Fan W. Literature-based discovery on the World Wide Web. ACM Transactions on Internet Technology (TOIT) 2002; 2: 261 - 275.

Weeber M, Vos R, Baayen RH. Using concepts in literature-based discovery: Simulating Swanson's raynaud - fish oil and migraine - magnesium discoveries. JASIST 2001; 52: 548-557.

Hristovski D, Stare J, Peterlin B, Dzeroski S. Supporting discovery in medicine by association rule mining in Medline and UMLS. Medinfo 2001; 10: 1344-8.

Weeber M, Klein H, Aronson AR, Mork JG, de Jong-van den Berg LTW, Vos R.Text-based discovery in biomedicine: The Architecture of the DAD-system. Proc. AMIA Symp. 2000; 903-907.

Valdes-Perez RE. Principles of human-computer collaboration for knowledge discovery in science. Artificial Intelligence 1999; 107: 335-346.

Kostoff RN. Science and technology innovation. Technovation 1999; 19: 593-604.

Lindsay RK, Gordon MD. Literature-based discovery by lexical statistics. JASIS 1999; 50: 574-587.

Gordon MD. Using textual information for discovery and innovation. Proc. 62nd annual meeting of ASIS 1999; 36: 771-772.

Qin J. Discovering semantic patterns in bibliographically coupled documents. Library Trends 1999; 48: 109-132.

Cory KA. Discovering hidden analogies in an online humanities database. Library Trends 1999; 48: 60-71.

Small H. A passage through science: crossing disciplinary boundaries. Library Trends 1999; 48: 72-108.

Hearst MA. Untangling text data mining. Proc. ACL 1999.

Finn R. Program Uncovers Hidden Connections In The Literature. The Scientist 1998 May 11: 12-13.

Valdez-Perez RE. Text-Based Informatics. The Scientist 1998 July 6: 10.

Ross BM. In reply. Arch Gen. Psychiat. 1998; 55: 753.

Gordon MD, Dumais S. Using latent semantic indexing for literature based discovery. JASIS 1998; 49: 674-685.

Spasser MA. The enacted fate of undiscovered public knowledge. JASIS 1997; 48: 707-717.

Trybula WJ. Data mining and knowledge discovery. Ann. Rev. Info. Sci. Technol. 1997; 32: 197-229.

Gordon MD, Lindsay RK. Toward discovery support systems: a replication, re-examination, and extension of Swanson's work on literature-based discovery of a connection between Raynaud's and fish oil. JASIS 1996; 47: 116-128.

The Process of Scientific Discovery:

Smalheiser NR. How many scientists does it take to change a paradigm? New ideas to explain scientific observations are everywhere--we just need to learn how to see them. EMBO Rep. 2013 Oct;14(10):861-5. doi: 10.1038/embor.2013.125.

Grinnell F. Everyday Practice of Science: Where Intuition and Passion meet Objectivity and Logic. Oxford University Press, New York, NY. Dec 2008.

Hubel DH. The way biomedical research is organized has dramatically changed over the past half-century: are the changes for the better? Neuron. 2009 Oct 29;64(2):161-3.

Nabel GJ. Philosophy of science: The coordinates of truth. Science. 2009 Oct 2;326(5949):53-4.

Alon U. How to choose a good scientific problem. Mol Cell. 2009 Sep 24;35(6):726-8.

Lawrence PA. Real lives and white lies in the funding of scientific research: the granting system turns young scientists into bureaucrats and then betrays them. PLoS Biol. 2009 Sep;7(9):e1000197.

Adams DJ, Beniston LJ, Childs PR. Promoting creativity and innovation in biotechnology. Trends Biotechnol. 2009 Aug;27(8):445-7.

O'Malley MA, Elliott KC, Haufe C, Burian RM. Philosophies of funding. Cell. 2009 Aug 21;138(4):611-5.

DeHaan RL. Teaching creativity and inventive problem solving in science. CBE Life Sci Educ. 2009 Fall;8(3):172-81.

Porter TM. How science became technical. ISIS 2009 June; 100: 292-309

Shneider AM. Four stages of a scientific discipline; four types of scientist. Trends Biochem Sci. 2009 May;34(5):217-23.

Sussman, R. Serendipity. J Biol Chem. 2009 Apr 17; 284(16): 10285-10290.

Tanner KD. Learning to see inequity in science. CBE Life Sci Educ. 2009 Winter;8(4):265-70.

Cohen, S. Origins of growth factors: NGF and EGF. J Biol Chem. 2008; 283(49): 33793-33797.

Ledford H. Collaborations: with all good intentions. Nature 2008; 452(7188): 682-684.

van Holde KE. Learning how to be a scientist. J Biol Chem. 2008; 283(8): 4461-4463.

Silva AJ. The science of research: the principles underlying the discovery of cognitive and other biological mechanisms. J Physiol Paris. 2007; 101(4-6):203-213.

Vicens Q, Bourne PE. Ten simple rules for a successful collaboration. PLoS Comput Biol 2007; 3(3): e44.

Erren TC, Cullen P, Erren M, Bourne PE. Ten simple rules for doing your best research, according to Hamming. PLoS Comput Biol 2007; 3(10): e213.

Snyder SH. The audacity principle in science. Proc American Philosophical Society 2005; 149(2), 141-158.

Thagard P. Ulcers and bacteria I: discovery and acceptance. Studies in History and Philosophy of Science Part C: Biological and Biomedical Sciences 1998; 29(1), 107-136.
html version at author's website.

Kaiser JF. You and your research. Transcript of the Bell Communications Research Colloquium Seminar given by Richard W. Hamming on March 7, 1986.

Richmond, PA. What are we looking for? Attention to the nature of scientific discovery would produce better information retrieval systems. Science 1963;139:737-739.

MicroRNA and bioinformatics studies:

Dwivedi Y, Roy B, Lugli G, Rizavi H, Zhang H, and Smalheiser NR. (2015) Chronic corticosterone-mediated dysregulation of microRNA network in prefrontal cortex of rats: relevance to depression pathophysiology. Transl Psychiatry 5: e682.

Lugli, G., Cohen, A.M., Bennett, D.A., Shah, R.C., Fields, C. J., Hernandez, A. G., and Smalheiser, N. R. (2015) Plasma Exosomal miRNAs in persons with and without Alzheimer Disease: Altered expression and prospects for biomarkers. PLoS ONE 10 (10): e0139233.

Smalheiser, N.R., Zhang, H. and Dwivedi, Y. (2014) Enoxacin elevates miRNA expression in frontal cortex and prevents learned helplessness in rats. Frontiers in Psychiatry 5: 6. PMC3918929 Selected as being in the top 10% of articles in the journal and invited for a Tier 2 follow up article.

Smalheiser, N.R., Lugli, G., Zhang, H., Rizavi, H., Cook, E.H. and Dwivedi, Y. (2014) Expression of microRNAs and other small RNAs in Prefrontal Cortex in Schizophrenia, Bipolar Disorder and Depressed Subjects. PLoS ONE 9: e86469. PMC3903529. Selected to be included in the PLOS ONE Human Genetics Editor's Picks Collection.

Smalheiser, N.R., Zhang, H. and Dwivedi, Y. (2014) Enoxacin elevates miRNA expression in frontal cortex and prevents learned helplessness in rats. Frontiers in Psychiatry 5: 6. PMC3918929 Selected as being in the top 10% of articles in the journal and invited for a Tier 2 follow up article.

Smalheiser, N. R. (2014) The RNA-centered view of the synapse: noncoding RNAs and synaptic plasticity. Phil. Trans. Roy. Soc. B. 369: pii: 20130504.

Smalheiser, N. R. and Gomes, O. L. A. (2014) Eukaryotic Argonaute-DNA binding? Biology Direct 10:27.

Smalheiser, N. R., Lugli, G., Rizavi, H., Torvik, V. I., Turecki, G. and Dwivedi, Y.(2012) MicroRNA Expression is Down-Regulated and Reorganized in Prefrontal Cortex of Depressed Suicide. PLoS ONE 7: e33201.

Lugli, G., Larson, J., Demars, M.P. and Smalheiser, N. R. (2012) Primary microRNA precursor transcripts are localized at postsynaptic densities in adult mouse forebrain. J. Neurochem 123: 459-466. Recommended by Faculty of 1000.

Smalheiser, N. R. The search for endogenous siRNAs in the mammalian brain. Exp. Neurol. 2012; 235: 455-463.

Smalheiser, N. R., Lugli, G., Thimmapuram, J., Cook, E. H. and Larson, J. (2011) Mitochondrial small RNAs that are up-regulated during olfactory discrimination training in mice. Mitochondrion 11: 994-995. doi:10.1016/j.mito.2011.08.014

Piriyapongsa, J., Jordan, I.K., Conley, A. B., Tom Ronan and Smalheiser, N.R. Transcription factor binding sites are highly enriched within microRNA precursor sequences. Biology Direct. 2011; 6: 61. http://www.biology-direct.com/content/6/1/61

Smalheiser NR, Lugli G, Rizavi HS, Zhang H, Torvik VI, Pandey GN, Davis JM, Dwivedi Y. MicroRNA expression in rat brain exposed to repeated inescapable shock: differential alterations in learned helplessness vs. non-learned helplessness. Int J Neuropsychopharmacol. 2011; 28:1-11.

Smalheiser NR, Lugli G, Thimmapuram J, Cook EH, Larson J. Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training RNA 2011 Jan;17(1):166-81.

Smalheiser NR, Lugli G, Lenon AL, Davis JM, Torvik VI, Larson J. Olfactory discrimination training up-regulates and reorganizes expression of microRNAs in adult mouse hippocampus. ASN Neuro. 2010 Feb 26;2(1):e00028.

Smalheiser NR. Do Neural Cells Communicate with Endothelial Cells via Secretory Exosomes and Microvesicles?. Cardiovascular Psychiatry and Neurology 2009, Article ID 383086.

Smalheiser NR, Lugli, G. microRNA Regulation of Synaptic Plasticity. Neuromolecular Med. 2009;11(3):133-40.
A preprint version of this article is available here.

Smalheiser NR. Synaptic enrichment of microRNAs in adult mouse forebrain is related to structural features of their precursors. Biol Direct. 2008 Oct 29; 3(1): 44.

Smalheiser NR, Lugli G, Torvik VI, Mise N, Ikeda R, Abe K. Natural antisense transcripts are co-expressed with sense mRNAs in synaptoneurosomes of adult mouse forebrain. Neurosci Res. 2008 Dec; 62(4): 236-239.
A preprint is available for download here, as well as the supplementary Excel file.

Smalheiser NR. Regulation of mammalian microRNA processing and function by cellular signaling and subcellular localization. Biochim Biophys Acta. 2008 Nov; 1779(11): 678-681.
A preprint version of this article is available here.

Lugli G, Torvik VI, Larson J, Smalheiser NR. Expression of microRNAs and their precursors in synaptic fractions of adult mouse forebrain. Journal of Neurochemistry 2008; 106(2): 650-661.
A preprint version of this article is available here, as well as supplementary File S1 (.doc), and File S2 (.xls).

Smalheiser NR. Exosomal transfer of proteins and RNAs at synapses in the nervous system. Biology Direct 2007, 2:35.

Smalheiser NR, Torvik VI. Models of microRNA-target coordination. In: "microRNAs: From Basic Science to Disease Biology", (K. Appasani, Ed.), Cambridge University Press, 2008, pp. 221-226.

Smalheiser NR, Torvik VI. Alu elements within human mRNAs are probable microRNA targets. Trends in Genetics 2006; 22(10), 532-536. Supplements: file 1(pdf), file 2(xls).

Smalheiser NR, Torvik VI. Complications in mammalian microRNA target prediction. In: "MicroRNA: Protocols", ed. S.-Y. Ying, in the series "Methods in Molecular Biology", Humana Press, 2006, 119-128.

Smalheiser NR, Torvik VI. Mammalian microRNAs derived from genomic repeats. Trends in Genetics 2005; 21(6): 322-326. Supplements: file 1(pdf), file 2(pdf), file 3(xls).

Lugli G, Larson J, Martone ME, Jones Y, Smalheiser NR. Dicer and eIF2c are enriched at postsynaptic densities in adult mouse brain and are modified by neuronal activity in a calpain-dependent manner. J Neurochem. 2005 Aug;94(4):896-905. Supplemental figures.
This is an electronic version of an article published in Journal of Neurochemistry: complete citation information for the final version of the paper, as published in the print edition of Journal of Neurochemistry, is available on the Blackwell Synergy online delivery service, accessible via the journal's website at http://www.blackwellpublishing.com/jnc or http://www.blackwell-synergy.com/.

Smalheiser NR, Torvik VI. A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions. BMC Bioinformatics 2004;5:139.

Smalheiser NR, Torvik VI. A statistical approach predicts human microRNA targets. Genome Biology preprint repository 2004; 5: P4 (database deposited at BMC).

Smalheiser NR. EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues. Genome Biology 2003; 4:403. Link to Genome Biology.

Smalheiser NR. Conserved amphipathic helices near the N-terminus and C-terminus of the alpha subunit of Cranin(Dystroglycan). Cell Adhesion and Communication 1998; 5: 401-404.

Smalheiser NR. Proteins in unexpected locations. Molecular Biology of the Cell 1996; 7:1003-1014.

Other publications:
Zhou W, Smalheiser NR, Yu C. A tutorial on information retrieval: basic terms and concepts. J Biomed Discov Collab. 2006 Mar 13;1(1):2.

Torvik VI, Triantaphyllou E. Discovering rules that govern monotone phenomena. In: "Data Mining and Knowledge Discovery Approaches Based on Rule Induction Techniques" (Triantaphyllou and Felici, eds.) Massive Computing Series, Springer-Verlag, 2006, Chapter 4: 149-192.

Smalheiser NR. Bath toys--a source of gastrointestinal infection. N Engl J Med. 2004 Jan 29;350(5):521.

Torvik VI, Triantaphyllou E.Guided Inference of Nested Monotone Boolean Functions. Information Sciences 2003; 151: 171-200.

Lugli G, Krueger JM, Davis JM, Persico AM, Keller F, Smalheiser NR. Methodological factors influencing measurement and processing of plasma reelin in humans. BMC Biochemistry 2003;4:9.

Das A, Smalheiser NR, Markaryan A, Kaplan A. Evidence for binding of the ectodomain of amyloid precursor protein 695 and activated high molecular weight kininogen. Biochemica et Biophysica Acta (General Subjects) 2002; 1571: 225-238.

Kim HM, Qu T, Kriho V, Lacor P, Smalheiser NR, Pappas GD, Guidotti A, Costa E, Sugaya K. Reelin function in neural stem cell biology. Proc. Natl. Acad. Sci. 2002; 99: 4020:4025.

Smalheiser NR, Manev H, Costa E. RNAi and brain function: was McConnell on the right track? Trends Neurosci. 2001 Apr;24(4):216-8.

Smalheiser NR. Walter Pitts. Perspect Biol Med. 2000 Winter;43(2):217-26.

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Last modified: Feb 4, 2018