Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks

The KEGG resource for deciphering the genome

Kanehisa, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh063 · Cited by 5,121 · see citing works

The Gene Ontology (GO) database and informatics resource

Gene Ontology Consortium (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh036 · Cited by 4,533 · see citing works

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

Al‐Shahrour, F., Díaz‐Uriarte, R., & Dopazo, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg455 · Cited by 1,118 · see citing works

IntAct: an open source molecular interaction database

Hermjakob, H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh052 · Cited by 1,013 · see citing works

A literature network of human genes for high-throughput analysis of gene expression

Jenssen, T.-K., Lægreid, A., Komorowski, J., & Hovig, E. J. (2001) · Nature Genetics · doi:10.1038/88213 · Cited by 839 · see citing works

EcoCyc: a comprehensive database resource for Escherichia coli

Keseler, I. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki108 · Cited by 737 · see citing works

A gene network for navigating the literature

Hoffmann, R., & Valencia, A. (2004) · Nature Genetics · doi:10.1038/ng0704-664 · Cited by 535 · see citing works

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles

Friedman, C., Kra, P., Yu, H., Krauthammer, M. O., & Rzhetsky, A. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.suppl_1.s74 · Cited by 508 · see citing works

A literature network of human genes for high-throughput analysis of gene expression

Jenssen, T.-K., Lægreid, A., Komorowski, J., et al. (2001) · Nature Genetics · doi:10.1038/ng0501-21 · Cited by 487 · see citing works

Automatic extraction of biological information from scientific text: protein-protein interactions.

Blaschke, C., Andrade-Navarro, M. A., Ouzounis, C. A., & Valencia, A. (1999) · PubMed · Cited by 448 · see citing works

Automated extraction of information on protein–protein interactions from the biological literature

Ono, T., Hishigaki, H., Tanigami, A., & Takagi, T. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.2.155 · Cited by 398 · see citing works

Migraine and Magnesium: Eleven Neglected Connections

Swanson, D. R. (1988) · Perspectives in biology and medicine · doi:10.1353/pbm.1988.0009 · Cited by 396 · see citing works

BIOBIBLIOMETRICS: INFORMATION RETRIEVAL AND VISUALIZATION FROM CO-OCCURRENCES OF GENE NAMES IN MEDLINE ABSTRACTS

Stapley, B. J., & Benoît, G. (1999) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789814447331_0050 · Cited by 273 · see citing works

Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses

Smalheiser, N. R., & Swanson, D. R. (1998) · Computer Methods and Programs in Biomedicine · doi:10.1016/s0169-2607(98)00033-9 · Cited by 223 · see citing works

BioCreAtIvE Task 1A: gene mention finding evaluation

Yeh, A., Morgan, A. A., Colosimo, M., & Hirschman, L. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-s1-s2 · Cited by 205 · see citing works

Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts.

Sekimizu, T., Park, & Tsujii, J. (1998) · PubMed · Cited by 196 · see citing works

Evaluation of BioCreAtIvE assessment of task 2

Blaschke, C., Andrés‐León, E., Krallinger, M., & Valencia, A. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-s1-s16 · Cited by 139 · see citing works

The frame-based module of the SUISEKI information extraction system

Blaschke, C., & Valencia, A. (2002) · IEEE Intelligent Systems and their Applications · doi:10.1109/5254.999215 · Cited by 118 · see citing works

Information extraction in molecular biology

Blaschke, C. (2002) · Briefings in Bioinformatics · doi:10.1093/bib/3.2.154 · Cited by 110 · see citing works

The potential use of SUISEKI as a protein interaction discovery tool.

Blaschke, C., & Valencia, A. (2001) · PubMed · Cited by 83 · see citing works

Mining functional information associated with expression arrays

Blaschke, C., Oliveros, J. C., & Valencia, A. (2001) · Functional & Integrative Genomics · doi:10.1007/s101420000036 · Cited by 80 · see citing works

Life cycles of successful genes

Hoffmann, R., & Valencia, A. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(02)00014-8 · Cited by 69 · see citing works

Automatic annotation for biological sequences by extraction of keywords from MEDLINE abstracts. Development of a prototype system.

Andrade-Navarro, M. A., & Valencia, A. (1997) · PubMed · Cited by 57 · see citing works

Learning anchor verbs for biological interaction patterns from published text articles

Hatzivassiloglou, V., & Weng, W. (2002) · International Journal of Medical Informatics · doi:10.1016/s1386-5056(02)00054-0 · Cited by 27 · see citing works

A sentence sliding window approach to extract protein annotations from biomedical articles

Krallinger, M., Padrón, M. A. B., & Valencia, A. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-s1-s19 · Cited by 25 · see citing works

Search and retrieve

Valencia, A. (2002) · EMBO Reports · doi:10.1093/embo-reports/kvf104 · Cited by 23 · see citing works

The BioPAX community standard for pathway data sharing

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745 · see citing works

Literature mining for the biologist: from information retrieval to biological discovery

Jensen, L. J., Šarić, J., & Peer Bork, B. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1768 · Cited by 632 · see citing works

Text mining and its potential applications in systems biology

Ananiadou, S., Kell, D. B., & Tsujii, J. (2006) · Trends in biotechnology · doi:10.1016/j.tibtech.2006.10.002 · Cited by 324 · see citing works

Information retrieval and text mining technologies for chemistry

Krallinger, M., Rabal, O., Lourenço, A., Oyarzabal, J., & Valencia, A. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00851 · Cited by 281 · see citing works

Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web

Hull, D., Pettifer, S. R., & Kell, D. B. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000204 · Cited by 209 · see citing works

Building mammalian signalling pathways with RNAi screens

Moffat, J., & Sabatini, D. M. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1860 · Cited by 202 · see citing works

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

Westergaard, D., Stærfeldt, H., Tønsberg, C., Jensen, L. J., & Brunak, S. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005962 · Cited by 198 · see citing works

A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature

Tikk, D., Thomas, P. E., Palaga, P., Hakenberg, J., & Leser, U. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000837 · Cited by 171 · see citing works

Metabolomics, modelling and machine learning in systems biology – towards an understanding of the languages of cells

Kell, D. B. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2006.05136.x · Cited by 147 · see citing works

iHOP web services

Fernández, J. M., Hoffmann, R., & Valencia, A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm298 · Cited by 146 · see citing works

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text

Garten, Y., & Altman, R. B. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-s2-s6 · Cited by 125 · see citing works

Genetic studies of diseases

Wang, E., Lenferink, A. E. G., & O'Connor‐McCourt, M. D. (2007) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-007-7054-6 · Cited by 127 · see citing works

Online tools to support literature-based discovery in the life sciences

Weeber, M., Kors, J. A., & Mons, B. (2005) · Briefings in Bioinformatics · doi:10.1093/bib/6.3.277 · Cited by 106 · see citing works

Toward the design of ultrahigh-entropy alloys via mining six million texts

Pei, Z., Yin, J., Liaw, P. K., & Raabe, D. (2023) · Nature Communications · doi:10.1038/s41467-022-35766-5 · Cited by 100 · see citing works

Analysis of Biological Processes and Diseases Using Text Mining Approaches

Krallinger, M., Leitner, F., & Valencia, A. (2009) · Methods in molecular biology · doi:10.1007/978-1-60327-194-3_16 · Cited by 88 · see citing works

Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications

Vázquez, M., Krallinger, M., Leitner, F., & Valencia, A. (2011) · Molecular Informatics · doi:10.1002/minf.201100005 · Cited by 87 · see citing works

Biological network extraction from scientific literature: state of the art and challenges

Li, C., Liakata, M., & Rebholz‐Schuhmann, D. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbt006 · Cited by 81 · see citing works

Synapse proteomics of multiprotein complexes: en route from genes to nervous system diseases

Grant, S. G. N., Marshall, M. C., Page, K.-L., Cumiskey, M. A., & Armstrong, J. D. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi330 · Cited by 64 · see citing works

A text-mining system for extracting metabolic reactions from full-text articles

Czarnecki, J., Nobeli, I., Smith, A. M., & Shepherd, A. J. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-172 · Cited by 58 · see citing works

The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks

Hsing, M., Byler, K. G., & Cherkasov, A. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-80 · Cited by 66 · see citing works

BBP: Brucella genome annotation with literature mining and curation

Xiang, Z., Zheng, W., & He, Y. O. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-347 · Cited by 53 · see citing works

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival

Ness, B. V., Ramos, C., Haznadar, M., Hoering, A., Haessler, J., Crowley, J. J., Jacobus, S. J., Oken, M. M., Rajkumar, S. V., Greipp, P. R., et al. (2008) · BMC Medicine · doi:10.1186/1741-7015-6-26 · Cited by 52 · see citing works

Connecting the Dots between PubMed Abstracts

Hossain, M. S., Gresock, J., Edmonds, Y., Helm, R. F., Potts, M., & Ramakrishnan, N. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029509 · Cited by 50 · see citing works

Extraction of biological interaction networks from scientific literature

Skusa, A., Ruegg, A., & Köhler, J. (2005) · Briefings in Bioinformatics · doi:10.1093/bib/6.3.263 · Cited by 50 · see citing works

Network integration and graph analysis in mammalian molecular systems biology

Ma’ayan, A. (2008) · IET Systems Biology · doi:10.1049/iet-syb:20070075 · Cited by 45 · see citing works

Integrated Bio-Entity Network: A System for Biological Knowledge Discovery

Bell, L., Chowdhary, R., Liu, J. S., Niu, X., & Zhang, J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021474 · Cited by 37 · see citing works

Literature mining of host–pathogen interactions: comparing feature-based supervised learning and language-based approaches

Thieu, T., Joshi, S., Warren, S., & Korkin, D. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts042 · Cited by 36 · see citing works

ChiPPI: a novel method for mapping chimeric protein–protein interactions uncovers selection principles of protein fusion events in cancer

Frenkel‐Morgenstern, M., Gorohovski, A., Tagore, S., Sekar, V., Vázquez, M., & Valencia, A. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx423 · Cited by 36 · see citing works

Using uncertainty to link and rank evidence from biomedical literature for model curation

Zerva, C., Batista-Navarro, R., Day, P. J., & Ananiadou, S. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx466 · Cited by 35 · see citing works

Claudin 28b and F-actin are involved in rainbow trout gill pavement cell tight junction remodeling under osmotic stress

Sandbichler, A. M., Egg, M., Schwerte, T., & Pelster, B. (2011) · Journal of Experimental Biology · doi:10.1242/jeb.050062 · Cited by 34 · see citing works

CIDeR: multifactorial interaction networks in human diseases

Lechner, M., Höhn, V., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., Kastenmüller, G., Wägele, B., & Ruepp, A. (2012) · Genome biology · doi:10.1186/gb-2012-13-7-r62 · Cited by 31 · see citing works

Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications

Remmerie, N., Vijlder, T. D., Laukens, K., Dang, T. H., Lemière, F., Mertens, I., Valkenborg, D., Blust, R., & Witters, E. (2011) · Phytochemistry · doi:10.1016/j.phytochem.2011.01.003 · Cited by 33 · see citing works

ChiTaRS 2.1—an improved database of the chimeric transcripts and RNA-seq data with novel sense–antisense chimeric RNA transcripts

Frenkel‐Morgenstern, M., Gorohovski, A., Vučenović, D., Maestre, L., & Valencia, A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1199 · Cited by 33 · see citing works

Parameter estimate of signal transduction pathways

Arisi, I., Cattaneo, A., & Rosato, V. (2006) · BMC Neuroscience · doi:10.1186/1471-2202-7-s1-s6 · Cited by 32 · see citing works

Integrative computational biology for cancer research

Fortney, K., & Jurišica, I. (2011) · Human Genetics · doi:10.1007/s00439-011-0983-z · Cited by 31 · see citing works

Language models for materials discovery and sustainability: Progress, challenges, and opportunities

Pei, Z., Yin, J., & Zhang, J. (2025) · Progress in Materials Science · doi:10.1016/j.pmatsci.2025.101495 · Cited by 30 · see citing works

The cellular uptake of pharmaceutical drugs is mainly carrier-mediated and is thus an issue not so much of biophysics but of systems biology

Kell, D. B., & Dobson, P. D. (2009) · Cited by 30 · see citing works

Challenges in plant cellular pathway reconstruction based on gene expression profiling

van Baarlen, P., van Esse, H. P., Siezen, R. J., & Thomma, B. P. H. J. (2007) · Trends in Plant Science · doi:10.1016/j.tplants.2007.11.003 · Cited by 28 · see citing works

Reverse Differentiation as a Gene Filtering Tool in Genome Expression Profiling of Adipogenesis for Fat Marker Gene Selection and Their Analysis

Ullah, M., Stich, S., Häupl, T., Eucker, J., Sittinger, M., & Ringe, J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069754 · Cited by 26 · see citing works

KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways

Spasić, ‪., Simeonidis, E., Messiha, H. L., Paton, N. W., & Kell, D. B. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp175 · Cited by 20 · see citing works

In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae

Alves, R., & Albert Sorribas, B. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-10 · Cited by 19 · see citing works

Using the iHOP Information Resource to Mine the Biomedical Literature on Genes, Proteins, and Chemical Compounds

Hoffmann, R. (2007) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0116s20 · Cited by 19 · see citing works

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website

Good, B. M., Kawas, E. A., Kuo, B. Y.-L., & Wilkinson, M. D. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-534 · Cited by 19 · see citing works

Cancer systems biology: exploring cancer-associated genes on cellular networksPreprint

Wang, E., Lenferink, A. E. G., & O'Connor‐McCourt, M. D. (2007) · arXiv (Cornell University) · doi:10.48550/arxiv.0712.3753 · Cited by 19 · see citing works

PathNER: a tool for systematic identification of biological pathway mentions in the literature

Wu, C., Schwartz, J., & Nenadić, G. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-s3-s2 · Cited by 17 · see citing works

Bioinformatics and cancer research: building bridges for translational research

Goméz-López, G., & Valencia, A. (2008) · Clinical & Translational Oncology · doi:10.1007/s12094-008-0161-5 · Cited by 16 · see citing works

Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae

Mirzarezaee, M., Araabi, B. N., & Sadeghi, M. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-172 · Cited by 16 · see citing works

BioPP: a tool for web-publication of biological networks

Viswanathan, G. A., Nudelman, G., Patil, S., & Sealfon, S. C. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-168 · Cited by 16 · see citing works

Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology

Alves, R., Vilaprinyó, E., & Albert Sorribas, B. (2008) · Current Bioinformatics · doi:10.2174/157489308784340694 · Cited by 15 · see citing works

Gene expression in women conceiving spontaneously over the age of 45 years

Gielchinsky, Y., Bogoch, Y., Rechavi, G., Jacob‐Hirsch, J., Amariglio, N., Shveiky, D., Michal Linial, B., & Laufer, N. (2008) · Fertility and Sterility · doi:10.1016/j.fertnstert.2007.06.058 · Cited by 15 · see citing works

Novel metrics for evaluating the functional coherence of protein groups via protein semantic network

Zheng, B., & Lu, X. (2007) · Genome biology · doi:10.1186/gb-2007-8-7-r153 · Cited by 15 · see citing works

Neuroinformatics in clinical practice: are computers going to help neurological patients and their physicians?

Villoslada, P., & Oksenberg, J. R. (2006) · Future Neurology · doi:10.2217/14796708.1.2.159 · Cited by 14 · see citing works

Uncovering the Molecular Machinery of the Human Spindle—An Integration of Wet and Dry Systems Biology

Rojas, A. M., Santamaría, A., Malik, R., Jensen, T. S., Körner, R., Morilla, I., Juan, D., Krallinger, M., Hansen, D. A., Hoffmann, R., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031813 · Cited by 13 · see citing works

Functional Genomics, Proteomics, Metabolomics and Bioinformatics for Systems Biology

Ballereau, S. J., Glaab, E., Kolodkin, A. N., Chaiboonchoe, A., Biryukov, M., Vlassis, N. A., Ahmed, H., Pellet, J., Baliga, N. S., Hood, L., et al. (2013) · Springer eBooks · doi:10.1007/978-94-007-6803-1_1 · Cited by 10 · see citing works

Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices

Harmston, N., Filsell, W., & Stumpf, M. P. H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr640 · Cited by 9 · see citing works

Mixture of logistic models and an ensemble approach for protein-protein interaction extraction

Bell, L., Zhang, J., & Niu, X. (2011) · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) · doi:10.1145/2147805.2147853 · Cited by 7 · see citing works

Stochastic simulation and modelling of metabolic networks in a machine learning framework

Biba, M., Xhafa, F., Esposito, F., & Ferilli, S. (2011) · Simulation Modelling Practice and Theory · doi:10.1016/j.simpat.2011.05.002 · Cited by 6 · see citing works

High-Throughput Analyses and Curation of Protein Interactions in Yeast

Wodak, S. J., Vlasblom, J., & Pu, S. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-173-4_22 · Cited by 6 · see citing works

BioKB - Text Mining and Semantic Technologies for Biomedical Content Discovery

Biryukov, M., Grouès, V., Satagopam, V., & Schneider, R. (2018) · Figshare · doi:10.6084/m9.figshare.6994121 · Cited by 6 · see citing works

Integration of Biological Data with Semantic Networks

Hsing, M., & Cherkasov, A. R. (2006) · Current Bioinformatics · doi:10.2174/157489306777827946 · Cited by 6 · see citing works

Text Mining

Krallinger, M., Leitner, F., Vázquez, M., & Valencia, A. (2014) · Elsevier eBooks · doi:10.1016/b978-0-444-53632-7.01107-2 · Cited by 5 · see citing works

A guide for building biological pathways along with two case studies: hair and breast development

Trindade, D. R., Orsine, L. A., Barbosa-Silva, A., Donnard, E. R., & Ortega, J. M. (2014) · Methods · doi:10.1016/j.ymeth.2014.10.006 · Cited by 5 · see citing works

Defrosting the Digital Library

Hull, D., Pettifer, S. R., & Kell, D. B. (2011) · Apple Academic Press eBooks · doi:10.1201/b14542-2 · Cited by 4 · see citing works

Mining Host-Pathogen Interactions

Korkin, D., Thieu, T., Joshi, S., & Warre, S. (2011) · InTech eBooks · doi:10.5772/22016 · Cited by 4 · see citing works

METSP: A Maximum-Entropy Classifier Based Text Mining Tool for Transporter-Substrate Identification with Semistructured Text

Zhao, M., Chen, Y., Qu, D., & Qu, H. (2015) · BioMed Research International · doi:10.1155/2015/254838 · Cited by 4 · see citing works

Identification, modeling and simulation of key pathways underlying certain cancers

Guo, H., Zhu, Y., Li, D., & He, F. (2011) · Hereditas (Beijing) · doi:10.3724/sp.j.1005.2011.00809 · Cited by 4 · see citing works

Knowledge Acquisition from the Biomedical Literature

Hirschman, L., Hayes, W. S., & Valencia, A. (2007) · Springer eBooks · doi:10.1007/978-0-387-48438-9_4 · Cited by 3 · see citing works

Methods in biomedical text mining

Rzhetsky, A., & Rodriguez‐Esteban, R. (2007) · Cited by 3 · see citing works

Collection of Disease Networks by Hybrid Curation Method and the Application for Pathway Analysis

Kushida, T., Asanuma, T., Okuda, Y., Shidahara, Y., & Takagi, T. (2009) · ... International Conference on Complex, Intelligent and Software Intensive Systems · doi:10.1109/cisis.2009.79 · Cited by 3 · see citing works

Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005)

Hahn, U., & Valencia, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl084 · Cited by 3 · see citing works

Insights into Global Mechanisms and Disease by Gene Expression Profiling

Sánchez‐Cabo, F., Rainer, J., Dopazo, A., Trajanoski, Z., & Hackl, H. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-027-0_13 · Cited by 2 · see citing works

Impact of Hydration on the α-Helical Structure of S-Peptide in RNase-S

Chathoth, N. E., Elangovan, R., & Anjukandi, P. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c00938 · Cited by 1 · see citing works

Biological Knowledge Extraction

Leitner, F., Hoffmann, R., & Valencia, A. (2008) · Humana Press eBooks · doi:10.1007/978-1-59745-440-7_22 · Cited by 1 · see citing works

Using Machine Learning Techniques for Modelling and Simulation of Metabolic Networks

Biba, M., Xhafa, F., Esposito, F., & Ferilli, S. (2011) · ... International Conference on Complex, Intelligent and Software Intensive Systems · doi:10.1109/cisis.2011.22 · Cited by 1 · see citing works

Knowledge-Driven, Data-Assisted Integrative Pathway Analytics

Reddy, P. S., Murray, S., & Liu, W. (2013) · IGI Global eBooks · doi:10.4018/978-1-4666-3604-0.ch009 · Cited by 1 · see citing works

Mining Information on Protein Function from Text

Krallinger, M., & Valencia, A. (2007) · doi:10.1002/9783527619368.ch34 · Cited by 1 · see citing works

Fine-Grained Protein Mutation Extraction from Biological Literature

Wang, R., Siu, S. W. I., & Böckmann, R. A. (2009) · International Conference on Electronics Computer Technology · doi:10.1109/icect.2009.10 · Cited by 1 · see citing works

Understanding the hormonal regulation of mouse lactogenesis by transcriptomics and literature analysis

Ling, M. H. (2009) · Minerva Access (University of Melbourne) · Cited by 1 · see citing works

The fully automated construction of metabolic pathways using text mining and knowledge-based constraints

Czarnecki, J. (2015) · Birkbeck Institutional Research Online (BiRO) - Theses · doi:10.18743/pub.00040135

Detecting Dysregulated Processes and Pathways

Stöckel, D., & Lenhof, H. (2014) · Wiley eBooks · doi:10.1002/9783527672165.ch14

Elicitation of Protein-Protein Interactions from Biomedical Literature Using Association Rule Discovery

Samuel, J. J. (2010) · doi:10.12794/metadc30508

Mining Time-series Sequences of Reactions for Biologically Active Patterns in Metabolic Pathways.

Biba, M., Esposito, F., Ferilli, S., Mauro, N. D., & Basile, T. M. A. (2007)

Biological Network Modeling and Analysis

Janowski, S., Kaltschmidt, B., & Kaltschmidt, C. (2014) · Approaches in Integrative Bioinformatics · doi:10.1007/978-3-642-41281-3_8 · Cited by 1 · see citing works

Connecting Text Mining and Pathways using the PathText Resource

Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., Kitano, H., Tsuruoka, Y., Ananiadou, S., & Tsujii, J. (2008) · Language Resources and Evaluation Conference (LREC) · doi:10.63317/2ni9suv85xzx

HETEROGENEOUS MOLECULAR NETWORKS

Schächter, V. (2007) · Complex systems and interdisciplinary science · doi:10.1142/9789812772367_0007

Knowledge-Driven, Data-Assisted Integrative Pathway Analytics

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