Machine learning in bioinformatics (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Machine learning in bioinformatics" in English language version.

refsWebsite

Global rank English rank

118nih.gov

4^th place

77doi.org

2^nd place

16harvard.edu

18^th place

17^th place

15semanticscholar.org

11^th place

8^th place

6worldcat.org

5^th place

4arxiv.org

69^th place

59^th place

3handle.net

102^nd place

76^th place

3secondarymetabolites.org

low place

1springer.com

274^th place

309^th place

1ieee.org

652^nd place

515^th place

1drive.google.com

1,343^rd place

1,354^th place

1oup.com

485^th place

440^th place

1unam.mx

769^th place

1,834^th place

1portico.org

low place

1frontiersin.org

4,679^th place

low place

1glos.ac.uk

low place

1arb-silva.de

low place

1secondgenome.com

low place

1opentreeoflife.org

low place

1web.archive.org

1^st place

1msu.edu

1,844^th place

1,231^st place

arb-silva.de

"Silva". arb-silva.de. Retrieved July 30, 2021.

arxiv.org

Soueidan H, Nikolski M (2019). "Machine learning for metagenomics: methods and tools". Metagenomics. 1. arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.
McClintock BT, Langrock R, Gimenez O, Cam E, Borchers DL, Glennie R, Patterson TA (December 2020). "Uncovering ecological state dynamics with hidden Markov models". Ecology Letters. 23 (12): 1878–1903. arXiv:2002.10497. Bibcode:2020EcolL..23.1878M. doi:10.1111/ele.13610. PMC 7702077. PMID 33073921.
Wang S, Peng J, Ma J, Xu J (January 2016). "Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields". Scientific Reports. 6: 18962. arXiv:1512.00843. Bibcode:2016NatSR...618962W. doi:10.1038/srep18962. PMC 4707437. PMID 26752681.
Soueidan, Hayssam; Nikolski, Macha (January 1, 2017). "Machine learning for metagenomics: methods and tools". Metagenomics. 1 (1). arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.

doi.org

Chicco D (December 2017). "Ten quick tips for machine learning in computational biology". BioData Mining. 10 (35): 35. doi:10.1186/s13040-017-0155-3. PMC 5721660. PMID 29234465.
Larrañaga P, Calvo B, Santana R, Bielza C, Galdiano J, Inza I, et al. (March 2006). "Machine learning in bioinformatics". Briefings in Bioinformatics. 7 (1): 86–112. doi:10.1093/bib/bbk007. PMID 16761367.
Pérez-Wohlfeil E, Torrenoa O, Bellis LJ, Fernandes PL, Leskosek B, Trellesa O (December 2018). "Training bioinformaticians in High Performance Computing". Heliyon. 4 (12): e01057. Bibcode:2018Heliy...401057P. doi:10.1016/j.heliyon.2018.e01057. PMC 6299036. PMID 30582061.
Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y (May 2018). "Sixty-five years of the long march in protein secondary structure prediction: the final stretch?". Briefings in Bioinformatics. 19 (3): 482–494. doi:10.1093/bib/bbw129. PMC 5952956. PMID 28040746.
Shastry KA, Sanjay HA (2020). "Machine Learning for Bioinformatics". In Srinivasa K, Siddesh G, Manisekhar S (eds.). Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Algorithms for Intelligent Systems. Singapore: Springer. pp. 25–39. doi:10.1007/978-981-15-2445-5_3. ISBN 978-981-15-2445-5. S2CID 214350490. Retrieved June 28, 2021.
Soueidan H, Nikolski M (2019). "Machine learning for metagenomics: methods and tools". Metagenomics. 1. arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.
Rabiner L, Juang B (January 1986). "An introduction to hidden Markov models". IEEE ASSP Magazine. 3 (1): 4–16. doi:10.1109/MASSP.1986.1165342. ISSN 1558-1284. S2CID 11358505.
Jackson CH, Sharples LD, Thompson SG, Duffy SW, Couto E (July 2003). "Multistate Markov models for disease progression with classification error". Journal of the Royal Statistical Society, Series D (The Statistician). 52 (2): 193–209. doi:10.1111/1467-9884.00351. S2CID 9824404.
Amoros R, King R, Toyoda H, Kumada T, Johnson PJ, Bird TG (May 30, 2019). "A continuous-time hidden Markov model for cancer surveillance using serum biomarkers with application to hepatocellular carcinoma". Metron. 77 (2): 67–86. doi:10.1007/s40300-019-00151-8. PMC 6820468. PMID 31708595.
Eddy SR (October 1, 1998). "Profile hidden Markov models". Bioinformatics. 14 (9): 755–63. doi:10.1093/bioinformatics/14.9.755. PMID 9918945.
McClintock BT, Langrock R, Gimenez O, Cam E, Borchers DL, Glennie R, Patterson TA (December 2020). "Uncovering ecological state dynamics with hidden Markov models". Ecology Letters. 23 (12): 1878–1903. arXiv:2002.10497. Bibcode:2020EcolL..23.1878M. doi:10.1111/ele.13610. PMC 7702077. PMID 33073921.
Zhang W, Itoh K, Tanida J, Ichioka Y (November 1990). "Parallel distributed processing model with local space-invariant interconnections and its optical architecture". Applied Optics. 29 (32): 4790–7. Bibcode:1990ApOpt..29.4790Z. doi:10.1364/AO.29.004790. PMID 20577468.
Fukushima K (2007). "Neocognitron". Scholarpedia. 2 (1): 1717. Bibcode:2007SchpJ...2.1717F. doi:10.4249/scholarpedia.1717.
Hubel DH, Wiesel TN (March 1968). "Receptive fields and functional architecture of monkey striate cortex". The Journal of Physiology. 195 (1): 215–43. doi:10.1113/jphysiol.1968.sp008455. PMC 1557912. PMID 4966457.
Fukushima K (1980). "Neocognitron: a self organizing neural network model for a mechanism of pattern recognition unaffected by shift in position". Biological Cybernetics. 36 (4): 193–202. doi:10.1007/BF00344251. PMID 7370364. S2CID 206775608.
Matsugu M, Mori K, Mitari Y, Kaneda Y (2003). "Subject independent facial expression recognition with robust face detection using a convolutional neural network". Neural Networks. 16 (5–6): 555–9. doi:10.1016/S0893-6080(03)00115-1. PMID 12850007.
Fioravanti D, Giarratano Y, Maggio V, Agostinelli C, Chierici M, Jurman G, Furlanello C (March 2018). "Phylogenetic convolutional neural networks in metagenomics". BMC Bioinformatics. 19 (Suppl 2): 49. doi:10.1186/s12859-018-2033-5. PMC 5850953. PMID 29536822.
Ji, Yanrong; Zhou, Zhihan; Liu, Han; Davuluri, Ramana V (August 9, 2021). Kelso, Janet (ed.). "DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome". Bioinformatics. 37 (15): 2112–2120. doi:10.1093/bioinformatics/btab083. ISSN 1367-4803. PMC 11025658. PMID 33538820.
Gündüz, Hüseyin Anil; Binder, Martin; To, Xiao-Yin; Mreches, René; Bischl, Bernd; McHardy, Alice C.; Münch, Philipp C.; Rezaei, Mina (September 11, 2023). "A self-supervised deep learning method for data-efficient training in genomics". Communications Biology. 6 (1): 928. doi:10.1038/s42003-023-05310-2. ISSN 2399-3642. PMC 10495322. PMID 37696966.
Breiman, Leo (2001). "Radom Forests". Machine Learning. 45 (1): 5–32. Bibcode:2001MachL..45....5B. doi:10.1023/A:1010933404324. S2CID 89141.
Karim MR, Beyan O, Zappa A, Costa IG, Rebholz-Schuhmann D, Cochez M, Decker S (January 2021). "Deep learning-based clustering approaches for bioinformatics". Briefings in Bioinformatics. 22 (1): 393–415. doi:10.1093/bib/bbz170. PMC 7820885. PMID 32008043.
Lorbeer B, Kosareva A, Deva B, Softić D, Ruppel P, Küpper A (March 1, 2018). "Variations on the Clustering Algorithm BIRCH". Big Data Research. 11: 44–53. doi:10.1016/j.bdr.2017.09.002.
Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, et al. (January 2020). "A computational framework to explore large-scale biosynthetic diversity". Nature Chemical Biology. 16 (1): 60–68. doi:10.1038/s41589-019-0400-9. PMC 6917865. PMID 31768033.
Shastry KA, Sanjay HA (2020). "Machine Learning for Bioinformatics". Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Algorithms for Intelligent Systems. Springer Singapore. pp. 25–39. doi:10.1007/978-981-15-2445-5_3. ISBN 978-981-15-2444-8. S2CID 214350490.
Libbrecht MW, Noble WS (June 2015). "Machine learning applications in genetics and genomics". Nature Reviews. Genetics. 16 (6): 321–32. doi:10.1038/nrg3920. PMC 5204302. PMID 25948244.
Degroeve S, De Baets B, Van de Peer Y, Rouzé P (2002). "Feature subset selection for splice site prediction". Bioinformatics. 18 (Suppl 2): S75-83. doi:10.1093/bioinformatics/18.suppl_2.s75. PMID 12385987.
Huang S, Cai N, Pacheco PP, Narrandes S, Wang Y, Xu W (January 2018). "Applications of Support Vector Machine (SVM) Learning in Cancer Genomics". Cancer Genomics & Proteomics. 15 (1): 41–51. doi:10.21873/cgp.20063. PMC 5822181. PMID 29275361.
Angermueller C, Pärnamaa T, Parts L, Stegle O (July 2016). "Deep learning for computational biology". Molecular Systems Biology. 12 (7): 878. doi:10.15252/msb.20156651. PMC 4965871. PMID 27474269.
Cao C, Liu F, Tan H, Song D, Shu W, Li W, et al. (February 2018). "Deep Learning and Its Applications in Biomedicine". Genomics, Proteomics & Bioinformatics. 16 (1): 17–32. doi:10.1016/j.gpb.2017.07.003. PMC 6000200. PMID 29522900.
Zou J, Huss M, Abid A, Mohammadi P, Torkamani A, Telenti A (January 2019). "A primer on deep learning in genomics". Nature Genetics. 51 (1): 12–18. doi:10.1038/s41588-018-0295-5. PMC 11180539. PMID 30478442. S2CID 205572042.
Zeng Z, Shi H, Wu Y, Hong Z (2015). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1155/2015/674296. PMC 4615216. PMID 26525745.
Zeng Z, Shi H, Wu Y, Hong Z (2012). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1016/B978-0-12-385467-4.00006-3. PMC 4615216. PMID 26525745.
Zeng Z, Shi H, Wu Y, Hong Z (2017). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1155/2015/674296. PMC 4615216. PMID 26525745.
Mathé C, Sagot MF, Schiex T, Rouzé P (October 2002). "Current methods of gene prediction, their strengths and weaknesses". Nucleic Acids Research. 30 (19): 4103–17. doi:10.1093/nar/gkf543. PMC 140543. PMID 12364589.
Pratas D, Silva RM, Pinho AJ, Ferreira PJ (May 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5 (10203): 10203. Bibcode:2015NatSR...510203P. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.
Pauling L, Corey RB, Branson HR (April 1951). "The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain". Proceedings of the National Academy of Sciences of the United States of America. 37 (4): 205–11. Bibcode:1951PNAS...37..205P. doi:10.1073/pnas.37.4.205. PMC 1063337. PMID 14816373.
Wang S, Peng J, Ma J, Xu J (January 2016). "Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields". Scientific Reports. 6: 18962. arXiv:1512.00843. Bibcode:2016NatSR...618962W. doi:10.1038/srep18962. PMC 4707437. PMID 26752681.
Riesenfeld CS, Schloss PD, Handelsman J (2004). "Metagenomics: genomic analysis of microbial communities". Annual Review of Genetics. 38 (1): 525–52. doi:10.1146/annurev.genet.38.072902.091216. PMID 15568985.
Soueidan, Hayssam; Nikolski, Macha (January 1, 2017). "Machine learning for metagenomics: methods and tools". Metagenomics. 1 (1). arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.
Lin Y, Wang G, Yu J, Sung JJ (April 2021). "Artificial intelligence and metagenomics in intestinal diseases". Journal of Gastroenterology and Hepatology. 36 (4): 841–847. doi:10.1111/jgh.15501. PMID 33880764. S2CID 233312307.
Dang T, Kishino H (January 2020). "Detecting significant components of microbiomes by random forest with forward variable selection and phylogenetics". bioRxiv 10.1101/2020.10.29.361360.
Fioravanti D, Giarratano Y, Maggio V, Agostinelli C, Chierici M, Jurman G, Furlanello C (March 2018). "Phylogenetic convolutional neural networks in metagenomics". BMC Bioinformatics. 19 (Suppl 2): 49. doi:10.1186/s12859-018-2033-5. PMC 5850953. PMID 29536822.
Dhungel E, Mreyoud Y, Gwak HJ, Rajeh A, Rho M, Ahn TH (January 2021). "MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning". BMC Bioinformatics. 22 (1): 25. doi:10.1186/s12859-020-03933-4. PMC 7814621. PMID 33461494.
Xun W, Liu Y, Li W, Ren Y, Xiong W, Xu Z, et al. (January 2021). "Specialized metabolic functions of keystone taxa sustain soil microbiome stability". Microbiome. 9 (1): 35. doi:10.1186/s40168-020-00985-9. PMC 7849160. PMID 33517892.
Pirooznia M, Yang JY, Yang MQ, Deng Y (2008). "A comparative study of different machine learning methods on microarray gene expression data". BMC Genomics. 9 Suppl 1 (1): S13. doi:10.1186/1471-2164-9-S1-S13. PMC 2386055. PMID 18366602.
d'Alché-Buc F, Wehenkel L (December 2008). "Machine learning in systems biology". BMC Proceedings. 2 Suppl 4 (4): S1. doi:10.1186/1753-6561-2-S4-S1. PMC 2654969. PMID 19091048.
Topol EJ (January 2019). "High-performance medicine: the convergence of human and artificial intelligence". Nature Medicine. 25 (1): 44–56. doi:10.1038/s41591-018-0300-7. hdl:10654/45728. PMID 30617339. S2CID 57574615.
Jiang F, Jiang Y, Zhi H, Dong Y, Li H, Ma S, et al. (December 2017). "Artificial intelligence in healthcare: past, present and future". Stroke and Vascular Neurology. 2 (4): 230–243. doi:10.1136/svn-2017-000101. PMC 5829945. PMID 29507784.
Mirtskhulava L, Wong J, Al-Majeed S, Pearce G (March 2015). "Artificial Neural Network Model in Stroke Diagnosis" (PDF). 2015 17th UKSim-AMSS International Conference on Modelling and Simulation (UKSim). pp. 50–53. doi:10.1109/UKSim.2015.33. ISBN 978-1-4799-8713-9. S2CID 6391733.
Titano JJ, Badgeley M, Schefflein J, Pain M, Su A, Cai M, et al. (September 2018). "Automated deep-neural-network surveillance of cranial images for acute neurologic events". Nature Medicine. 24 (9): 1337–1341. doi:10.1038/s41591-018-0147-y. PMID 30104767. S2CID 51976344.
Krallinger M, Erhardt RA, Valencia A (March 2005). "Text-mining approaches in molecular biology and biomedicine". Drug Discovery Today. 10 (6): 439–45. doi:10.1016/S1359-6446(05)03376-3. PMID 15808823.
Pratas D, Hosseini M, Silva R, Pinho A, Ferreira P (June 20–23, 2017). "Visualization of Distinct DNA Regions of the Modern Human Relatively to a Neanderthal Genome". Pattern Recognition and Image Analysis. Lecture Notes in Computer Science. Vol. 10255. pp. 235–242. doi:10.1007/978-3-319-58838-4_26. ISBN 978-3-319-58837-7.
Bardgett RD, Caruso T (March 2020). "Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375 (1794): 20190112. doi:10.1098/rstb.2019.0112. PMC 7017770. PMID 31983338.
Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, et al. (May 2018). "Bacterial-fungal interactions: ecology, mechanisms and challenges". FEMS Microbiology Reviews. 42 (3): 335–352. doi:10.1093/femsre/fuy008. hdl:21.11116/0000-0002-C1E7-F. PMID 29471481.
Ansari MZ, Yadav G, Gokhale RS, Mohanty D (July 2004). "NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases". Nucleic Acids Research. 32 (Web Server issue): W405-13. doi:10.1093/nar/gkh359. PMC 441497. PMID 15215420.
Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, et al. (January 2020). "A computational framework to explore large-scale biosynthetic diversity". Nature Chemical Biology. 16 (1): 60–68. doi:10.1038/s41589-019-0400-9. PMC 6917865. PMID 31768033.
Doroghazi JR, Albright JC, Goering AW, Ju KS, Haines RR, Tchalukov KA, et al. (November 2014). "A roadmap for natural product discovery based on large-scale genomics and metabolomics". Nature Chemical Biology. 10 (11): 963–8. doi:10.1038/nchembio.1659. PMC 4201863. PMID 25262415.
Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, et al. (July 2014). "Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters". Cell. 158 (2): 412–421. doi:10.1016/j.cell.2014.06.034. PMC 4123684. PMID 25036635.
Goering AW, McClure RA, Doroghazi JR, Albright JC, Haverland NA, Zhang Y, et al. (February 2016). "Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer". ACS Central Science. 2 (2): 99–108. doi:10.1021/acscentsci.5b00331. PMC 4827660. PMID 27163034.
Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, et al. (November 2018). "Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites". Scientific Reports. 8 (1): 16600. Bibcode:2018NatSR...816600A. doi:10.1038/s41598-018-34954-y. PMC 6226438. PMID 30413766.
Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, et al. (April 2015). "Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species". Chemistry & Biology. 22 (4): 460–471. doi:10.1016/j.chembiol.2015.03.010. PMC 4409930. PMID 25865308.
Nielsen JC, Grijseels S, Prigent S, Ji B, Dainat J, Nielsen KF, et al. (April 2017). "Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species". Nature Microbiology. 2 (6): 17044. doi:10.1038/nmicrobiol.2017.44. PMID 28368369. S2CID 22699928.
McClure RA, Goering AW, Ju KS, Baccile JA, Schroeder FC, Metcalf WW, et al. (December 2016). "Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations". ACS Chemical Biology. 11 (12): 3452–3460. doi:10.1021/acschembio.6b00779. PMC 5295535. PMID 27809474.
Cao L, Shcherbin E, Mohimani H (August 2019). "A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota". mSystems. 4 (4): e00387–19, /msystems/4/4/msys.00387–19.atom. doi:10.1128/mSystems.00387-19. PMC 6712304. PMID 31455639.
Olm MR, Bhattacharya N, Crits-Christoph A, Firek BA, Baker R, Song YS, et al. (December 2019). "Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria". Science Advances. 5 (12): eaax5727. Bibcode:2019SciA....5.5727O. doi:10.1126/sciadv.aax5727. PMC 6905865. PMID 31844663.
Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, et al. (November 2019). "Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome". Science. 366 (6465): 606–612. Bibcode:2019Sci...366..606C. doi:10.1126/science.aaw9285. hdl:1887/3188901. PMID 31672892. S2CID 207814746.
Pascal Andreu, Victória; Augustijn, Hannah E.; van den Berg, Koen; van der Hooft, Justin J. J.; Fischbach, Michael A.; Medema, Marnix H. (October 26, 2021). Shank, Elizabeth Anne (ed.). "BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes". mSystems. 6 (5): e0093721. doi:10.1128/mSystems.00937-21. ISSN 2379-5077. PMC 8547482. PMID 34581602.
Agrawal P, Khater S, Gupta M, Sain N, Mohanty D (July 2017). "RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links". Nucleic Acids Research. 45 (W1): W80 – W88. doi:10.1093/nar/gkx408. PMC 5570163. PMID 28499008.
Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJ (February 2021). "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLOS Computational Biology. 17 (2): e1008724. Bibcode:2021PLSCB..17E8724H. doi:10.1371/journal.pcbi.1008724. PMC 7909622. PMID 33591968.
Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJ (February 2021). "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLOS Computational Biology. 17 (2): e1008724. Bibcode:2021PLSCB..17E8724H. doi:10.1371/journal.pcbi.1008724. PMC 7909622. PMID 33591968.
Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, et al. (NCBI Resource Coordinators) (January 2018). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research. 46 (D1): D8 – D13. doi:10.1093/nar/gkx1095. PMC 5753372. PMID 29140470.
Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJ, et al. (January 2020). "MIBiG 2.0: a repository for biosynthetic gene clusters of known function". Nucleic Acids Research. 48 (D1): D454 – D458. doi:10.1093/nar/gkz882. PMC 7145714. PMID 31612915.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. (January 2013). "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools". Nucleic Acids Research. 41 (Database issue): D590-6. doi:10.1093/nar/gks1219. PMC 3531112. PMID 23193283.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. (July 2006). "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB". Applied and Environmental Microbiology. 72 (7): 5069–72. Bibcode:2006ApEnM..72.5069D. doi:10.1128/AEM.03006-05. PMC 1489311. PMID 16820507.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. (March 2012). "An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea". The ISME Journal. 6 (3): 610–8. Bibcode:2012ISMEJ...6..610M. doi:10.1038/ismej.2011.139. PMC 3280142. PMID 22134646.
Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, et al. (October 2015). "Synthesis of phylogeny and taxonomy into a comprehensive tree of life". Proceedings of the National Academy of Sciences of the United States of America. 112 (41): 12764–9. Bibcode:2015PNAS..11212764H. doi:10.1073/pnas.1423041112. PMC 4611642. PMID 26385966.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. (January 2014). "Ribosomal Database Project: data and tools for high throughput rRNA analysis". Nucleic Acids Research. 42 (Database issue): D633-42. doi:10.1093/nar/gkt1244. PMC 3965039. PMID 24288368.

drive.google.com

Zhang W (1988). "Shift-invariant pattern recognition neural network and its optical architecture". Proceedings of Annual Conference of the Japan Society of Applied Physics.

frontiersin.org

journal.frontiersin.org

"Machine Learning in Molecular Systems Biology". Frontiers. Retrieved June 9, 2017.

glos.ac.uk

eprints.glos.ac.uk

Mirtskhulava L, Wong J, Al-Majeed S, Pearce G (March 2015). "Artificial Neural Network Model in Stroke Diagnosis" (PDF). 2015 17th UKSim-AMSS International Conference on Modelling and Simulation (UKSim). pp. 50–53. doi:10.1109/UKSim.2015.33. ISBN 978-1-4799-8713-9. S2CID 6391733.

handle.net

hdl.handle.net

Topol EJ (January 2019). "High-performance medicine: the convergence of human and artificial intelligence". Nature Medicine. 25 (1): 44–56. doi:10.1038/s41591-018-0300-7. hdl:10654/45728. PMID 30617339. S2CID 57574615.
Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, et al. (May 2018). "Bacterial-fungal interactions: ecology, mechanisms and challenges". FEMS Microbiology Reviews. 42 (3): 335–352. doi:10.1093/femsre/fuy008. hdl:21.11116/0000-0002-C1E7-F. PMID 29471481.
Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, et al. (November 2019). "Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome". Science. 366 (6465): 606–612. Bibcode:2019Sci...366..606C. doi:10.1126/science.aaw9285. hdl:1887/3188901. PMID 31672892. S2CID 207814746.

harvard.edu

ui.adsabs.harvard.edu

Pérez-Wohlfeil E, Torrenoa O, Bellis LJ, Fernandes PL, Leskosek B, Trellesa O (December 2018). "Training bioinformaticians in High Performance Computing". Heliyon. 4 (12): e01057. Bibcode:2018Heliy...401057P. doi:10.1016/j.heliyon.2018.e01057. PMC 6299036. PMID 30582061.
McClintock BT, Langrock R, Gimenez O, Cam E, Borchers DL, Glennie R, Patterson TA (December 2020). "Uncovering ecological state dynamics with hidden Markov models". Ecology Letters. 23 (12): 1878–1903. arXiv:2002.10497. Bibcode:2020EcolL..23.1878M. doi:10.1111/ele.13610. PMC 7702077. PMID 33073921.
Zhang W, Itoh K, Tanida J, Ichioka Y (November 1990). "Parallel distributed processing model with local space-invariant interconnections and its optical architecture". Applied Optics. 29 (32): 4790–7. Bibcode:1990ApOpt..29.4790Z. doi:10.1364/AO.29.004790. PMID 20577468.
Fukushima K (2007). "Neocognitron". Scholarpedia. 2 (1): 1717. Bibcode:2007SchpJ...2.1717F. doi:10.4249/scholarpedia.1717.
Breiman, Leo (2001). "Radom Forests". Machine Learning. 45 (1): 5–32. Bibcode:2001MachL..45....5B. doi:10.1023/A:1010933404324. S2CID 89141.
Pratas D, Silva RM, Pinho AJ, Ferreira PJ (May 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5 (10203): 10203. Bibcode:2015NatSR...510203P. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.
Pauling L, Corey RB, Branson HR (April 1951). "The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain". Proceedings of the National Academy of Sciences of the United States of America. 37 (4): 205–11. Bibcode:1951PNAS...37..205P. doi:10.1073/pnas.37.4.205. PMC 1063337. PMID 14816373.
Wang S, Peng J, Ma J, Xu J (January 2016). "Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields". Scientific Reports. 6: 18962. arXiv:1512.00843. Bibcode:2016NatSR...618962W. doi:10.1038/srep18962. PMC 4707437. PMID 26752681.
Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, et al. (November 2018). "Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites". Scientific Reports. 8 (1): 16600. Bibcode:2018NatSR...816600A. doi:10.1038/s41598-018-34954-y. PMC 6226438. PMID 30413766.
Olm MR, Bhattacharya N, Crits-Christoph A, Firek BA, Baker R, Song YS, et al. (December 2019). "Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria". Science Advances. 5 (12): eaax5727. Bibcode:2019SciA....5.5727O. doi:10.1126/sciadv.aax5727. PMC 6905865. PMID 31844663.
Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, et al. (November 2019). "Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome". Science. 366 (6465): 606–612. Bibcode:2019Sci...366..606C. doi:10.1126/science.aaw9285. hdl:1887/3188901. PMID 31672892. S2CID 207814746.
Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJ (February 2021). "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLOS Computational Biology. 17 (2): e1008724. Bibcode:2021PLSCB..17E8724H. doi:10.1371/journal.pcbi.1008724. PMC 7909622. PMID 33591968.
Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJ (February 2021). "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLOS Computational Biology. 17 (2): e1008724. Bibcode:2021PLSCB..17E8724H. doi:10.1371/journal.pcbi.1008724. PMC 7909622. PMID 33591968.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. (July 2006). "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB". Applied and Environmental Microbiology. 72 (7): 5069–72. Bibcode:2006ApEnM..72.5069D. doi:10.1128/AEM.03006-05. PMC 1489311. PMID 16820507.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. (March 2012). "An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea". The ISME Journal. 6 (3): 610–8. Bibcode:2012ISMEJ...6..610M. doi:10.1038/ismej.2011.139. PMC 3280142. PMID 22134646.
Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, et al. (October 2015). "Synthesis of phylogeny and taxonomy into a comprehensive tree of life". Proceedings of the National Academy of Sciences of the United States of America. 112 (41): 12764–9. Bibcode:2015PNAS..11212764H. doi:10.1073/pnas.1423041112. PMC 4611642. PMID 26385966.

ieee.org

ieeexplore.ieee.org

Rabiner L, Juang B (January 1986). "An introduction to hidden Markov models". IEEE ASSP Magazine. 3 (1): 4–16. doi:10.1109/MASSP.1986.1165342. ISSN 1558-1284. S2CID 11358505.

msu.edu

rdp.cme.msu.edu

"RDP Release 11 -- Sequence Analysis Tools". rdp.cme.msu.edu. Archived from the original on August 19, 2020. Retrieved July 30, 2021.

nih.gov

pubmed.ncbi.nlm.nih.gov

Chicco D (December 2017). "Ten quick tips for machine learning in computational biology". BioData Mining. 10 (35): 35. doi:10.1186/s13040-017-0155-3. PMC 5721660. PMID 29234465.
Larrañaga P, Calvo B, Santana R, Bielza C, Galdiano J, Inza I, et al. (March 2006). "Machine learning in bioinformatics". Briefings in Bioinformatics. 7 (1): 86–112. doi:10.1093/bib/bbk007. PMID 16761367.
Pérez-Wohlfeil E, Torrenoa O, Bellis LJ, Fernandes PL, Leskosek B, Trellesa O (December 2018). "Training bioinformaticians in High Performance Computing". Heliyon. 4 (12): e01057. Bibcode:2018Heliy...401057P. doi:10.1016/j.heliyon.2018.e01057. PMC 6299036. PMID 30582061.
Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y (May 2018). "Sixty-five years of the long march in protein secondary structure prediction: the final stretch?". Briefings in Bioinformatics. 19 (3): 482–494. doi:10.1093/bib/bbw129. PMC 5952956. PMID 28040746.
Amoros R, King R, Toyoda H, Kumada T, Johnson PJ, Bird TG (May 30, 2019). "A continuous-time hidden Markov model for cancer surveillance using serum biomarkers with application to hepatocellular carcinoma". Metron. 77 (2): 67–86. doi:10.1007/s40300-019-00151-8. PMC 6820468. PMID 31708595.
Eddy SR (October 1, 1998). "Profile hidden Markov models". Bioinformatics. 14 (9): 755–63. doi:10.1093/bioinformatics/14.9.755. PMID 9918945.
McClintock BT, Langrock R, Gimenez O, Cam E, Borchers DL, Glennie R, Patterson TA (December 2020). "Uncovering ecological state dynamics with hidden Markov models". Ecology Letters. 23 (12): 1878–1903. arXiv:2002.10497. Bibcode:2020EcolL..23.1878M. doi:10.1111/ele.13610. PMC 7702077. PMID 33073921.
Zhang W, Itoh K, Tanida J, Ichioka Y (November 1990). "Parallel distributed processing model with local space-invariant interconnections and its optical architecture". Applied Optics. 29 (32): 4790–7. Bibcode:1990ApOpt..29.4790Z. doi:10.1364/AO.29.004790. PMID 20577468.
Hubel DH, Wiesel TN (March 1968). "Receptive fields and functional architecture of monkey striate cortex". The Journal of Physiology. 195 (1): 215–43. doi:10.1113/jphysiol.1968.sp008455. PMC 1557912. PMID 4966457.
Fukushima K (1980). "Neocognitron: a self organizing neural network model for a mechanism of pattern recognition unaffected by shift in position". Biological Cybernetics. 36 (4): 193–202. doi:10.1007/BF00344251. PMID 7370364. S2CID 206775608.
Matsugu M, Mori K, Mitari Y, Kaneda Y (2003). "Subject independent facial expression recognition with robust face detection using a convolutional neural network". Neural Networks. 16 (5–6): 555–9. doi:10.1016/S0893-6080(03)00115-1. PMID 12850007.
Fioravanti D, Giarratano Y, Maggio V, Agostinelli C, Chierici M, Jurman G, Furlanello C (March 2018). "Phylogenetic convolutional neural networks in metagenomics". BMC Bioinformatics. 19 (Suppl 2): 49. doi:10.1186/s12859-018-2033-5. PMC 5850953. PMID 29536822.
Ji, Yanrong; Zhou, Zhihan; Liu, Han; Davuluri, Ramana V (August 9, 2021). Kelso, Janet (ed.). "DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome". Bioinformatics. 37 (15): 2112–2120. doi:10.1093/bioinformatics/btab083. ISSN 1367-4803. PMC 11025658. PMID 33538820.
Gündüz, Hüseyin Anil; Binder, Martin; To, Xiao-Yin; Mreches, René; Bischl, Bernd; McHardy, Alice C.; Münch, Philipp C.; Rezaei, Mina (September 11, 2023). "A self-supervised deep learning method for data-efficient training in genomics". Communications Biology. 6 (1): 928. doi:10.1038/s42003-023-05310-2. ISSN 2399-3642. PMC 10495322. PMID 37696966.
Karim MR, Beyan O, Zappa A, Costa IG, Rebholz-Schuhmann D, Cochez M, Decker S (January 2021). "Deep learning-based clustering approaches for bioinformatics". Briefings in Bioinformatics. 22 (1): 393–415. doi:10.1093/bib/bbz170. PMC 7820885. PMID 32008043.
Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, et al. (January 2020). "A computational framework to explore large-scale biosynthetic diversity". Nature Chemical Biology. 16 (1): 60–68. doi:10.1038/s41589-019-0400-9. PMC 6917865. PMID 31768033.
Libbrecht MW, Noble WS (June 2015). "Machine learning applications in genetics and genomics". Nature Reviews. Genetics. 16 (6): 321–32. doi:10.1038/nrg3920. PMC 5204302. PMID 25948244.
Degroeve S, De Baets B, Van de Peer Y, Rouzé P (2002). "Feature subset selection for splice site prediction". Bioinformatics. 18 (Suppl 2): S75-83. doi:10.1093/bioinformatics/18.suppl_2.s75. PMID 12385987.
Huang S, Cai N, Pacheco PP, Narrandes S, Wang Y, Xu W (January 2018). "Applications of Support Vector Machine (SVM) Learning in Cancer Genomics". Cancer Genomics & Proteomics. 15 (1): 41–51. doi:10.21873/cgp.20063. PMC 5822181. PMID 29275361.
Angermueller C, Pärnamaa T, Parts L, Stegle O (July 2016). "Deep learning for computational biology". Molecular Systems Biology. 12 (7): 878. doi:10.15252/msb.20156651. PMC 4965871. PMID 27474269.
Cao C, Liu F, Tan H, Song D, Shu W, Li W, et al. (February 2018). "Deep Learning and Its Applications in Biomedicine". Genomics, Proteomics & Bioinformatics. 16 (1): 17–32. doi:10.1016/j.gpb.2017.07.003. PMC 6000200. PMID 29522900.
Zou J, Huss M, Abid A, Mohammadi P, Torkamani A, Telenti A (January 2019). "A primer on deep learning in genomics". Nature Genetics. 51 (1): 12–18. doi:10.1038/s41588-018-0295-5. PMC 11180539. PMID 30478442. S2CID 205572042.
Zeng Z, Shi H, Wu Y, Hong Z (2015). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1155/2015/674296. PMC 4615216. PMID 26525745.
Zeng Z, Shi H, Wu Y, Hong Z (2012). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1016/B978-0-12-385467-4.00006-3. PMC 4615216. PMID 26525745.
Zeng Z, Shi H, Wu Y, Hong Z (2017). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1155/2015/674296. PMC 4615216. PMID 26525745.
Mathé C, Sagot MF, Schiex T, Rouzé P (October 2002). "Current methods of gene prediction, their strengths and weaknesses". Nucleic Acids Research. 30 (19): 4103–17. doi:10.1093/nar/gkf543. PMC 140543. PMID 12364589.
Pratas D, Silva RM, Pinho AJ, Ferreira PJ (May 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5 (10203): 10203. Bibcode:2015NatSR...510203P. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.
Pauling L, Corey RB, Branson HR (April 1951). "The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain". Proceedings of the National Academy of Sciences of the United States of America. 37 (4): 205–11. Bibcode:1951PNAS...37..205P. doi:10.1073/pnas.37.4.205. PMC 1063337. PMID 14816373.
Wang S, Peng J, Ma J, Xu J (January 2016). "Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields". Scientific Reports. 6: 18962. arXiv:1512.00843. Bibcode:2016NatSR...618962W. doi:10.1038/srep18962. PMC 4707437. PMID 26752681.
Riesenfeld CS, Schloss PD, Handelsman J (2004). "Metagenomics: genomic analysis of microbial communities". Annual Review of Genetics. 38 (1): 525–52. doi:10.1146/annurev.genet.38.072902.091216. PMID 15568985.
Lin Y, Wang G, Yu J, Sung JJ (April 2021). "Artificial intelligence and metagenomics in intestinal diseases". Journal of Gastroenterology and Hepatology. 36 (4): 841–847. doi:10.1111/jgh.15501. PMID 33880764. S2CID 233312307.
Fioravanti D, Giarratano Y, Maggio V, Agostinelli C, Chierici M, Jurman G, Furlanello C (March 2018). "Phylogenetic convolutional neural networks in metagenomics". BMC Bioinformatics. 19 (Suppl 2): 49. doi:10.1186/s12859-018-2033-5. PMC 5850953. PMID 29536822.
Dhungel E, Mreyoud Y, Gwak HJ, Rajeh A, Rho M, Ahn TH (January 2021). "MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning". BMC Bioinformatics. 22 (1): 25. doi:10.1186/s12859-020-03933-4. PMC 7814621. PMID 33461494.
Xun W, Liu Y, Li W, Ren Y, Xiong W, Xu Z, et al. (January 2021). "Specialized metabolic functions of keystone taxa sustain soil microbiome stability". Microbiome. 9 (1): 35. doi:10.1186/s40168-020-00985-9. PMC 7849160. PMID 33517892.
Pirooznia M, Yang JY, Yang MQ, Deng Y (2008). "A comparative study of different machine learning methods on microarray gene expression data". BMC Genomics. 9 Suppl 1 (1): S13. doi:10.1186/1471-2164-9-S1-S13. PMC 2386055. PMID 18366602.
d'Alché-Buc F, Wehenkel L (December 2008). "Machine learning in systems biology". BMC Proceedings. 2 Suppl 4 (4): S1. doi:10.1186/1753-6561-2-S4-S1. PMC 2654969. PMID 19091048.
Topol EJ (January 2019). "High-performance medicine: the convergence of human and artificial intelligence". Nature Medicine. 25 (1): 44–56. doi:10.1038/s41591-018-0300-7. hdl:10654/45728. PMID 30617339. S2CID 57574615.
Jiang F, Jiang Y, Zhi H, Dong Y, Li H, Ma S, et al. (December 2017). "Artificial intelligence in healthcare: past, present and future". Stroke and Vascular Neurology. 2 (4): 230–243. doi:10.1136/svn-2017-000101. PMC 5829945. PMID 29507784.
Titano JJ, Badgeley M, Schefflein J, Pain M, Su A, Cai M, et al. (September 2018). "Automated deep-neural-network surveillance of cranial images for acute neurologic events". Nature Medicine. 24 (9): 1337–1341. doi:10.1038/s41591-018-0147-y. PMID 30104767. S2CID 51976344.
Krallinger M, Erhardt RA, Valencia A (March 2005). "Text-mining approaches in molecular biology and biomedicine". Drug Discovery Today. 10 (6): 439–45. doi:10.1016/S1359-6446(05)03376-3. PMID 15808823.
Bardgett RD, Caruso T (March 2020). "Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375 (1794): 20190112. doi:10.1098/rstb.2019.0112. PMC 7017770. PMID 31983338.
Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, et al. (May 2018). "Bacterial-fungal interactions: ecology, mechanisms and challenges". FEMS Microbiology Reviews. 42 (3): 335–352. doi:10.1093/femsre/fuy008. hdl:21.11116/0000-0002-C1E7-F. PMID 29471481.
Ansari MZ, Yadav G, Gokhale RS, Mohanty D (July 2004). "NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases". Nucleic Acids Research. 32 (Web Server issue): W405-13. doi:10.1093/nar/gkh359. PMC 441497. PMID 15215420.
Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, et al. (January 2020). "A computational framework to explore large-scale biosynthetic diversity". Nature Chemical Biology. 16 (1): 60–68. doi:10.1038/s41589-019-0400-9. PMC 6917865. PMID 31768033.
Doroghazi JR, Albright JC, Goering AW, Ju KS, Haines RR, Tchalukov KA, et al. (November 2014). "A roadmap for natural product discovery based on large-scale genomics and metabolomics". Nature Chemical Biology. 10 (11): 963–8. doi:10.1038/nchembio.1659. PMC 4201863. PMID 25262415.
Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, et al. (July 2014). "Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters". Cell. 158 (2): 412–421. doi:10.1016/j.cell.2014.06.034. PMC 4123684. PMID 25036635.
Goering AW, McClure RA, Doroghazi JR, Albright JC, Haverland NA, Zhang Y, et al. (February 2016). "Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer". ACS Central Science. 2 (2): 99–108. doi:10.1021/acscentsci.5b00331. PMC 4827660. PMID 27163034.
Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, et al. (November 2018). "Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites". Scientific Reports. 8 (1): 16600. Bibcode:2018NatSR...816600A. doi:10.1038/s41598-018-34954-y. PMC 6226438. PMID 30413766.
Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, et al. (April 2015). "Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species". Chemistry & Biology. 22 (4): 460–471. doi:10.1016/j.chembiol.2015.03.010. PMC 4409930. PMID 25865308.
Nielsen JC, Grijseels S, Prigent S, Ji B, Dainat J, Nielsen KF, et al. (April 2017). "Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species". Nature Microbiology. 2 (6): 17044. doi:10.1038/nmicrobiol.2017.44. PMID 28368369. S2CID 22699928.
McClure RA, Goering AW, Ju KS, Baccile JA, Schroeder FC, Metcalf WW, et al. (December 2016). "Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations". ACS Chemical Biology. 11 (12): 3452–3460. doi:10.1021/acschembio.6b00779. PMC 5295535. PMID 27809474.
Cao L, Shcherbin E, Mohimani H (August 2019). "A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota". mSystems. 4 (4): e00387–19, /msystems/4/4/msys.00387–19.atom. doi:10.1128/mSystems.00387-19. PMC 6712304. PMID 31455639.
Olm MR, Bhattacharya N, Crits-Christoph A, Firek BA, Baker R, Song YS, et al. (December 2019). "Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria". Science Advances. 5 (12): eaax5727. Bibcode:2019SciA....5.5727O. doi:10.1126/sciadv.aax5727. PMC 6905865. PMID 31844663.
Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, et al. (November 2019). "Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome". Science. 366 (6465): 606–612. Bibcode:2019Sci...366..606C. doi:10.1126/science.aaw9285. hdl:1887/3188901. PMID 31672892. S2CID 207814746.
Pascal Andreu, Victória; Augustijn, Hannah E.; van den Berg, Koen; van der Hooft, Justin J. J.; Fischbach, Michael A.; Medema, Marnix H. (October 26, 2021). Shank, Elizabeth Anne (ed.). "BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes". mSystems. 6 (5): e0093721. doi:10.1128/mSystems.00937-21. ISSN 2379-5077. PMC 8547482. PMID 34581602.
Agrawal P, Khater S, Gupta M, Sain N, Mohanty D (July 2017). "RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links". Nucleic Acids Research. 45 (W1): W80 – W88. doi:10.1093/nar/gkx408. PMC 5570163. PMID 28499008.
Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJ (February 2021). "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLOS Computational Biology. 17 (2): e1008724. Bibcode:2021PLSCB..17E8724H. doi:10.1371/journal.pcbi.1008724. PMC 7909622. PMID 33591968.
Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJ (February 2021). "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLOS Computational Biology. 17 (2): e1008724. Bibcode:2021PLSCB..17E8724H. doi:10.1371/journal.pcbi.1008724. PMC 7909622. PMID 33591968.
Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, et al. (NCBI Resource Coordinators) (January 2018). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research. 46 (D1): D8 – D13. doi:10.1093/nar/gkx1095. PMC 5753372. PMID 29140470.
Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJ, et al. (January 2020). "MIBiG 2.0: a repository for biosynthetic gene clusters of known function". Nucleic Acids Research. 48 (D1): D454 – D458. doi:10.1093/nar/gkz882. PMC 7145714. PMID 31612915.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. (January 2013). "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools". Nucleic Acids Research. 41 (Database issue): D590-6. doi:10.1093/nar/gks1219. PMC 3531112. PMID 23193283.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. (July 2006). "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB". Applied and Environmental Microbiology. 72 (7): 5069–72. Bibcode:2006ApEnM..72.5069D. doi:10.1128/AEM.03006-05. PMC 1489311. PMID 16820507.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. (March 2012). "An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea". The ISME Journal. 6 (3): 610–8. Bibcode:2012ISMEJ...6..610M. doi:10.1038/ismej.2011.139. PMC 3280142. PMID 22134646.
Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, et al. (October 2015). "Synthesis of phylogeny and taxonomy into a comprehensive tree of life". Proceedings of the National Academy of Sciences of the United States of America. 112 (41): 12764–9. Bibcode:2015PNAS..11212764H. doi:10.1073/pnas.1423041112. PMC 4611642. PMID 26385966.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. (January 2014). "Ribosomal Database Project: data and tools for high throughput rRNA analysis". Nucleic Acids Research. 42 (Database issue): D633-42. doi:10.1093/nar/gkt1244. PMC 3965039. PMID 24288368.

ncbi.nlm.nih.gov

Chicco D (December 2017). "Ten quick tips for machine learning in computational biology". BioData Mining. 10 (35): 35. doi:10.1186/s13040-017-0155-3. PMC 5721660. PMID 29234465.
Pérez-Wohlfeil E, Torrenoa O, Bellis LJ, Fernandes PL, Leskosek B, Trellesa O (December 2018). "Training bioinformaticians in High Performance Computing". Heliyon. 4 (12): e01057. Bibcode:2018Heliy...401057P. doi:10.1016/j.heliyon.2018.e01057. PMC 6299036. PMID 30582061.
Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y (May 2018). "Sixty-five years of the long march in protein secondary structure prediction: the final stretch?". Briefings in Bioinformatics. 19 (3): 482–494. doi:10.1093/bib/bbw129. PMC 5952956. PMID 28040746.
Amoros R, King R, Toyoda H, Kumada T, Johnson PJ, Bird TG (May 30, 2019). "A continuous-time hidden Markov model for cancer surveillance using serum biomarkers with application to hepatocellular carcinoma". Metron. 77 (2): 67–86. doi:10.1007/s40300-019-00151-8. PMC 6820468. PMID 31708595.
McClintock BT, Langrock R, Gimenez O, Cam E, Borchers DL, Glennie R, Patterson TA (December 2020). "Uncovering ecological state dynamics with hidden Markov models". Ecology Letters. 23 (12): 1878–1903. arXiv:2002.10497. Bibcode:2020EcolL..23.1878M. doi:10.1111/ele.13610. PMC 7702077. PMID 33073921.
Hubel DH, Wiesel TN (March 1968). "Receptive fields and functional architecture of monkey striate cortex". The Journal of Physiology. 195 (1): 215–43. doi:10.1113/jphysiol.1968.sp008455. PMC 1557912. PMID 4966457.
Fioravanti D, Giarratano Y, Maggio V, Agostinelli C, Chierici M, Jurman G, Furlanello C (March 2018). "Phylogenetic convolutional neural networks in metagenomics". BMC Bioinformatics. 19 (Suppl 2): 49. doi:10.1186/s12859-018-2033-5. PMC 5850953. PMID 29536822.
Ji, Yanrong; Zhou, Zhihan; Liu, Han; Davuluri, Ramana V (August 9, 2021). Kelso, Janet (ed.). "DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome". Bioinformatics. 37 (15): 2112–2120. doi:10.1093/bioinformatics/btab083. ISSN 1367-4803. PMC 11025658. PMID 33538820.
Gündüz, Hüseyin Anil; Binder, Martin; To, Xiao-Yin; Mreches, René; Bischl, Bernd; McHardy, Alice C.; Münch, Philipp C.; Rezaei, Mina (September 11, 2023). "A self-supervised deep learning method for data-efficient training in genomics". Communications Biology. 6 (1): 928. doi:10.1038/s42003-023-05310-2. ISSN 2399-3642. PMC 10495322. PMID 37696966.
Karim MR, Beyan O, Zappa A, Costa IG, Rebholz-Schuhmann D, Cochez M, Decker S (January 2021). "Deep learning-based clustering approaches for bioinformatics". Briefings in Bioinformatics. 22 (1): 393–415. doi:10.1093/bib/bbz170. PMC 7820885. PMID 32008043.
Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, et al. (January 2020). "A computational framework to explore large-scale biosynthetic diversity". Nature Chemical Biology. 16 (1): 60–68. doi:10.1038/s41589-019-0400-9. PMC 6917865. PMID 31768033.
Libbrecht MW, Noble WS (June 2015). "Machine learning applications in genetics and genomics". Nature Reviews. Genetics. 16 (6): 321–32. doi:10.1038/nrg3920. PMC 5204302. PMID 25948244.
Huang S, Cai N, Pacheco PP, Narrandes S, Wang Y, Xu W (January 2018). "Applications of Support Vector Machine (SVM) Learning in Cancer Genomics". Cancer Genomics & Proteomics. 15 (1): 41–51. doi:10.21873/cgp.20063. PMC 5822181. PMID 29275361.
Angermueller C, Pärnamaa T, Parts L, Stegle O (July 2016). "Deep learning for computational biology". Molecular Systems Biology. 12 (7): 878. doi:10.15252/msb.20156651. PMC 4965871. PMID 27474269.
Cao C, Liu F, Tan H, Song D, Shu W, Li W, et al. (February 2018). "Deep Learning and Its Applications in Biomedicine". Genomics, Proteomics & Bioinformatics. 16 (1): 17–32. doi:10.1016/j.gpb.2017.07.003. PMC 6000200. PMID 29522900.
Zou J, Huss M, Abid A, Mohammadi P, Torkamani A, Telenti A (January 2019). "A primer on deep learning in genomics". Nature Genetics. 51 (1): 12–18. doi:10.1038/s41588-018-0295-5. PMC 11180539. PMID 30478442. S2CID 205572042.
Zeng Z, Shi H, Wu Y, Hong Z (2015). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1155/2015/674296. PMC 4615216. PMID 26525745.
Zeng Z, Shi H, Wu Y, Hong Z (2012). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1016/B978-0-12-385467-4.00006-3. PMC 4615216. PMID 26525745.
Zeng Z, Shi H, Wu Y, Hong Z (2017). "Survey of Natural Language Processing Techniques in Bioinformatics". Computational and Mathematical Methods in Medicine. 2015 (D1): 674296. doi:10.1155/2015/674296. PMC 4615216. PMID 26525745.
"GenBank and WGS Statistics". www.ncbi.nlm.nih.gov. Retrieved November 25, 2023.
Mathé C, Sagot MF, Schiex T, Rouzé P (October 2002). "Current methods of gene prediction, their strengths and weaknesses". Nucleic Acids Research. 30 (19): 4103–17. doi:10.1093/nar/gkf543. PMC 140543. PMID 12364589.
Pratas D, Silva RM, Pinho AJ, Ferreira PJ (May 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5 (10203): 10203. Bibcode:2015NatSR...510203P. doi:10.1038/srep10203. PMC 4434998. PMID 25984837.
Pauling L, Corey RB, Branson HR (April 1951). "The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain". Proceedings of the National Academy of Sciences of the United States of America. 37 (4): 205–11. Bibcode:1951PNAS...37..205P. doi:10.1073/pnas.37.4.205. PMC 1063337. PMID 14816373.
Wang S, Peng J, Ma J, Xu J (January 2016). "Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields". Scientific Reports. 6: 18962. arXiv:1512.00843. Bibcode:2016NatSR...618962W. doi:10.1038/srep18962. PMC 4707437. PMID 26752681.
Fioravanti D, Giarratano Y, Maggio V, Agostinelli C, Chierici M, Jurman G, Furlanello C (March 2018). "Phylogenetic convolutional neural networks in metagenomics". BMC Bioinformatics. 19 (Suppl 2): 49. doi:10.1186/s12859-018-2033-5. PMC 5850953. PMID 29536822.
Dhungel E, Mreyoud Y, Gwak HJ, Rajeh A, Rho M, Ahn TH (January 2021). "MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning". BMC Bioinformatics. 22 (1): 25. doi:10.1186/s12859-020-03933-4. PMC 7814621. PMID 33461494.
Xun W, Liu Y, Li W, Ren Y, Xiong W, Xu Z, et al. (January 2021). "Specialized metabolic functions of keystone taxa sustain soil microbiome stability". Microbiome. 9 (1): 35. doi:10.1186/s40168-020-00985-9. PMC 7849160. PMID 33517892.
Pirooznia M, Yang JY, Yang MQ, Deng Y (2008). "A comparative study of different machine learning methods on microarray gene expression data". BMC Genomics. 9 Suppl 1 (1): S13. doi:10.1186/1471-2164-9-S1-S13. PMC 2386055. PMID 18366602.
d'Alché-Buc F, Wehenkel L (December 2008). "Machine learning in systems biology". BMC Proceedings. 2 Suppl 4 (4): S1. doi:10.1186/1753-6561-2-S4-S1. PMC 2654969. PMID 19091048.
Jiang F, Jiang Y, Zhi H, Dong Y, Li H, Ma S, et al. (December 2017). "Artificial intelligence in healthcare: past, present and future". Stroke and Vascular Neurology. 2 (4): 230–243. doi:10.1136/svn-2017-000101. PMC 5829945. PMID 29507784.
Bardgett RD, Caruso T (March 2020). "Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375 (1794): 20190112. doi:10.1098/rstb.2019.0112. PMC 7017770. PMID 31983338.
Ansari MZ, Yadav G, Gokhale RS, Mohanty D (July 2004). "NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases". Nucleic Acids Research. 32 (Web Server issue): W405-13. doi:10.1093/nar/gkh359. PMC 441497. PMID 15215420.
Navarro-Muñoz JC, Selem-Mojica N, Mullowney MW, Kautsar SA, Tryon JH, Parkinson EI, et al. (January 2020). "A computational framework to explore large-scale biosynthetic diversity". Nature Chemical Biology. 16 (1): 60–68. doi:10.1038/s41589-019-0400-9. PMC 6917865. PMID 31768033.
Doroghazi JR, Albright JC, Goering AW, Ju KS, Haines RR, Tchalukov KA, et al. (November 2014). "A roadmap for natural product discovery based on large-scale genomics and metabolomics". Nature Chemical Biology. 10 (11): 963–8. doi:10.1038/nchembio.1659. PMC 4201863. PMID 25262415.
Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, et al. (July 2014). "Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters". Cell. 158 (2): 412–421. doi:10.1016/j.cell.2014.06.034. PMC 4123684. PMID 25036635.
Goering AW, McClure RA, Doroghazi JR, Albright JC, Haverland NA, Zhang Y, et al. (February 2016). "Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer". ACS Central Science. 2 (2): 99–108. doi:10.1021/acscentsci.5b00331. PMC 4827660. PMID 27163034.
Amiri Moghaddam J, Crüsemann M, Alanjary M, Harms H, Dávila-Céspedes A, Blom J, et al. (November 2018). "Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites". Scientific Reports. 8 (1): 16600. Bibcode:2018NatSR...816600A. doi:10.1038/s41598-018-34954-y. PMC 6226438. PMID 30413766.
Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, et al. (April 2015). "Molecular networking and pattern-based genome mining improves discovery of biosynthetic gene clusters and their products from Salinispora species". Chemistry & Biology. 22 (4): 460–471. doi:10.1016/j.chembiol.2015.03.010. PMC 4409930. PMID 25865308.
McClure RA, Goering AW, Ju KS, Baccile JA, Schroeder FC, Metcalf WW, et al. (December 2016). "Elucidating the Rimosamide-Detoxin Natural Product Families and Their Biosynthesis Using Metabolite/Gene Cluster Correlations". ACS Chemical Biology. 11 (12): 3452–3460. doi:10.1021/acschembio.6b00779. PMC 5295535. PMID 27809474.
Cao L, Shcherbin E, Mohimani H (August 2019). "A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota". mSystems. 4 (4): e00387–19, /msystems/4/4/msys.00387–19.atom. doi:10.1128/mSystems.00387-19. PMC 6712304. PMID 31455639.
Olm MR, Bhattacharya N, Crits-Christoph A, Firek BA, Baker R, Song YS, et al. (December 2019). "Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria". Science Advances. 5 (12): eaax5727. Bibcode:2019SciA....5.5727O. doi:10.1126/sciadv.aax5727. PMC 6905865. PMID 31844663.
Pascal Andreu, Victória; Augustijn, Hannah E.; van den Berg, Koen; van der Hooft, Justin J. J.; Fischbach, Michael A.; Medema, Marnix H. (October 26, 2021). Shank, Elizabeth Anne (ed.). "BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes". mSystems. 6 (5): e0093721. doi:10.1128/mSystems.00937-21. ISSN 2379-5077. PMC 8547482. PMID 34581602.
Agrawal P, Khater S, Gupta M, Sain N, Mohanty D (July 2017). "RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links". Nucleic Acids Research. 45 (W1): W80 – W88. doi:10.1093/nar/gkx408. PMC 5570163. PMID 28499008.
Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJ (February 2021). "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLOS Computational Biology. 17 (2): e1008724. Bibcode:2021PLSCB..17E8724H. doi:10.1371/journal.pcbi.1008724. PMC 7909622. PMID 33591968.
Huber F, Ridder L, Verhoeven S, Spaaks JH, Diblen F, Rogers S, van der Hooft JJ (February 2021). "Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships". PLOS Computational Biology. 17 (2): e1008724. Bibcode:2021PLSCB..17E8724H. doi:10.1371/journal.pcbi.1008724. PMC 7909622. PMID 33591968.
National Center for Biotechnology Information; U.S. National Library of Medicine. "National Center for Biotechnology Information". ncbi.nlm.nih.gov. Retrieved July 30, 2021.
Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, et al. (NCBI Resource Coordinators) (January 2018). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research. 46 (D1): D8 – D13. doi:10.1093/nar/gkx1095. PMC 5753372. PMID 29140470.
Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJ, et al. (January 2020). "MIBiG 2.0: a repository for biosynthetic gene clusters of known function". Nucleic Acids Research. 48 (D1): D454 – D458. doi:10.1093/nar/gkz882. PMC 7145714. PMID 31612915.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. (January 2013). "The SILVA ribosomal RNA gene database project: improved data processing and web-based tools". Nucleic Acids Research. 41 (Database issue): D590-6. doi:10.1093/nar/gks1219. PMC 3531112. PMID 23193283.
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. (July 2006). "Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB". Applied and Environmental Microbiology. 72 (7): 5069–72. Bibcode:2006ApEnM..72.5069D. doi:10.1128/AEM.03006-05. PMC 1489311. PMID 16820507.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. (March 2012). "An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea". The ISME Journal. 6 (3): 610–8. Bibcode:2012ISMEJ...6..610M. doi:10.1038/ismej.2011.139. PMC 3280142. PMID 22134646.
Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, et al. (October 2015). "Synthesis of phylogeny and taxonomy into a comprehensive tree of life". Proceedings of the National Academy of Sciences of the United States of America. 112 (41): 12764–9. Bibcode:2015PNAS..11212764H. doi:10.1073/pnas.1423041112. PMC 4611642. PMID 26385966.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. (January 2014). "Ribosomal Database Project: data and tools for high throughput rRNA analysis". Nucleic Acids Research. 42 (Database issue): D633-42. doi:10.1093/nar/gkt1244. PMC 3965039. PMID 24288368.

opentreeoflife.org

tree.opentreeoflife.org

"opentree". tree.opentreeoflife.org. Retrieved July 30, 2021.

oup.com

academic.oup.com

Ji, Yanrong; Zhou, Zhihan; Liu, Han; Davuluri, Ramana V (August 9, 2021). Kelso, Janet (ed.). "DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome". Bioinformatics. 37 (15): 2112–2120. doi:10.1093/bioinformatics/btab083. ISSN 1367-4803. PMC 11025658. PMID 33538820.

portico.org

access.portico.org

Soueidan, Hayssam; Nikolski, Macha (January 1, 2017). "Machine learning for metagenomics: methods and tools". Metagenomics. 1 (1). arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.

secondarymetabolites.org

mibig.secondarymetabolites.org

"MIBiG: Minimum Information about a Biosynthetic Gene cluster". mibig.secondarymetabolites.org. Retrieved July 30, 2021.
MiBiG

antismash-db.secondarymetabolites.org

"antiSMASH database". antismash-db.secondarymetabolites.org.

secondgenome.com

greengenes.secondgenome.com

"greengenes.secondgenome.com". greengenes.secondgenome.com. Retrieved July 30, 2021.

semanticscholar.org

api.semanticscholar.org

Shastry KA, Sanjay HA (2020). "Machine Learning for Bioinformatics". In Srinivasa K, Siddesh G, Manisekhar S (eds.). Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Algorithms for Intelligent Systems. Singapore: Springer. pp. 25–39. doi:10.1007/978-981-15-2445-5_3. ISBN 978-981-15-2445-5. S2CID 214350490. Retrieved June 28, 2021.
Soueidan H, Nikolski M (2019). "Machine learning for metagenomics: methods and tools". Metagenomics. 1. arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.
Rabiner L, Juang B (January 1986). "An introduction to hidden Markov models". IEEE ASSP Magazine. 3 (1): 4–16. doi:10.1109/MASSP.1986.1165342. ISSN 1558-1284. S2CID 11358505.
Jackson CH, Sharples LD, Thompson SG, Duffy SW, Couto E (July 2003). "Multistate Markov models for disease progression with classification error". Journal of the Royal Statistical Society, Series D (The Statistician). 52 (2): 193–209. doi:10.1111/1467-9884.00351. S2CID 9824404.
Fukushima K (1980). "Neocognitron: a self organizing neural network model for a mechanism of pattern recognition unaffected by shift in position". Biological Cybernetics. 36 (4): 193–202. doi:10.1007/BF00344251. PMID 7370364. S2CID 206775608.
Breiman, Leo (2001). "Radom Forests". Machine Learning. 45 (1): 5–32. Bibcode:2001MachL..45....5B. doi:10.1023/A:1010933404324. S2CID 89141.
Shastry KA, Sanjay HA (2020). "Machine Learning for Bioinformatics". Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Algorithms for Intelligent Systems. Springer Singapore. pp. 25–39. doi:10.1007/978-981-15-2445-5_3. ISBN 978-981-15-2444-8. S2CID 214350490.
Zou J, Huss M, Abid A, Mohammadi P, Torkamani A, Telenti A (January 2019). "A primer on deep learning in genomics". Nature Genetics. 51 (1): 12–18. doi:10.1038/s41588-018-0295-5. PMC 11180539. PMID 30478442. S2CID 205572042.
Soueidan, Hayssam; Nikolski, Macha (January 1, 2017). "Machine learning for metagenomics: methods and tools". Metagenomics. 1 (1). arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.
Lin Y, Wang G, Yu J, Sung JJ (April 2021). "Artificial intelligence and metagenomics in intestinal diseases". Journal of Gastroenterology and Hepatology. 36 (4): 841–847. doi:10.1111/jgh.15501. PMID 33880764. S2CID 233312307.
Topol EJ (January 2019). "High-performance medicine: the convergence of human and artificial intelligence". Nature Medicine. 25 (1): 44–56. doi:10.1038/s41591-018-0300-7. hdl:10654/45728. PMID 30617339. S2CID 57574615.
Mirtskhulava L, Wong J, Al-Majeed S, Pearce G (March 2015). "Artificial Neural Network Model in Stroke Diagnosis" (PDF). 2015 17th UKSim-AMSS International Conference on Modelling and Simulation (UKSim). pp. 50–53. doi:10.1109/UKSim.2015.33. ISBN 978-1-4799-8713-9. S2CID 6391733.
Titano JJ, Badgeley M, Schefflein J, Pain M, Su A, Cai M, et al. (September 2018). "Automated deep-neural-network surveillance of cranial images for acute neurologic events". Nature Medicine. 24 (9): 1337–1341. doi:10.1038/s41591-018-0147-y. PMID 30104767. S2CID 51976344.
Nielsen JC, Grijseels S, Prigent S, Ji B, Dainat J, Nielsen KF, et al. (April 2017). "Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species". Nature Microbiology. 2 (6): 17044. doi:10.1038/nmicrobiol.2017.44. PMID 28368369. S2CID 22699928.
Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, et al. (November 2019). "Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome". Science. 366 (6465): 606–612. Bibcode:2019Sci...366..606C. doi:10.1126/science.aaw9285. hdl:1887/3188901. PMID 31672892. S2CID 207814746.

springer.com

link.springer.com

Shastry KA, Sanjay HA (2020). "Machine Learning for Bioinformatics". In Srinivasa K, Siddesh G, Manisekhar S (eds.). Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Algorithms for Intelligent Systems. Singapore: Springer. pp. 25–39. doi:10.1007/978-981-15-2445-5_3. ISBN 978-981-15-2445-5. S2CID 214350490. Retrieved June 28, 2021.

unam.mx

link-springer-com.pbidi.unam.mx

Shastry KA, Sanjay HA (2020). "Machine Learning for Bioinformatics". Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Algorithms for Intelligent Systems. Springer Singapore. pp. 25–39. doi:10.1007/978-981-15-2445-5_3. ISBN 978-981-15-2444-8. S2CID 214350490.

web.archive.org

"RDP Release 11 -- Sequence Analysis Tools". rdp.cme.msu.edu. Archived from the original on August 19, 2020. Retrieved July 30, 2021.

worldcat.org

search.worldcat.org

Soueidan H, Nikolski M (2019). "Machine learning for metagenomics: methods and tools". Metagenomics. 1. arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.
Rabiner L, Juang B (January 1986). "An introduction to hidden Markov models". IEEE ASSP Magazine. 3 (1): 4–16. doi:10.1109/MASSP.1986.1165342. ISSN 1558-1284. S2CID 11358505.
Ji, Yanrong; Zhou, Zhihan; Liu, Han; Davuluri, Ramana V (August 9, 2021). Kelso, Janet (ed.). "DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome". Bioinformatics. 37 (15): 2112–2120. doi:10.1093/bioinformatics/btab083. ISSN 1367-4803. PMC 11025658. PMID 33538820.
Gündüz, Hüseyin Anil; Binder, Martin; To, Xiao-Yin; Mreches, René; Bischl, Bernd; McHardy, Alice C.; Münch, Philipp C.; Rezaei, Mina (September 11, 2023). "A self-supervised deep learning method for data-efficient training in genomics". Communications Biology. 6 (1): 928. doi:10.1038/s42003-023-05310-2. ISSN 2399-3642. PMC 10495322. PMID 37696966.
Soueidan, Hayssam; Nikolski, Macha (January 1, 2017). "Machine learning for metagenomics: methods and tools". Metagenomics. 1 (1). arXiv:1510.06621. doi:10.1515/metgen-2016-0001. ISSN 2449-7657. S2CID 17418188.
Pascal Andreu, Victória; Augustijn, Hannah E.; van den Berg, Koen; van der Hooft, Justin J. J.; Fischbach, Michael A.; Medema, Marnix H. (October 26, 2021). Shank, Elizabeth Anne (ed.). "BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes". mSystems. 6 (5): e0093721. doi:10.1128/mSystems.00937-21. ISSN 2379-5077. PMC 8547482. PMID 34581602.