In Press | Submitted | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 Undergraduate/High School Contributions – Bolded and Italicized Below

In Press
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Gal, K., Karger, D., Geller, S., Hoernle, N., Segal, A., Zhang, A.X., Igo, M; Facciotti, M.T., Kim, H.G., Sripathi, K. New Methods for Confusion Detection in Course Forums: Student, Teacher and Machine. IEEE Transactions on Learning Technologies. ** Revisions Submitted **.
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Shusterman, E., Kim, H.G., Facciotti, M.T., Igo, M.M., Sripathi, K., Karger, D., Segal, A. and Gal, K. Seeding Course Forums using the Teacher-in-the-Loop. LAK21: 11th International Learning Analytics and Knowledge Conference. 2021. Apr 12 2021. pp. 22-31. DOI:
Sharma, G., Yao, A.I., Smaldone, G.T., Liang, J., Long, M., Facciotti, M.T. and Singer M. Global gene expression analysis of the Myxococcus xanthus developmental time course. Genomics. 2021. Jan;113(1 Pt 1):120-134. PMID: 33276008
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Seitzer, P.M., Yao, A.I., Cisneros, A., Facciotti, M.T.. The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances. Microorganisms. 2020. Nov 30;8(12):1900. PMID: 33266086
Geller, S.A., Hoernle, N., Gal, K., Segal, A., Zhang, A.X., Kim, H.G., Karger, D., Facciotti, M.T. and Igo, M.M. (2020) # Confused and beyond: detecting confusion in course forums using students’ hashtags. Proceedings of the Tenth International Conference on Learning Analytics & Knowledge. 2020. Mar 23 2020. pp.589-594. DOI:
Rodriguez-Medina, J., Kim, H.G., Castro, J., Contreras, C.M., Glon, C.L., Goyal, A., Guo, B.Y., Knowles, S., Lin, J.C., McGuiness, C.L., Sorkin, E., Stefani, J., Yegireddi, S.J., Chaganti, S., Cui, D., Deck, S.L., Deokule, Y., Douglas, H., Kenaston, M., O’Brien, A., Patterson, E., Schoppa, N., Vo, D.T., Tran, K., Tran, TL., Pérez-Irizarry, V., Carrasquillo-Nieves, K., Montalvo-Rodriguez, R., Yao, A.I., Albeck, J.G., Facciotti, M.T., Nord, A.S., and Furrow, R.E. (2020) Draft Genome Sequences of 16 Halophilic Prokaryotes Isolated from Diverse Environments. Microbiology Resource Announcements. Feb 20;9(8):e01540-19. PMID: 32079635
Furrow, R.E., Kim, H.G., Abdelrazek, S., Dahlhausen, K., Yao, A.I., Eisen, J.A., Goldman, M.S., Albeck, J.G., and Facciotti, M.T.. (2020) Combining Microbial Culturing With Mathematical Modeling in an Introductory Course-Based Undergraduate Research Experience. Frontiers in Microbiology. 2020. Nov 6;11:581903. PMID: 33250873
Yao, A. I., Lucero, S., & Facciotti, M. T. (2020) Prototyping Biomolecules to Machines: A Case Study of Launching and Sustaining an Academic Biomaker Lab. International Journal of Academic Makerspaces and Making (IJAMM). link to paper.  Work originally appeared as conference abstract in 2017 prior to publication as journal article.
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Payne, S., Facciotti, M.T., Van Cott, K., Yao, A.I., Wilson, M., Sutter, S., Rodríguez-Acevedo, K.L., and Blum, P (2019) Conservation of an Ancient Oxidation Response That Controls Archaeal Epigenetic Traits Through Chromatin Protein Networks. bioRxiv. 2019. DOI: ###This article is not peer reviewed###
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Seitzer, P.M., Jeanniard, J., Ma, F.R., Van Etten, J.L., Facciotti, M.T., and Dunigan, D (2018) Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes. Viruses. 2018. Oct 20;10(10):576. PMID: 30347809
Yogev, E., Gal, K., Karger, D., Facciotti, M.T. and Igo, M.M. (2018) Classifying and visualizing students’ cognitive engagement in course readings. Proceedings of the Fifth Annual ACM Conference on Learning at Scale. 2018. Jun 26 2018. pp.1-10. DOI:
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Becker, E.A., Easlon, E.J., Potter, S.C., Guzman-Alvarez, A., Spear, J.M., Facciotti, M.T., Igo, M.M., Singer, M., and Pagliarulo, C. (2017) The Effects of Practice-Based Training on Graduate Teaching Assistants’ Classroom Practices. CBE Life Sci Educ. 2017. 2017;16(4):ar58. PMID: 29146664
Zhang A.X., Igo, M.M., Facciotti, M.T., and Karger, D. (2017) Using student annotated hashtags and emojis to collect nuanced affective states. L@S ’17: Proceedings of the Fourth (2017) ACM Conference on Learning @ Scale. Apr 2017. pp 319-322. DOI:
Fruend, G., O’Brien, T.E., Vinson, L., Carlin, D.A., Yao, A.I., Man, W.S., Tagkopoulos, I., Facciotti, M.T., Tantillo, D.J. and Siegel, J.B. (2017) Elucidating Substrate Promiscuity within the FabI Enzyme Family. ACS Chemical Biology. 2017. 12 (9), 2465-2473. PMID: 28820936
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Becker E.A., Yao A.I., Seitzer, P.M., Kind, T., Wang, T., Eigenheer, R., Shao, K.S.Y., Yarov-Yarovoy, V. and Facciotti, M.T. (2016) A large and phylogenetically diverse class of type 1 opsins lacking a canonical retinal binding site. PLoS One. Jun 21;11(6):e0156543. doi: 10.1371/journal.pone.0156543. eCollection 2016. PMID: 27327432
Sánchez-Nieves, R., Facciotti, M.T., Saavedra-Collado, S., Dávila-Santiago, L., Rodríguez-Carrero, R., and Montalvo-Rodríguez, R. (2016) Draft genome of Haloarcula rubripromontorii strain SL3, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico. Genom Data. 7:287-9. doi: 10.1016/j.gdata.2016.02.005. eCollection 2016. PMID: 26981428
Sánchez-Nieves, R., Facciotti, M.T., Saavedra-Collado, S., Dávila-Santiago, L., Rodríguez-Carrero, R., and Montalvo-Rodríguez. R. (2016) Draft genome sequence of Halorubrum tropicale strain V5, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico. Genom Data. 7:284-6. doi: 10.1016/j.gdata.2016.02.004. eCollection 2016 Mar. PMID: 26981427
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Rudrappa, D. Yao, A.I., White, D., Pavlik, B., Singh, R., Facciotti, M.T. and Blum, P. (2015) Identification of an Archaeal Mercury Regulon by Chromatin Immunoprecipitation. 161(12):2423-33. doi: 10.1099/mic.0.000189. PMID: 26408318
Rai, N., Ferreiro, A., Neckelmann, A., Soon, A., Yao, A.I., Siegel, J., Facciotti, M.T., and Tagkopoulos, I. (2015) RiboTALE: a versatile and modular tool for the multi-dimensional control of gene expression. Scientific Reports May 29;5:10658. doi: 10.1038/srep10658. PMID: 26023068
Persson, T., Demina, I.V., Battenberg, K., Vigil-Stenman, T., Heuvel, B.V., Pujic, P., Facciotti, M.T., Wilbanks, E.G., O’Brien, A., Fournier, P., Hernandez, M.A.C., Herrara, A.M., Médigue, C., Normand, P., Pawloski, K., and Berry, A. (2015) Who invented Nod factors? A phylogenetically basal Frankia strain contains the canonical nod genes.PLoS One May 28;10(5):e0127630. doi: 10.1371/journal.pone.0127630. eCollection 2015 PMID: 26020781
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Becker, E.A.*, Seitzer, P.M.*, Tritt, A., Larsen, D., Krusor, M., Yao, A.I., Wu, D., Madern, D., Eisen, J.E., Darling, A.E., and Facciotti, M.T. (2014). Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PLoS Genetics. 10(11): e1004784. publisher link PMID: 25393412 *Contributed Equally
Plaisier, C.L., Lo, F., Ashworth, J., Brooks, A.N., Beer, K.D., Kaur, A., Pan, M., Reiss, D.J., Facciotti, M.T., and Baliga, N.S.  (2014). Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. BMC Systems Biology 8:122 publisher link
Wang, T., Oppawsky, C., Duan, Y., Tittor, J., Oesterhelt, D., and Facciotti, M.T.  (2014). Stable closure of the cytoplasmic half-channel is required for efficient proton transport at physiological membrane potentials in the bacteriorhodopsin catalytic cycle. Biochemistry. 53(14):2380-90 PMID: 24660845
Wilbanks, E.G., Jaekel, U., Salman, V., Humphrey, P.T., Eisen, J.A. Eisen, Facciotti, M.T., Buckley,D.H., Zinder, S.H., Druschel, G.K., Fike, D.A., and Orphan, V.J. (2014). Microscale Sulfur Cycling in the Phototrophic Pink Berry Consortia of the Sippewissett Salt Marsh. Environ Microbiol PMID: 24428801 (January 15, 2014).
Neches, R.Y., Seitzer, P.M., Wilbanks, E.G., and Facciotti, M.T.  (2014) In a fit of pique: Analyzing microbial ChIP-Seq data with Pique. PeerJ PrePrints 2:e290v2 publisher link ###This article is not peer reviewed###
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Warnecke, T., Becker, E.A., Facciotti, M.T., Nislow, C. and Lehner, B. (2013). Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution. PLoS Computational Biology. PMID:24278010 9,e1003373.
Facciotti, M.T. (2013). Thermodynamically inspired classifier for molecular phenotypes of health and disease. Proceedings of the National Academy of Sciences. PMID:24204030 Nov 7, 2013.doi:10.1073/pnas.1317876110
Wang, T., Facciotti, M.T.* and Duan, Y. (2013). Schiff Base Switch II Precedes the Retinal Thermal Isomerization in the Photocycle of Bacteriorhodopsin. PLoS ONE 8, e69882. PMID:23922839.*Co-corresponding author
Gilmore, S.F., Yao, A.I., Tietel, Z., Kind, T., Facciotti, M.T., Parikh, A.N. (2013). The role of squalene in the organization of monolayers derived from lipid extracts of Halobacterium salinarum. Langmuir. 29. 7922-30. PMID:23713788.
Wang, T., Sessions, A.O., Lunde, C.S., Rouhani, S., Glaeser, R.M., Duan, Y., and Facciotti, M.T. (2013). Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway. Structure. 21. 290-7. PMID:23394942.
Seitzer, P., Huynh, T. A., & Facciotti, M. T. (2013). JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. BMC Bioinformatics. 14(1). 18. doi:10.1186/1471-2105-14-18. PMID:23324080.
Yao, A.I., Fenton, T.A., Owsley, K., Seitzer, P., Larsen, D.J., Sit, H., Lau, J., Nair, A., Tantiongloc, J., Tagkopoulos, I., Facciotti, M.T. (2013). Promoter activity arising from the fusion of standard BioBrick™ parts. ACS Synthetic Biology. doi: 10.1021/sb300114d. 2(2), 111-120. PMID:23656374.
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Köhler, S, Seitzer P, Facciotti M.T., & Ludäscher B. (2012). Improved Motif Detection in Large Sequence Sets with Random Sampling in a Kepler workflow. Procedia Computer Science. 9. 1999. publisher link
Seitzer P., Larsen D.J. Wilbanks E.G., and Facciotti M.T. (2012). A Monte Carlo-based framework to enhance the discovery and interpretation of regulatory sequence motifs. BMC Bioinformatics. 13(11). doi:10.1186. PMID: 23181585 **Highly Accessed**
Tritt, A., Eisen, J.A., Facciotti, M.T. and Darling, A.E. (2012). A user-friendly pipeline for de novo assembly of microbial genomes. PLoS One. Sept 13. 7(9): e42304. PMID: 23028432
Sun C., Alkhoury K., Wang Y.I., Foster G.A., Radecke C.E., Tam K., Edwards C.M., Facciotti M.T., Armstrong E.J., Knowlton A.A, Newman J.W., Passerini A.G., and Simon S.I. (2012). IRF-1 and miRNA126 modulate inflammatory VCAM-1 expression in response to a high fat meal. Circulation Research. Aug 8. PMID: 22874466
Lynch, E.A., Langille, M.G.I, Darling, A.E., Wilbanks, E.G., Haitliner, C., Shao, K.S.Y., Starr, M.O., Teilling, C., Harkins, T., Edwards, R., Eisen, J.A., and Facciotti, M.T. (2012). Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux. PLoS One. Jul 24. PMID: 22848480.
Wilbanks, E.G., Larsen, D.J., Neches, R.Y.,Yao, A.I., Wu, C, Kjolby, R.S. and Facciotti, M.T. (2012). A workflow for genome-wide mapping of archaeal transcription factors with ChIP-Seq. Nucleic Acids Research. May;40(10):e74. PMID: 22323522.
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Yao A.I. and Facciotti M.T. Regulatory Multidimensionality of Gas Vesicle Biogenesis in Halobacterium salinarum NRC-1. 2011. Archaea. vol. 2011. Article ID 716456. Aug 7. PMID: 2022110395.
Darling A., Tritt A., Eisen J.A., and Facciotti M.T. 2011. Mauve Assembly Metrics. Bioinformatics. Aug 2. PMID: 21810901.
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Wilbanks E.G., Facciotti M.T. 2010. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One. Jul;5(7):e11471 PMID:20628599
Facciotti M.T.*, Pang, W.L., Lo, F.Y., Whitehead, K., Koide, T., Masumura, K., Pan, M., Kaur, A., Larsen D.J., Reiss, D.J., Hoang, L., Kalisiak, E., Northern, T., Trauger, S.A., Siuzdak, G., and Baliga, N.S. 2010. Large scale physiological readjustment during growth in a simple batch culture enables rapid, comprehensive and inexpensive systems analysis. BMC Systems Biology. May;14(4):64 PMID:20470417 *Co-corresponding author
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Koide, T., Reiss, D.J., Bare, C.J., Facciotti, M.T., Schmid, A.K., Pan, M., Marzolf, B., Van, P.T., Lo, F., Pratrap, A., Deutsch, E.W., Peterson, A. Martin, D., Baliga, N.S. 2009. Prevalence of transcription promoters within archaeal operons and coding sequences. Mol. Syst. Biology. Jun;5:285 PMID:19536208
Facciotti M.T. 2009. Training interdisciplinary scientists for systems biology. J. Invest. Medicine Feb;57(2):471-3 PMID:19174700
Benedyk M, Berglund L, Facciotti M, Mobley W, and Zucker D. 2009. Strategies for innovation and interdisciplinary translational research: research and career benefits and barriers. J. Invest. Medicine. Feb;57(2):477-81. PMID:19174698
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Van, P., Schmid, A., King, N., Kaur, A., Pan, M., Whitehead, K., Koide, T., Facciotti, M.T., Goo, Y. A., Deutsch, E., Reiss, D., Mallick, P., Baliga, N.S. 2008. Halobacterium salinarum NRC-1 PeptideAtlas; towards strategies for target proteomics and improved proteome coverage. Journal of Proteome Research. published online July 25, 2008. PMID: 1865250
Johnson, M.H., Facciotti, M.T., Reiss, D.J., Whitehead, K., Schmid, A., Kaur, A., Pan, M., Shannon, P., Tenenbaum, D., Baliga, N.S. 2008. QS437. Integrated Biological and Computational Analysis of Important But Largely Under-Studied Organisms. The Journal of Surgical Research. 144:2 441-444. Conference Abstract.
Larjo, A., Lähdesmäki, H., Facciotti, M.T., Baliga, N.S., Hli-Harja, O., Shmulevich. 2008. Active Learning of Bayesian Network Structure in a Realistic Setting. Proceedings of the 5th International Workshop on Computational Systems Biology (WCSB 2008). 85-88. Conference Proceedings.
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Bonneau, R., Facciotti, M.T., Reiss, D.J., Schmid, A., Pan, M., Kaur, A., Thorsson, V., Shannon, P., Johnson M., Bare, C.J., Longabaugh, W., Vuthoori, M., Whitehead, K., Madar, A., Suzuki, L., Mori, T., Chang, D., DiRuggiero, J., Johnson, C., Hood, L. and Baliga N.S. 2007. A predictive model for transcriptional control of physiology in a free living cell. Cell131(7). 1354-1365.  PMID: 18160043
Reiss, D.J., Facciotti M.T., and Baliga, N.S. 2007. Model-based deconvolution of genome-wide DNA binding. BioinformaticsPMID: 18056063
Facciotti, M.T., Reiss, D.J., Pan, M., Kaur, A., Vuthoori, M., Bonneau, R., Shannon, P., Srivastava, A., Donahoe, S.M., Hood, L., and Baliga, N.S.  2007.  Structure of a general transcription factor specified global gene regulatory network.  PNAS104(11). 4630-4635.PMID: 117360575
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Kaur, A., Pan, M., Meislin, M., Facciotti, M.T., El-Geweley, R. and Baliga, N.S.  2006.  A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Research. 16(7).  841-854. PMID: 16751342
Bonneau, R., Reiss, D.J., Shannon, P. Facciotti, M.T., Hood, L. Baliga, N.S., and Thorsson, V.  2006.  The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data-sets de novo.  Genome Biology7(6).  R36. PMID: 16686963
Lunde, C.S., Rouhani, S., Facciotti, M.T., and Glaeser, R.M.  2006. Membrane-Protein Stability in a Phospholipid-based Crystallization Medium.  Journal of Structural Biology154(3). 223-231. PMID: 16600634
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Facciotti, M.T., Bonneau, R., Hood, L., and Baliga, N.S.  2004.  Systems Biology Experimental Design – Considerations for Building Predictive Gene Regulatory Network Models for Prokaryotic Systems.  Current Genomics. 5(7). 527-544.
Baliga, N.S., Bonneau, R. Facciotti, M.T., Pan, M., Glusman, G., Deutsch, E.W., Shannon, P., Chiu, Y., Weng, R.S., Gan, R.R., Hung, P., Date, S.V., Marcotte, E., Hood, L., and Ng, W.V.  2004.  Genome sequence of Haloarcula marismortui:  A halophilic archaeon from the Dead Sea.  Genome Research. 14(11).  2221-2234. PMID: 15520287
Facciotti, M.T., Rouhani, S. and Glaeser, R.M.  2004.  Energy transduction in transmembrane ion pumps.  Trends in Biochemical Sciences. 29(8).445-451. PMID: 15362229
Facciotti, M.T., Rouhani, S. and Glaeser, R.M.  2004.  Crystal structures of bR(D85S) favor a model of bacteriorhodopsin as an hydroxyl-ion pump.  FEBS Letters. 564(3). 301-306.PMID: 15111113
Facciotti, M.T., Cheung, V., Lunde, C.S., Rouhani, S., Baliga, N., and Glaeser, R.M.  2004. Specificity of anion-binding in the substrate-pocket of bacteriorhodopsin.  Biochemistry.43(17).  4934-4943. PMID: 15109251
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Facciotti, M.T., Cheung, V., Nguyen, D., Rouhani, S., and Glaeser, R.M. 2003. Crystal structure of the bromide-bound D85S mutant of bacteriorhodopsin:  principles of ion pumping.  Biophysical Journal. 85.  451-458.  PMID: 12829500
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Rouhani, S., Facciotti, M.T., Woodcock, G., Cheung, V., Cunningham., Nguyen, D., Rad, B., Lin, C., Lunde, C.S., and Glaeser, R.M.  2002.  Crystallization of membrane proteins from media composed of connected-bilayer gels.  Biopolymers. 66.  300-316. PMID: 12539259
Kennis, J.T.M., Larsen, D.S., Ohta, K., Facciotti, M.T., Glaeser, R.M., and Fleming, G.R. 2002. Ultrafast protein dynamics of bacteriorhodopsin probed by photon echo and transient absorption spectroscopy.  Journal of Physical Chemistry B.  106(23).  6067-6080.
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Facciotti, M.T., Rouhani, S., Burkard, F.T., Betancourt, F.M., Downing, K.H., Rose, R.B., McDermott, G., and Glaeser, R.M.  2001.  Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle.  Biophysical Journal. 81.  3442-3455. PMID: 11721006
Rouhani, S., Cartailler, J-P., Facciotti, M.T., Walian, P., Needleman, R., Lanyi, J.K., Glaeser, R.M., and Luecke, H.  2001. Crystal structure of the D85S mutant of bacteriorhodopsin:  Model of an O-like photocycle intermediate.  Journal of Molecular Biology313.  615-628.PMID: 11676543
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Glaeser, R., Facciotti, M.T., Walian, P., Rouhani, S., Holton, J., MacDowell, A., Celestre, R., Cambie, D., and Padmore, H.  2000. Characterization of conditions required for X-ray diffraction experiments with protein microcrystals.  Biophysical Journal.  78. 3178-3185.PMID: 10827994
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Facciotti, M.T., Bertain, P.B., and Yuan, L.  1999.  Improved stearate phenotype in transgenic canola expressing a modified acyl-acyl carrier protein thioesterase.  Nature Biotechnology. 17. 593-597. PMID: 10385326
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Facciotti, M.T. and Yuan, L. 1998. Molecular dissection of the plant acyl-acyl carrier protein thioesterases.  FETT Lipid100:4-5. 167-172.


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