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April 2024-present: Currently we have positions for graduate students, undergraduate students, and postdocs to do research in our lab. April 2024: Check out Prof. Saiz preprint on “Actionable forecasting as a determinant of function in noisy biological systems” published in arXiv. —————————————-2024—————————————-2024—————————————-2024—————————————- November 2023: Check out Prof. Saiz report with the National Academies of Sciences, Engineering, and Medicine in The National Academies Press. September 2023: Our best wishes to Ninghui Hao, who just started her Master of Science in Biomedical Informatics at Harvard Medical School. July 2023: Check out Andy Fell’s piece entitled “Bringing COVID-19 Data into Focus” on our latest paper “Dynamics-informed deconvolutional neural networks for super-resolution identification of regime changes in epidemiological time series“, just published in Science Advances. June 2023: Our latest paper on “Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites” has been accepted in Scientific Reports. June 2023: Our latest paper on “Dynamics-informed deconvolutional neural networks for super-resolution identification of regime changes in epidemiological time series” has been accepted in Science Advances. May 2023: Check out Prof. Saiz preprint on “Chaperone-driven entropic separation of amyloid nanofilament bundles” published in bioRxiv. March 2023: Check out Prof. Saiz preprint on “The unreasonable effectiveness of equilibrium gene regulation through the cell cycle” published in bioRxiv. —————————————-2023—————————————-2023—————————————-2023—————————————- December 2022: Prof. Saiz will be teaching two courses in Winter: BIM 152 (Molecular Control of Biosystems) for undergraduate students and BIM 189C (Computational tools and Applications in Bioengineering and Biomedicine) for undergraduate students. September 2022: Check out Prof. Saiz preprint on “Dynamics-informed deconvolutional neural networks for super-resolution identification of regime changes in epidemiological time series” published in medRxiv. July 2022: Our latest paper on “Robustness of DNA Looping Across Multiple Cell Divisions in Individual Bacteria” has been accepted in PNAS. January 2022: Prof. Saiz will be teaching two courses in Winter: BIM 152 (Molecular Control of Biosystems) for undergraduate students and BIM 189C (Computational tools and Applications in Bioengineering and Biomedicine) for undergraduate students. —————————————-2022—————————————-2022—————————————-2022—————————————- December 2021: Check out Prof. Saiz preprint on “Robustness of DNA Looping Across Multiple Divisions in Individual Bacteria” published in bioRxiv. November 2021: Check out Prof. Saiz report with the National Academies of Sciences, Engineering, and Medicine in The National Academies Press. October 2021: Our latest paper on “Cell-to-cell and type-to-type heterogeneity of signaling networks: Insights from the crowd” has been published in Molecular Systems Biology. October 2021: Our latest paper on “Reliably quantifying the evolving worldwide dynamic state of the COVID-19 outbreak from death records, clinical parametrization, and demographic data” has been published in Scientific Reports. October 2021: Our latest paper on “Ascertaining the initiation of epidemic resurgences: an application to the COVID-19 second surges in Europe and the Northeast United States” has been published in Royal Society Open Science. September 2021: Check out Prof. Saiz preprint on “Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites” published in bioRxiv. September 2021: Our latest paper on “All-or-none amyloid disassembly via chaperone-triggered fibril unzipping favors clearance of α-synuclein toxic species” has been published in PNAS. April 2021: Our latest paper on “Computational Design of Single-Stranded DNA Hairpin Aptamers Immobilized on a Biosensor Substrate” has been accepted in Scientific Reports. March 2021: Check out Prof. Saiz preprint on “Cell-to-cell and type-to-type heterogeneity of signaling networks: Insights from the crowd” published in bioRxiv. January 2021: Check out Prof. Saiz preprint on “Similarities and differences of the COVID-19 second surge in Europe and the Northeast United States” published in medRxiv. —————————————-2021—————————————-2021—————————————-2021—————————————- December 2020: Check out Prof. Saiz COVID19 Web App on “COVID-19 Dynamics” at https://covid19dynamics.herokuapp.com/. November 2020: Check out Prof. Saiz preprint on “The evolving worldwide dynamic state of the COVID-19 outbreak” published in medRxiv. —————————————-2020—————————————-2020—————————————-2020—————————————- September 2018: Check out Prof. Saiz article on “Kinetically Restricted Solid-Solid Phase Transition in cis-Ceramide Monolayers” published in Langmuir. —————————————-2018—————————————-2018—————————————-2018—————————————- October 2017: Check out Prof. Saiz article on “Computing at the front-end by receptor networks” published in Cell Systems. August 2017: Check out the special issue on “Signaling at Membranes” published in the Journal of Membrane Biology with Prof. Saiz as the guest editor. August 2017: Check out Prof. Saiz article on “Insights into signaling and the functional complexity of biological membranes” published in the Journal of Membrane Biology. May 26th, 2017: Congratulations to Iman Jeddi for successfully defending her dissertation on Computational Modeling and Analysis of Single-Stranded DNA Aptamers for Biosensing Applications. Dr. Jeddi is the latest PhD student to graduate from the Saiz lab. Spring Quarter 2017: Prof. Saiz will be teaching two courses in Spring: BIM 152 (Molecular Control of Biosystems) for undergraduate students and BIM 189C (Computational tools and Applications in Bioengineering and Biomedicine) for undergraduate students. March 2017: Our latest paper on “Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors” has been accepted in Scientific Reports. February 2017: Check out Prof. Saiz article on “How Will Kinetics and Thermodynamics Inform Our Future Efforts to Understand and Build Biological Systems?” published in Cell Systems; other authors include Jennifer Doudna. February 2017: Our latest paper on “Predicting human olfactory perception from chemical features of odor molecules” has just been published in Science. February 2017: Check out what Science News is saying about our Science paper [Artificial intelligence grows a nose]. February 2017: Check out what ACS’ C&EN (Chemical & Engineering News) is saying about our Science paper [Computers predict molecules’ scent from their structures]. —————————————-2017—————————————-2017—————————————-2017—————————————- May 2016: Prof. Saiz visited Lehigh University and gave a talk on ‘Multilevel modeling of cellular networks in biomedicine’ as part of the Seminar Series of the Department of Chemical and Biomolecular Engineering. Spring Quarter 2016: Prof. Saiz will be teaching two courses in Spring: BIM 152 (Molecular Control of Biosystems) for undergraduate students and BIM 189C (Computational tools and Applications in Bioengineering and Biomedicine) for undergraduate students. —————————————-2016—————————————-2016—————————————-2016—————————————- October 7-10, 2015: Biomedical Engineering Society annual meeting: Iman gave a talk on our work on DNA aptamers at the platform session on ‘Molecules and Molecular Systems’ and Prof. Saiz gave the opening talk of the Bioinformatics, Computational and Systems Biology track at the ‘From Molecules to Cells and Organs in Health and Disease’ platform session. October 7-10, 2015: Biomedical Engineering Society annual meeting: Prof. Saiz was chair (organizer) of the Bioinformatics, Computational and Systems Biology track of the 2015 BMES meeting at Tampa (Florida) and delivered the opening talk of the meeting (Meeting Announcement PDF; Oral Platform Sessions PDF & Poster Sessions PDF of the Bioinformatics, Computational and Systems Biology track. June 2015-: Prof. Saiz is the editor of the special issue on “Signaling at Membranes” of the Journal of Membrane Biology. If you are an expert in the field and are interested in contributing a paper for the special issue, do not hesitate to contact her [at lsaiz@ucdavis.edu]. 2014-2015: Biomedical Engineering Society 2015 annual meeting: Prof. Saiz is the current chair of the Bioinformatics, Computational and Systems Biology track and will be organizing the sessions on the topic at Tampa (Florida) [check it out]. Spring Quarter 2015: Prof. Saiz will be teaching two courses in Spring: BIM 152 (Molecular Control of Biosystems) for undergraduate students and BIM 289C (Molecular Systems Biology and Biomedicine) for graduate students. —————————————-2015—————————————-2015—————————————-2015—————————————- June 9th, 2014: Our latest paper on “Suppression and enhancement of transcriptional noise by DNA looping” has been published [check it out]. May 23rd, 2014: Our latest paper on “Suppression and enhancement of transcriptional noise by DNA looping” has been accepted for publication. May 19th, 2014: Congratulations to Iman Jeddi for successfully defending her PhD thesis proposal!! April 5th, 2014: Our latest paper on “Determinants of protein-ligand complex formation in the thyroid hormone receptor: A Molecular Dynamics simulation study” has been published in Computational and Theoretical Chemistry [check it out]. March 27th, 2014: Our latest paper on “Determinants of protein-ligand complex formation in the thyroid hormone receptor: A Molecular Dynamics simulation study” has been accepted in Computational and Theoretical Chemistry. March 1st, 2014: Our latest paper on “Literature-based automated reconstruction, expansion, and refinement of the TGF-β superfamily ligand-receptor network” has been published in Journal of Membrane Biology [check it out]. February 14th, 2014: Our latest Biophysical Journal article awarded the distinction of “Best of 2013” [check it out]. February 12th, 2014: Congratulations to Daniel Nicklas for successfully defending his dissertation. Dr. Nicklas is the first PhD student to graduate from the Saiz lab. January 28th, 2014: Our latest paper on “Literature-based automated reconstruction, expansion, and refinement of the TGF-β superfamily ligand-receptor network” has been accepted in Journal of Membrane Biology. —————————————-2014—————————————-2014—————————————-2014—————————————- December 25th, 2013: “TherapySim” has just been released. TherapySim is a Python software package to predict potential therapeutic targets in signaling networks. Software can be downloaded at http://sourceforge.net/projects/therapysim together with the Python implementation tutorials [check it out]. December 20th, 2013: Our latest paper on “Characterization of negative feedback network motifs in the TGF-β signaling pathway” has been published in PLoS ONE [check it out]. December 10th, 2013: Our latest paper on “In silico identification of potential therapeutic targets in the TGF-β signal transduction pathway” has just been accepted and published in Molecular BioSystems [check it out]. November 6th, 2013: Our latest paper on “Characterization of negative feedback network motifs in the TGF-β signaling pathway” has been accepted in PLoS One. September, 25-28th 2013: BMES annual meeting: Danny will be presenting a poster on our work on TGF-beta and BMP signaling pathways. August 30th, 2013: Our latest Biophysical Journal paper has been highlighted in Cell Press’ “Spotlight in Quantitative Cell Biology” with the best (recent) Biophysical Journal papers on the topic [check it out]. July, 13-17th 2013: 9th European Biophysics Congress: Prof. Saiz gave an invited talk at the Symposium on “Systems Biology” at the 9th European Biophysics Congress in Lisbon (Portugal). July, 2013: Check out the abstract from our lab on “Negative feedback and crosstalk in the TGF-beta signaling pathway” published in European Biophysics Journal, 42 (Suppl 1), S73 (2013). Congratulations Aireen, Danny, and Victor. June, 2013: Our latest paper has just been published in the Journal of the Royal Society Interface [check it out]. June, 18th 2013: Our latest paper has just been published in the Biophysical Journal [check it out]. May, 2013: Our latest paper has just been published in ACS Synthetic Biology [check it out]. February, 2013: Biophysical Society annual meeting: Prof. Saiz has been invited to co-chair the session Platform BK: Systems Biophysics. She has also an oral presentation in that session on her recent work on control of gene expression by modulated self-assembly. Summer 2012-Spring 2013: Priam is continuing his internship at Genentech while doing research in our lab for another quarter! —————————————-2013—————————————-2013—————————————-2013—————————————- December, 12th 2012: “CplexA” is now available for Mathematica, Python, and Matlab. Software can be downloaded at http://cplexa.sourceforge.net/ and Mathematica, Matlab, and Python implementation tutorials are available at http://cplexa.sourceforge.net/ [check it out]. October, 24-27th 2012: BMES annual meeting: Danny presented a poster on our work on TGF-beta and BMP signaling pathways.
Summer/Fall 2012: Priam is continuing his internship at Genentech while doing research in our lab for another quarter! September, 27-28th 2012: UCDMC Annual Cancer Center Symposium: Danny presented a poster on our work on TGF-beta and BMP signaling pathways! August, 29th 2012: IRIS Undergraduate Research Conference: Our lab participated in the GREAT summer program hosting a GREAT student. Aireen presented a poster on our work at the IRIS conference. July, 17th 2012: New lab location: Our lab just moved to 3303A GBSF. June, 28th 2012: Daniel Nicklas successfully defended his PhD proposal. May, 2012: BMEGG Graduate Research Conference: Our lab participated in the first annual BME graduate research conference. Julie presented a poster on our work on stochastic modeling of gene regulation networks. April, 2012: Our latest paper has just been published as an invited topical review in the Journal of Physics: Condensed Matter [check it out]. January, 2012: Our latest Biophysical Journal article has been highlighted in the Biophysical Society Newsletter. January, 2012: BMES/BESA Undergraduate Research Fair: Our lab participated in the annual undergraduate research fair. We presented a poster on our work on computational modeling of signaling networks. —————————————-2012—————————————-2012—————————————-2012—————————————- November, 2011: Our latest article has just been published in the Biophysical Journal [read more] ! … and it has been highlighted as featured article!! October, 2011: BMES annual meeting: Danny will be giving a talk at the Platform Session on “Mathematical and Computational Models of Cellular and Molecular Processes” (Track: Systems Biology, Bioinformatics and Computational Bioengineering) in October! September, 2011: UCDMC Annual Cancer Center Symposium: Danny presented a poster on our work on TGF-beta and BMP signaling pathways! June, 2011: Our latest article just published in advance in Nucleic Acids Research has been highlighted as a featured article [read more]. “Featured articles represent the top 5% of papers in terms of originality, significance and scientific excellence”! May 20th, 2011: Our latest article has just been published in advance in Nucleic Acids Research [read more] ! February, 2011: Biophysical Society Annual Meeting: Check out Jonathan’s abstract at Biophysical Journal, 100, 164a (2011) on our work on TGF-beta and BMP signaling pathways! —————————————- 2011—————————————-2011—————————————-2011—————————————- August, 2010:GREAT Undergraduate Research Conference: Our lab participated in the GREAT summer program hosting two GREAT students. Yan and Teng presented a talk and a poster, respectively, on our work at the GREAT UG Research conference. July, 2010: Visiting undergraduate students Ms. Yan Li and Mr. Teng Li have joined the lab for summer research. June, 18th 2010: Our latest article has just been published in advance in Bioinformatics! June, 1st 2010: UG Course BIM189A: Molecular Control of Biosystems (Professor Saiz): Today we are having the final course project presentations. The following is the list of topics chosen by the undergraduate students for their research projects: – Hemoglobin – Environmental Biosensors – Bistable Caspase Regulation (apoptosis) – Arabinose Operon and its Application as an Oscillatory Gene Circuit – Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria – TGF-beta signaling pathway – Thiamine Pyrophosphate Riboswitch – Development of a Toggle Switch or Oscillatory Behavior in E. Coli – DNA Looping in the lac operon – Gal operon in yeast – Different Mechanisms of Bistability in Biological Systems.
May, 2010: The article entitled “Computer Simulation Studies of Model Biological Membranes” (Saiz and Klein; Accounts of Chemical Research, 2002) has been cited over 100 times!
April, 19th 2010: Check out our recently developed (and just released) open source software (CplexA) and corresponding tutorial. CplexA is a Mathematica package to compute the needed quantities to study macromolecular assembly and its effects in gene regulation (based on our papers published in Bioinformatics and in Nature/EMBO Molecular Systems Biology available in “Publications”). CplexA and the tutorial are available at http://sourceforge.net/projects/cplexa/.
Spring 2010: I will be teaching an interdisciplinary graduate course on “Molecular Systems Biology and Biomedicine” during the Spring 2010 Quarter (see Teaching). I will be teaching a new undergrad elective course on “Molecular Control of Biosystems” during the Spring 2010 Quarter (see Teaching). April, 19th 2010: Graduate Student Jonathan Ho (Biophysics Graduate Group) has joined the lab. —————————————-2010—————————————-2010—————————————-2010—————————————- September 2009: Congratulations Chao Zhu!!!… for graduating with a B.S. in Biotechnology and starting your graduate studies at the Pharmacology and Toxicology Graduate Program, UC Davis. June 2009: Graduate Student Ms. Elena Zaurova (Applied Mathematics Graduate Group) has joined the lab. June 2009: Visiting undergraduate student Ms. Rui Wang has joined the lab for summer research. January 2009: Graduate Student Colin Middleton has joined the lab. January 2009: Our research has been covered in the last edition of a classic biology textbook!: Coverage of research in classic textbooks: Discussion of our results on the thermodynamics of macromolecular assembly (Vilar & Saiz, 2005) in the last edition J.D. Watson et al., Molecular Biology of the Gene, 6th edition (Benjamin Cummins, New York, 2008), p. 587. October 2008: Another of our predictions confirmed!: Our prediction of alternative conformations of lac repressor-looped DNA complexes in vivo has just received further experimental support from in vitro experiments by the Gelles Lab (Brandeis) in the September 2008 issue of PLoS Biology! See our predictions in (Saiz and Vilar (2006) In vivo evidence of alternative loop geometries in DNA-protein complexes, arXiv:q-bio/0602012v1) and in Curr. Opin. Struct. Biol. (Saiz and Vilar, 2006) and the detailed paper in PLoS One (Saiz and Vilar, 2007). October 2008: Postdoctoral Fellow Le Yang has joined the lab. September 2008: Prof. Saiz has been appointed as Editorial Board member of the Journal of Membrane Biology. June 2008: Undergraduate students Chao Zhu (Biotechnology, UC Davis) and Harpreet Singh (Biomedical Engineering, UC Davis) have joined the lab. April 2008: Dr. Monica Pickholz, researcher at Unicamp (Brazil), is visiting the lab. New Course in Spring 2008: I will be teaching an interdisciplinary graduate course on Molecular and Multiscale Approaches to Systems Biology during the Spring 2008 Quarter (see Teaching). Note: advertised as BIM 289C Part 1 in the UC Davis Spring 2008 class schedule and registration guide. October 2007 I have just moved to the Biomedical Engineering Department of the University of California, Davis. The brand new lab for our group is up and running! |