News
BioMoDeL News
BioMoDeL's Rohith Mohan Received his PhD Degree
9/26/2018. Congratulations to Rohith Mohan for defending successfully his dissertation and receiving his PhD degree. Rohith's dissertation title is: Mapping the Druggability of Complement C3 and its Derivatives, and Inhibitor Design.
Dr Reed Harrison Started his Postdoctoral Fellowship at UCSD
September 2018. Newly minted BioMoDeL PhD, Reed Harrison started his postdoctoral fellowship in the group of Peter Wang, Bioengineering, UCSD.
BioMoDeL's Reed Harrison Received his PhD Degree
8/27/2018. Congratulations to Reed Harrison for defending successfully his dissertation and receiving his PhD degree. Reed's dissertation title is: Multi-Scale Design of Surveillance and Regulation Within the Complement System.
New Paper from Professor Elaine Haberer's Lab with BioMoDeL Contributions
July 2018. Ngo-Duc T-T, Plank JM, Chen G, Harrison RES, Morikis D, Liu H, Haberer ED (2018) M13 bacteriophage spheroids as scaffolds for directed synthesis of spiky gold nanostructures, Nanoscale, View Online. DOI: 10.1039/c8nr03229g.
New Paper from Professor Jiayu Liao's Lab with BioMoDeL Contribution
July 2018. Malik-Chaudhry HK, Gaieb Z, Saavedra A, Reyes M, Kung R, Le F, Morikis D, Liao J (2018) Dissecting Distinct Roles of NEDDylation E1 Ligase Heterodimer APPBP1 and UBA3 Reveals Potential Evolution Process for Activation of Ubiquitin-related Pathways, Scientific Reports 8: 10108 (10 pages). DOI: 10.1038/s41598-018-28214-2.
BioMoDeL Presented at the 19th UC Systemwide Bioengineering Symposium
BioMoDeL graduate students, Reed Harrison, Rohith Mohan, Nehemiah Zewde, and Rohaine Hsu, presented their work at the 19th UC Systemwide Bioengineering Symposium that took place in Riverside. Another collaborative project was also presented by Professor David Lo's postdoctoral fellow Casey Gries.
BioMoDeL Graduate Student Receives Best Poster Presentation Award
BioMoDeL graduate student Reed Harrison received the award for best poster presentation at the computational bioengineering track at the 19th University of California Systemwide Bioengineering Symposium. The symposium was hosted by our department, and was held in Riverside during June 21-21.
BioMoDeL Contributed to the Success of the 19th UC Systemwide Bioengineering Symposium
The 19th University of California Systemwide Bioengineering Symposium has come to end, and was a great success! All BioMoDeL graduate students gave oral or poster presentations, and volunteered for various organizational tasks during the conference. Professor Morikis was a member of the organizing committee, and chaired sessions.
June 2018. Mohan RR, Wilson M, Gorham RD Jr, Harrison RES, Morikis VA, Kieslich CA, Orr AA, Coley AV, Tamamis P, Morikis D (2018) Virtual screening of chemical compounds for discovery of complement C3 ligands, ACS Omega 3:6427–6438.
June 2018. Zewde N, Morikis D (2017) A Computational Model for the Evaluation of Complement System Regulation under Homeostasis, Disease, and Drug Intervention, PLOS ONE 13(6): e0198644 (28 pages, 177 pages supplementary information).
Three BioMoDeL students serve in the Student Editorial Board of UCR’s Undergraduate Research Journal
Undergraduate BioMoDeL student-researchers Siddharth Sai, Jayapriya Vengadesan, and Nolan Winicki served in the Student Editorial Board of Volume XII of the UCR Undergraduate Research Journal.
New BioMoDeL Paper at UCR Undergraduate Research Journal
Undergraduate BioMoDeL researcher and Bioengineering junior, Nolan Winicki, has published the paper with title " Identification of Targetable Surfaces of Cks1 for Development of New Cancer Therapeutics" in volume XII of UCR Undergraduate Research Journal. Co-authors in the paper are Reed Harrison, BioMoDeL graduate student, Professor Jefferson Perry of UCR's Department of Biochemistry, and Professor Morikis.
New BioMoDeL Paper at UCR Undergraduate Research Journal
BioMoDeL undergraduate researcher and Bioengineering junior, Nolan Winicki, has published the paper with title "Identification of Targetable Surfaces of Cks1 for Development of New Cancer Therapeutics" in volume XII of UCR Undergraduate Research Journal. Co-authors in the paper are Reed Harrison, BioMoDeL graduate student, Professor Jeff Perry of UCR's Department of Biochemistry, and Professor Morikis.
Four BioMoDeL Students Present at the UCR Undergraduate Research Symposium
Undergraduate student-researchers, Nolan Winicki (3d year), Sharon Gupta (4th year), Vivian Luong (4th year), and Siddharth Sai (3d year) presented their research at the UCR Undergraduate Research Symposium that took place in May 7-8, 2018.
BioMoDeL Graduate Student Receives Dissertation Year Fellowship Award
Nehemiah Zewde, fourth year graduate student, received a one-quarter Dissertation Year Program (DYP) fellowship award for 2018-2019. Nehemiah is expected to complete his doctoral degree in bioengineering by summer 2019. The DYP award is administered by UCR's Graduate Division.
BioMoDeL Graduate Student Receives Best Teaching Assistant Award
Rohith Mohan, fifth year graduate student, received the 2017-2018 Best Teaching Assistant Award in Bioengineering by UCR's Graduate Division.
High Schooler Mentee Advances to California State Fair
Congratulations to high school student Maanasi Kademani of Riverside's Martin Luther King High School, last year’s BioMoDeL award winner and lab mentee since then, for winning gold medal at the 2018 Riverside County Science and Engineering Fair. The title of her project was “Structure and Sequence Conservation of Rhodopsin Across Ectothermic and Endothermic Vertebrates”. Maanasi will be advancing with her project to the California State Fair to be held at the California Science Center in Los Angeles, in late April 2018.
High School Student Receives BioMoDeL Award for Science Fair Project
Congratulations to Hailee Hammond of Eleanor Roosevelt High School - Corona-Norco, for receiving the 2018 BioMoDeL award at the Riverside County Science and Engineering Fair, for her project "Natural Neutralizing PPI's".
BMC Biophysics Launches Call for Papers for a Thematic Series on Biophysics of Disease
March 12, 2018. BMC Biophysics is currently accepting manuscripts for the thematic series Biophysics of Disease. Deadline for submission is October 12, 2018. Professor Morikis, Editor-in-Chief of BMC Biophysics, will also serve as the Editor of the Thematic Series.
March 12-16, 2018. We celebrate Biophysics Week. Numerous events are sponsored by the Biophysical Society.
BioMoDeL Graduate Students Volunteer in Science Olympiad
March 3, 2018. Graduate students Rohith Mohan and Reed Harrison volunteered at the Inland Empire Regional Inland Empire Science Olympiad at Ramona High School, Riverside, CA for the 3rd consecutive year. They returned as judges and Proctors for the Protein Modeling event and as test-writers for the Microbe Mission event.
BioMoDeL Graduate Student Presents at the Biophysical Society Annual Meeting
Graduate student Reed Harrison presented his research in a poster at the 2018 annual meeting of the Biophysical Society that took place in San Francisco, 2/17-21/2018.
BioMoDeL Alumnus Publishes Major Paper
Dr. Alex Cheung, BioMoDeL undergraduate researcher alumnus, BS Bioengineering UCR, PhD Harvard, published a major research paper in Nature Biotechnology with title "Scaffolds that mimic antigen-presenting cells enable ex vivo expansion of primary T cells" for work he did in the Mooney lab at Harvard University. The work is featured in the journal cover.
Welcome to our newest BioMoDeL member, Rohaine Hsu, first year bioengineering graduate student.
Q&A Blog Introducing Professor Morikis as the Editor-in-Chief for BMC Biophysics
A Q&A Blog is posted by the BioMed Central Series journals, Introducing Professor Morikis as the Editor-in-Chief for BMC Biophysics. Professor Morikis has been Editor-in-Chief of BMC Biophysics since July 2017, and was a Section Editor since the time of launching of the journal in 2011.
BioMoDeL Graduate Student Presents Departmental Seminar
11/29/2017. Graduate student Reed Harrison gave a research presentation at the graduate student part of the departmental seminars. The presentation was on the role of electrostatics in structural differences of two variants of the immune system protein C3b, and the role of these differences in predisposition to age-related macular degeneration.
November 2017. Zewde N, Morikis D (2017) A Computational Model for the Evaluation of Complement System Regulation under Homeostasis, Disease, and Drug Intervention, bioRxiv doi: 10.1101/225029.
BioMoDeL Undergraduate Student Presented at SCCUR Conference
11/18/2017. BioMoDeL undergraduate student-researcher Siddharth Sai presented his research at the annual Southern California Conference for Undergraduate Research (SCCUR), held at Cal Poly Pomona University. Presentation title: Computational Analysis of Helical Interactions In Resistin. This is a collaborative research project with Professor Meera Nair of UCR's School of Medicine, and was co-supervised by BioMoDeL graduate student Rohith Mohan.
BioMoDeL Graduate Student Presented his Research
11/16/2017. BioMoDeL graduate student Reed Harrison presented his research at the UCR Bioengineering Graduate Student-Faculty Evening Social. Presentation title: Molecular Basis for the Link between Macular Degeneration and a Single Nucleotide Polymorphism.
Professor Morikis Presented BioMoDeL Research
11/17/2017. Professor Morikis presented one of BioMoDeL's research projects at the UCR Data Science seminars. Presentation title: A Computational ODE Model for the Evaluation of Immune System Pathway Dynamics in Homeostasis and Disease.
11/15-16/2017. BioMoDeL attended the conference "Multi-scale Systems Biology Methods for Studying Biomedical Processes in Patients under Stress or with Chronic or Acute Diseases", held at UCR.
BioMoDeL Graduate Student Presents Departmental Seminar
11/8/2017. Graduate student Rohith Mohan gave a research presentation at the graduate student part of the departmental seminars. The title of his talk was “AESOP: A Python Library for Investigating Electrostatics in Protein Interactions”.
BioMoDeL is Awarded Supercomputer Time
10/31/2017. BioMoDeL received a grant of 460,000 Anton2 molecular dynamics simulation units from the Pittsburgh Supercomputing Center. Anton2 is the fastest supercomputer built to perform molecular dynamics simulations.
Professor Morikis Presents at AIChE 2017
10/31/2017. Professor Morikis was invited speaker at the Annual Meeting of the American Association of Chemical Engineers (AIChE) in Minneapolis, in a special session in honor and memory of the late Professor Chris Floudas (Princeton University and Texas A&M). Professor Floudas, a pioneer in developing computational methods for engineering research and applications, was a collaborator for 19 years in a variety of projects, and a friend of BioMoDeL.
Professor Morikis Presents at Peptide Conference
10/26/2017. Professor Morikis presented BioMoDeL research on peptide design at the 12th Annual Peptide Therapeutics Symposium at the Salk Institute in La Jolla.
Professor Morikis Presents at Conference
10/20/2017. Professor Morikis presented BioMoDeL research on Multiscale Computational Modeling of Proteins, Complexes, and Pathways at the Annual Retreat of UCR's Institute for Integrative Genome Biology.
BioMoDeL Graduate Student Presents at BMES
BioMoDeL graduate student Reed Harrison, presented his research in a poster at the 2017 BMES (BioMedical Engineering Society) Annual Meeting in Phoenix, AZ, 10/11-14/2017.
BioMoDeL Receives Recognition for Issued Patent
10/11/2017. BioMoDeL was recognized by UCR's Research and Economic Development Office and EPIC (Entrepreneurial Proof of Concept and Innovation Center) in a ceremony for UCR patents issued in 2016-2017. Awards were presented for 27 UCR inventions, among them ours for peptides that have the potential to treat age-related macular degeneration. For BioMoDeL technologies, see: https://www.ucreduotp.net/epic.
Professor Morikis is the Principal Investigator in a 4-year $1.5M R01 grant from NIH/NEI to perform research on the discovery of biomarkers for age-related macular degeneration. The project entails computational modeling and simulations, design, and virtual screening studies, fluorescence spectroscopy and imaging studies, cell studies, and primate and human tissue studies. An interdisciplinary team of experts has been assembled to perform or provide expertise on various aspects of the work, including Profs. Kaustabh Ghosh (UCR), Valentine Vullev (UCR), Trevor McGill and Martha Neuringer (Oregon Health and Science University), Lincoln Johnson (UCSB), Hyle Park (UCR), and SriniVas Sadda (UCLA).
Professor Morikis has been Appointed Editor-in-Chief of BMC Biophysics
7/20/2017. Professor Morikis has been appointed Editor-in-Chief of BMC Biophysics, a BioMed Central (BMC) journal. BMC is part of Springer Nature.
Participation at the 18th Annual UC Systemwide Bioengineering Symposium
Professor Morikis attended the 18th Annual UC Systemwide Bioengineering Symposium, held at UCLA. A poster with BioMoDeL's latest research on quantitative modeling of complement system dynamics was presented.
6/24/2017. BioMoDeL alumnus Chris Kieslich (PhD in Bioengineering, UCR, 2012) and Fani Boukouvala (PhD in Chemical & Biochemical Engineering, Rutgers University, 2013) got married in Athens, Greece! Congratulations! A mini BioMoDeL alumni reunion took place at the wedding.
BioMoDeL Graduate Student Starts Summer Internship at Boston Biotech
BioMoDeL graduate student Rohith Mohan has started his summer internship at Biogen, Boston, MA.
BioMoDeL Undergraduate Student-Researcher Receives Summer Research Fellowship
BioMoDeL undergraduate student-researcher Siddharth Sai has received an Undergraduate Education Summer Research Fellowship.
BioMoDeL Graduate Student Receives UC President's Dissertation-Year Fellowship
BioMoDeL graduate student Reed Harrison has received University of California’s President’s Dissertation-Year Fellowship for the 2017/2018 academic year.
BioMoDeL alumnus Wilson Rodriguez (undergraduate researcher, 2011-2013, BS in Bioengineering, 2013) and Linh Tong (UCR, BS in Chemical Engineering) got married in Santa Ana, CA! Congratulations!
New BioMoDeL Paper at UCR Undergraduate Research Journal
Undergraduate BioMoDeL researcher and Bioengineering sophomore, Siddharth Sai, has published the paper with title "In Silico Physicochemical Analysis of Helical Interactions in Resistin" in volume XI of UCR Undergraduate Research Journal. Co-authors in the paper are Rohith Mohan, BioMoDeL graduate student, Professor Meera Nair of UCR's School of Medicine, and Professor Morikis.
BioMoDeL Graduate Student Presented at CePCeB Postdoc Symposium
5/12/2017. BioMoDeL graduate student Reed Harrison presented his work at the 4th Center for Plant Cell Biology (CePCeB) Postdoc Symposium.
BioMoDeL Graduate Student Receives Best Teaching Assistant Award
Reed Harrison received the 2016-2017 Bioengineering Best Teaching Assistant Award by UCR's Graduate Division.
May 2017. Harrison RES, Mohan RR, Gorham RD Jr, Kieslich CA, Morikis D (2017) AESOP: A Python Library for Investigating Electrostatics in Protein Interactions, Biophysical Journal 112:1761-1766.
April 2017. Gaieb Z, Morikis D (2017) Conformational heterogeneity in CCR7 undergoes transitions to specific states upon ligand binding, Journal of Molecular Graphics and Modelling, in press - available online.
Inaugural BioMoDeL Award at the 2017 Riverside Science & Engineering Fair
3/28-29/2017. The first BioMoDeL Community Award at the Riverside Science & Engineering Fair went to Maanasi Kademani of Martin Luther King High School for her research project “A Comparative Study on the Effectiveness of Plant-Based AChE Inhibitors and Drug AChE Inhibitors for the Treatment of Alzheimer’s Disease”. The award is based on biophysical and bioengineering content of a research project, with potential medical significance, as well scientific methodology followed and professional presentation of the poster at the Science and Engineering Fair. Judging is performed by BioMoDeL graduate students. This award is accompanied with a $100 gift.
BioMoDeL alumnus presents his new work at webinar
3/27/2017. Recent BioMoDeL graduate Zied Gaieb, currently postdoctoral fellow at UCSD, presented his new work at a D3R (Drug Design Data Resource) webinar.
Seminar at the Math Department
3/20/2017. Professor Morikis presented BioMoDeL's research on "Computational Modeling of Protein Dynamics and Interactions" at the Interdisciplinary Seminar series, Department of Mathematics, UCR
We are saddened to hear that Dr Roberts of City of Hope passed away on 11/8/2016. Dr Roberts, a visionary in the field of neurobiochemistry, had discovered the presence of GABA in the brain in 1949, among numerous other contributions. Dr Roberts was a friend of BioMoDeL, a past collaborator, and a mentor to Professor Morikis.
New BioMoDeL Publication with Colleagues from the Spanish National Research Council, Madrid, Spain
March 2017. López-Perrote A, Harrison RES, Subías M, Alcorlo M, Rodríguez de Córdoba S, Morikis D, Llorca O (2017) Ionic tethering contributes to the conformational stability and function of complement C3b, Molecular Immunology 85:137-147.
BioMoDeL Graduate Students Participate in the Inland Empire Science Olympiad
March 2017. Reed Harrison and Rohith Mohan wrote, proctored, and graded the science exam for middle and high school students at the 2017 Inland Empire Science Olympiad.
BioMoDeL Alumnus Published Review Article
BioMoDeL alumnus Alex Cheung (undergraduate student researcher) has published a 2015 review article on "Engineered Materials for Cancer Immunotherapy" with his graduate advisor David Mooney (Harvard University). Cheung AS, Mooney DJ (2015) Nano Today 10: 511–531. DOI: 10.1016/j.nantod.2015.06.007.
Gaieb Z, Morikis D (2017) Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors, Computational and Structural Biotechnology 15:131-137.
BioMoDeL Alumni Publish Review Article
BioMoDeL alumni Ron Gorham (graduate student and postdoc) and Kaila Bennett (senior design project) publish joint review article on "Let’s Tie the Knot: Marriage of Complement and Adaptive Immunity in Pathogen Evasion, for Better or Worse". DOI=10.3389/fmicb.2017.00089. Ron and Kaila celebrated their one-year wedding anniversary with the writing of this review.
Newest BioMoDeL PhD Starts a Postdoctoral Fellowship at UCSD
Recent BioMoDeL PhD Zied Gaieb started his postdoctoral fellowship at UCSD in the groups of Professors Rommie Amaro and Michael Gilson.
BioMoDeL Participates in the 7th Annual Southern California Systems Biology Conference
1/28/2017. BioMoDeL graduate student Nehemiah Zewde gave a presentation with title "Mathematical Modeling of Complement System Dynamics", substituting for Professor Morikis.
Compstatin Analogs, with colleagues from Princeton University and University of Cyprus. US Patent 9512180. Issued 12/6/2016.
11/18/2016. Professor Morikis gave an invited talk at the 2016 Annual Meeting of the American Institute of Chemical Engineers (AIChE) in San Francisco. The title of his talk was "The Role of Electrostatics in the Function of a Protein Link Between Innate and Adaptive Immunity".
Professor Orestis Kalogirou visits BioMoDeL
11/09/2016. Professor Orestis Kalogirou from the Aristotle University of Thessaloniki, Greece (currently Fulbright Scholar at Harvard Medical School) visited BioMoDeL and the Department of Bioengineering, and gave a departmental colloquium presentation with title "Biomedical Applications of Magnetic Nanoparticles".
Mohan RR, Cabrera AP, Harrison RES, Gorham RD Jr, Johnson LV, Ghosh K, Morikis D (2016) Peptide Redesign for Inhibition of the complement system: Targeting age-related macular degeneration, Molecular Vision 22:1280-1290.
Our python version of AESOP is released
AESOP (Analysis of Electrostatic Structures Of Proteins) is now released as a python library. AESOP has three modules for the analysis of protein electrostatics: (i) alanine scan, (ii) directed mutagenesis, and (iii) electrostatic similarities. AESOP 0.0.14 is available for downloading from https://pypi.python.org/pypi/aesop/ . Documentation can be downloaded from: http://aesop.readthedocs.io . A webserver for alanine scans is at: https://aeolus.engr.ucr.edu/aesop/ .
Professor Walter Knapp Visits BioMoDeL
9/30/2016. Professor Walter Knapp of Freie Universität, Berlin, visited BioMoDeL & gave a joint Bioengineering/Physical Chemistry seminar on "Marriage of Quantum Chemistry and Electrostatics to Compute pKa's and Redox Potentials in Solution and Proteins"
Professor Rommie Amaro Visits BioMoDeL
9/28/2016. Professor Rommie Amaro of UCSD visited BioMoDeL and our department and presented a Bioengineering Colloquium on "Multi-Scale Dynamics: Molecules to Cells".
Professor Gennady Verkhivker visits BioMoDeL
9/27/2016. Professor Gennady Verkhivker of Chapman University visited BioModeL and gave a Biochemistry seminar on network-centric modeling of allosteric regulation.
BioMoDeL Paper is Featured in Journal Cover
Zied Gaieb's paper on the "Molecular mechanism of biased ligand conformational changes in CC chemokine receptor 7" is featured on the cover of the Journal of Chemical Information and Modeling.
Festschrift issue in honor of Professor Andy McCammon
The Festschrift issue of the Journal of Physical Chemistry B in honor of Professor Andy McCammon is published. Our paper "Electrostatic Steering Accelerates C3d:CR2 Association" is part of this issue. DOI: 10.1021/acs.jpcb.6b02095.
Congratulations alumnus Chris Kieslich
Congratulations to BioMoDeL alumnus Chris Kieslich for his new position as a Research Engineer at the Wallace H. Coulter Department of Biomedical Engineering of Georgia Tech.
August 14, 2016. We are mourning the loss of Professor Chris Floudas of Texas A&M University, who suddenly passed away today. Professor Floudas was a long-term collaborator and friend of BioMoDeL. Professors Floudas and Morikis and their research groups have been collaborating for 18 years on protein, peptide, and drug design projects. News, Texas A&M. News, Princeton.
August 4, 2016. Congratulations to Zied Gaieb for successfully defending his thesis and receiving his PhD degree.
August 2, 2016. BioMoDeL graduate student Reed Harrison has returned after performing research for two moths at the Spanish National Cancer Research Center in Madrid, Spain, with a prestigious Whitaker summer grant.
July 2016. News and Commentary: Kember C (2016) Targeting the Dark Horse of complement: the first generation of functionally selective C5aR2 ligands, Immunology & Cell Biology, in press – available on line. DOI: 10.1038/icb.2016.62; for our paper: Croker DE, Monk PN, Halai R, Kaeslin G, Schofield Z, Wu MCL, Clark RJ, Blaskovich MAT, Morikis D, Floudas CA, Cooper MA, Woodruff TM (2016) Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signaling, Immunology & Cell Biology, in press – available on line. DOI: 10.1038/icb.2016.43.
July 26, 2016. Professor Morikis gave a presentation on Knowledge-based Drug Discovery at the UCR Bourns College of Engineering MESA Program for K-12 STEM teachers.
June 10, 2016. BioMoDeL graduate students Zied Gaieb and Rohith Mohan presented their work at the 3d Annual CePCeB (cepceb.ucr.edu) Postdoc Symposium.
BioMoDeL graduate student Reed Harrison has received a Whitaker summer grant to perform research at CNIO (Centro National de Investigaciones Oncologicas – Spanish National Cancer Research Center), in Madrid, Spain.
May 2016. Congratulations to BioMoDeL graduate student Nehemiah Zewde for passing his oral qualifying exam.
April 2016. New tri-continent collaborative paper with colleagues from Univesity of Queensland, Sheffield University, and Texas A&M University: Croker DE, Monk PN, Halai R, Kaeslin G, Schofield Z, Wu MCL, Clark RJ, Blaskovich MAT, Morikis D, Floudas CA, Cooper MA, Woodruff TM (2016) Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signaling, Immunology & Cell Biology, in press – available on line. DOI: 10.1038/icb.2016.43.
April 2016. New publication: Mohan RR, Huber GA, Morikis D (2016) Electrostatic steering accelerates C3d:CR2 association, Journal of Physical Chemistry B, in press – available online. DOI: 10.1021/acs.jpcb.6b02095.
April 2016. Professor Morikis chaired a session and judged posters and oral presentations at the UCR 10th Annual Symposium for Undergraduate Research, Scholarship, and Creative Activity, April 19-20, 2016.
April 2016. Professor Morikis is featured as "Biophysicist in Profile" in the April 2016 Newsletter of the Biophysical Society: http://biophysics.cld.bz/Biophysical-Society-Newsletter-April-2016.
March 2016. New publication: Zewde N, Gorham RD Jr, Dorado A, Morikis D (2016) Quantitative modeling of the alternative pathway of the complement system, PLOS ONE 11:e0152337 (26 pages, 43 pages supplementary information). DOI: 10.1371/journal.pone.0152337.
3/15/2016. BioMoDeL graduate student Zied Gaieb gave a poster presentation on his research at the 251st American Chemical Society National Meeting & Exposition, 3/13-17/2016, San Diego, CA.
3/1/2016. BioMoDeL graduate student Zied Gaieb gave an oral presentation on his research at the 60th Annual Meeting of Biophysical Society, 2/27-3/2/2016, Los Angeles, CA.
2/28/2016. BioMoDeL graduate students Rohith Mohan and Reed Harrison presented posters of their research at the 60th Annual Meeting of Biophysical Society, 2/27-3/2/2016, Los Angeles, CA.
2/27/2016. Professor Morikis participated in the inaugural meeting of the Biophysical Society Bioengineering Subgroup, during the 60th Annual Meeting of the Biophysical Society, 2/27-3/2/2016, Los Angeles, CA.
Professor Morikis participated as a panelist at the 8th Annual Conference of the Arnold and Mabel Beckman Initiative for Macular Research (BIMR), January 14-16, at the Beckman Center of the National Academies of Sciences and Engineering, in Irvine, CA.
2015
December 2015. Professor Morikis has completed his sabbatical stay at CNIO (Centro National de Investigaciones Oncologicas – Spanish National Cancer Research Center), Madrid, Spain.
12/14/2015. Professor Morikis presented a seminar on "Discovery of Complement System Biomarkers using Virtual Screening" at CNIO (Centro National de Investigaciones Oncologicas – Spanish National Cancer Research Center), Madrid, Spain.
November 2015. New publication. Gorham RD Jr, Nuñez V, Lin J-H, Rooijakkers SHM, Vullev VI, Morikis D (2015) Discovery of small molecules for fluorescent detection of complement system activation product C3d, Journal of Medicinal Chemistry, in press – available online. DOI: 10.1021/acs.jmedchem.5b01062.
November 2015. New collaborative publication from Natasha Raikhel's lab. Zhang C, Brown MQ, van de Ven W, Zhang Z-M, Wu B, Young MC, Synek L, Borchardt D, Harrison R, Pan S, Luo N, Huang Y-M, Ghang Y-J, Ung N, Li R, Isley J, Morikis D, Song J, Guo W, Hooley RJ, Chang C, Yang Z, Zarsky V, Muday GK, Hicks GR, Raikhel NV (2015) Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis, Proceedings of the National Academy of Sciences (USA), in press – available online. DOI: 10.1073/pnas.1521248112.
11/25/2015. Professor Morikis attended the Madrid Macromolecular Structural Club meeting.
11/23/2015. Professor Morikis presented a seminar on "Evolution of Electrostatics in a Link between Innate and Adaptive Immunity" at CNIO (Centro National de Investigaciones Oncologicas – Spanish National Cancer Research Center), Madrid, Spain.
11/11/2015. Professor Morikis met with researchers and gave a presentation at the Centro de Investigaciones Biologicas (Center of Biological Research), Madrid, Spain.
10/24/2015. BioMoDeL alumni Ron Gorham (graduate student and postdoc) and Kaila Bennett (senior design and graduate student collaborator) got married in Lake Arrowhead, CA! Congratulations! A reunion of BioMoDeL alumni and current graduate students took place at the wedding!
BioMoDeL graduate student Rohith Mohan received funding from the NSF to attend the "Macromolecular Simulation Software Workshop" hosted by CECAM in Jülich, Germany, October 12-19, 2015.
10/13/2015. Professor Morikis gave a talk at the thematic meeting on Biophysics of Proteins at Surfaces: Assembly, Activation, Signaling, Madrid, Spain.
September 2015. BioMoDeL alumnus, Chris Kieslich (PhD 2012), has launched his new website: http://cakieslich.com/.
August 2015. New publication: Chen C, Gorham RD Jr., Gaieb Z, and Morikis D (2015) Electrostatic interactions between complement regulator CD46(SCR1-2) and adenovirus Ad11/Ad21 fiber protein knob, Molecular Biology International, 2015: Article ID 967465. 15 pages. DOI:10.1155/2015/967465. Link. Suppl.
August 2015. New collaborative publication from David Lo's lab: Bennett KM, Gorham RD, Gusti V, Trinh L, Morikis D, Lo DD (2015) Hybrid flagellin as a T cell independent vaccine scaffold, BMC Biotechnology, 15:71. DOI: 10.1186/s12896-015-0194-0. Link. Suppl.
June 2015. Congratulations to BioMoDeL graduate student Rohith Mohan for passing his oral qualifying exam.
June 2015. Congratulations to BioMoDeL graduate student Anthony Lira for receiving his MS in Bioengineering, 2015, UCR.
June 2015. Congratulations to BioMoDeL undergraduate student Sanychen Muk for receiving his BS in Bioengineering, 2015, UCR.
June 2015. Congratulations to BioMoDeL undergraduate student-researcher Sanychen Muk for publishing his work: Muk S, Gorham RD Jr, Morikis D (2015) Regulation of complement activation through factor D inhibition: a drug discovery study, UCR Undergraduate Research Journal, 9:85-90. Link.
June 2015. Professor Morikis presented the unveiling ceremony of volume IX of the UCR Undergraduate Research Journal. Professor Morikis has been the Chair of the Faculty Advisory Board (FAB) for the last three years, and has been with FAB since the journal inception in 2007.
June 2015. Congratulations to BioMoDeL graduate student Rohith Mohan for receiving a San Diego Supercomputer Center - University of California Graduate Summer Fellowship Award.
May 2015. Congratulations to BioMoDeL graduate student Reed Harrison for passing his oral qualifying exam.
May 2015. Thanks to NVIDIA for the donation of a TESLA K40 GPU to help accelerate our molecular dynamics simulations.
May 2015. Congratulations to our senior design team for placing at top 3 in the internal competition with their project MUSE (Mobile User Sign-language Equipment), or how to use muscle movement to interpret ASL (American Sign Language): Shane Eum, Annie Lee, Enoch Li, Henry Marshall, Sanychen Muk.
BioMoDeL is now in Benefunder, visit http://benefunder.org/causes/462/dimitrios-morikis.
BioMoDeL alumnus Nic Novak (summer 2008 NSF/REU intern) is co-founder of Magic.
Congratulations to BioMoDeL graduate students Zied Gaieb and Rohith Mohan for being among the five finalists for the NVIDIA GPU Award for Best GPU Poster at the American Chemical Society (ACS) National Meeting (Denver, CO; spring 2015). Link. The award is sponsored by the ACS Computers in Chemistry Division. NVIDIA is the Visual Computing Company.
February 2015. Congratulations to recent BioMoDeL alumnus Ron Gorham for receiving a Marie Curie Postdoctoral Fellowship. Ron just started his European Postdoctoral Fellowship at University Medical Center Utrecht.
January 2015. Congratulations to Ron Gorham for his excellent work at BioMoDeL, and for assuming a postdoctoral position at the University Medical Center Utrecht. Good Luck!
1/26/2015. Professor Morikis gave a talk on the development of biomarkers for early detection of complement system-mediated inflammatory diseases at the UCR School of Medicine.
New Publication: Harrison R, Gorham RD Jr, Morikis D (2015) Energetic evaluation of binding modes in the C3d and factor H (CCP 19-20) complex, Protein Science, In Press – available online. DOI:10.1002/pro.2650. Link. Suppl.
Bioengineering Undergraduate Advisor Professor Morikis participated in the Undergraduate Education task group at the UCR Bourns College of Engineering retreat, January 23-25, in Long Beach, CA.
Professor Morikis participated as a panelist and gave a presentation at the 7th Annual Conference of the Arnold and Mabel Beckman Initiative for Macular Research (BIMR), January 15-17, at the Beckman Center of the National Academies of Sciences and Engineering, in Irvine, CA.
January 2015. Congratulations to Phanourios Tamamis, BioMoDeL alumnus/Fulbright Fellow, for joining the Department of Chemical Engineering at Texas A&M University as Assistant Professor. Prior to this appointment, Phanourios was a Postdoctoral Fellow at the Department of Chemical & Biological Engineering of Princeton University.
2014
December 2014. Congratulations to BioMoDeL Postdoctoral Fellow Ron Gorham for receiving the Best Tech Talk award at the 12thAnnual CePCeB Symposium that took place on December 12 in UCR. Link.
New Publication: Gorham RD Jr, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive CK, Floudas CA, Radeke MJ, Johnson LV, Morikis D (2014) New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics, Journal of Medicinal Chemistry, in press – available online, DOI: 10.1021/jm501345y. Link.
New Publication. Mohan R, Gorham RD Jr, Morikis D (2014) A theoretical view of the C3d:CR2 binding controversy, Molecular Immunology, in press - available online. Link.
New Publication. Halai R, Bellows-Peterson ML, Branchett, W, Smadbeck J, Kieslich CA, Croker DE, Cooper MA, Morikis D, Woodruff TM, Floudas CA, Monk PN (2014) Derivation of ligands for the complement C3a receptor from the C-terminus of C5a, European Journal of Pharmacology 745:176-181. Link.
October 2014. Congratulations to BioMoDeL Postdoctoral Fellow Ron Gorham for receiving the Reviewer's Choice Award for his poster presentation at the 2014 Biomedical Engineering Society (BMES) Annual Meeting, October 22-25, San Antonio, TX
October 2014. Professor Morikis participated at the Video Bioinformatics IGERT Annual Retreat, in Lake Arrowhead, CA.
New publication. Tamamis P, Kieslich CA, Nikiforovich GV, Woodruff TM, Morikis D, Archontis G (2014) Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking, BMC Biophysics 7:5. Link.
August 2014. Congratulations to collaborating graduate student researcher Danh Do (Prof. Schiller's Lab, Biomedical Sciences) for successfully defending his PhD thesis: The Role of Bacterial Biofilms in Chronic Infection.
July 2014. Professor Morikis gave a talk with title Immunophysics and Immunoengineering in the Complement System at CIEMAT (Centro de Investgaciones Energeticas, Medioambientales y Tecnologicas, www.ciemat.es), Madrid, Spain.
July 2014. New grant received from the Beckman Initiative for Macular Research. The project entails the development of immune system-based biomarkers for the early detection of the onset of macular disease. PI: Dimitrios Morikis; Co-PIs: Lincoln Johnson (Center for the Study of Macular Degeneration, UC-Santa Barbara) and Valentine Vullev (Bioengineering, UCR).
July 2014. Congratulations to BioMoDeL graduate student Reed Harrison for receiving an IGERT graduate fellowship award in Video Bioinformatics for 2014-2015.
New publication. Ojha H, Panwar HS, Gorham RD Jr, Morikis D, Sahu A (2014) Viral regulators of complement activation: structure, function and evolution, Molecular Immunology 61:89-99. Link.
June 2014. Professor Morikis gave a presentation at the Computer Aided Drug Discovery and Development Symposium of the 95th Annual AAAS-Pacific Division Meeting, UCR. Link.
June 2014. Professors Morikis and Vullev co-organized the Multi-Scale Bioengineering Symposium of the 95th Annual AAAS-Pacific Division Meeting, UCR, and chaired the morning and afternoon sessions, respectively. Link.
June 2014. BioMoDeL collaborator Danh Do (graduate student, Prof. Schiller Lab) presented his work at the Cell & Molecular Biology Symposium of the 95th Annual AAAS-Pacific Division Meeting, UCR. Link.
June 2014. Congratulations to BioMoDeL graduate student Rohith Mohan for receiving an award for Best Oral Presentation at the 15th Annual UC Systemwide Bioengineering Symposium, UC-Irvine. Link.
June 2014. BioMoDeL researchers presented their work at the 15th Annual UC Systemwide Bioengineering Symposium, UC-Irvine: Ron Gorham (postdoctoral fellow), Zied Gaieb, Reed Harrison, Rohith Mohan (Graduate students), and Ilya Lederman (undergraduate student); also collaborator Harbani Malik (postdoctoral fellow - Prof. Liao Lab) presented common work with our group. Link. Photo.
June 2014. Congratulations to Ilya Lederman for completing his Chancellor's Research Fellowship with an oral presentation at the Annual UC Systemwide Bioengineering Symposium and a publication at the UCR Undergraduate Research Journal. Link. Link. Link.
June 2014. Congratulations to BioMoDeL students for receiving their BS in Bioengineering, 2014, UCR: Nehemiah Zewde, Ilya Lederman, and Belinda Le. Photo.
June 2014. BioMoDeL undergraduate student-researchers were honored at the UCR Undergraduate Research Journal Unveiling ceremony. Photo. Ceremony Photos.
New undergraduate research publication: Baddour B, Gorham, RD Jr, Morikis D (2014) Electrostatic analysis of complement factor D, UCR Undergraduate Research Journal 8:5-12. Link.
New undergraduate research publication: Lederman I, Morikis D (2014) Network analysis of intra-molecular interactions of the HIV-1 gp120 V3 loop, UCR Undergraduate Research Journal 8:25-32. Link.
New undergraduate research publication: Zewde N, Dorado A, Gorham RD Jr, Morikis D (2014) Quantitative modeling of the alternative pathway in complement immune system, UCR Undergraduate Research Journal 8:75-82. Link.
April 2014. Undergraduate BioMoDeL students Basil Baddour, Ilya Lederamn, and Nehemiah Zewde presented their research at the 8th Annual Undergraduate Research, Scholarship, and Creative Activity Symposium at UCR.
New publication. Liu Y, Kieslich CA, Morikis D, Liao J (2014) Comparative analysis of electrostatic similarity indices in a high-throughput computational protocol for alanine scans and electrostatic clustering: application to SUMO-SENP2 interaction, Protein Engineering Design & Selection 27: 117-126. Link.
March 2014. Congratulations to collaborating graduate student researcher Harbani Kaur Malik Chaudhry (Prof. Liao's Lab, Bioengineering) for successfully defending her PhD thesis: Development of in vitro Sensitive FRET Technology to Dissect Reaction Dynamics and Intermediates in NEDD8 Conjugation Cascade.
New publication. Gorham RD Jr, Rodriguez W, Morikis D (2014) Molecular analysis of the interaction between staphylococcal virulence factor Sbi-IV and complement C3d, Biophysical Journal 106:1164-1173. Link.
January 2014. New instrumentation grant from the Department of the Army, led by Prof. morikis (PI). This is a common facility to be housed at the Center for Bioengineering Research.
2013
December 2013. Welcome first year graduate students Reed Harrison and Rohith Mohan in joining BioMoDeL.
December 2013. Prof. Morikis gave a presentation at UCR’s NSF IGERT Video Bioinformatics 4th Retreat in Lake Arrowhead, CA.
November 2013. Prof. Morikis gave a presentation at the City of Hope, Duarte, CA
November 2013. Welcome to undergraduate student Belinda Le in joining BioMoDeL.
Congratulations to BioMoDeL alumna Aliana Lopez de Victoria for joining the Department of Chemistry of the University of Central Florida as a Postdoctoral Fellow.
October 2013. Welcome to undergraduate students Robin Riehn and Balmeet Singh in joining BioMoDeL.
August 19, 2013. Congratulations to Ron Gorham for receiving his PhD degree. Ron continues as Postdoctoral Fellow in BioMoDeL.
July 2013. Prof. Morikis gave an invited talk at the 7th International Discussion Meeting on Relaxations in Complex Systems (7IDMRCS): New Results, Directions and Opportunities, 7/21-26/2013, in Barcelona, Spain. He also chaired a Physics and Chemistry of Biosystems session. Link.
New publication. Gorham Jr RD, Forest DL, Tamamis P, López de Victoria A, Mazák-Kraszni M, KieslichCA, Banna CD, Bellows-Peterson ML, Larive CK, Floudas CA, Archontis G, Johnson LV, Morikis D (2013) Novel Compstatin Family Peptides Prevent Complement-associated Deposit Formation in Human Retinal Pigmented Epithelial Cell Cultures, Experimental Eye Research 116:96-108.
June 2013. Congratulations to graduate student Zied Gaieb for passing his oral qualifying exam.
June 2013. Welcome to high school summer student Adam Lawrence.
New publication. Kieslich CA, Shin D, López de Victoria A, González-Rivera G, Morikis D (2013) A preddictive model for HIV-1 coreceptor selection, AIDS Research & Human Retroviruses 29:1386-1394.
June 2013. Graduate students Ron Gorham and Zied Gaieb, and Dr. Morikis attended the 14th Annual University of California Systemwide Bioengineering Research Conference at UCSD, June 19-21. Ron and Zied presented posters of their research.
June 2013. Congratulation to lab member Wilson Rodriguez for receiving his BS in Bioengineering. Wilson will be joining LabAnswer in Orlando FL Wilson has been an undergraduate researcher at BioMoDeL for over two years.
June 2013. Congratulations to lab member Carl Chen for receiving his MS degree in Bioengineering.
June 2013. Congratulations to Senior Design Team members Michael Andraos, Jennalisa Crohn, Michael Hadoung, Ratna Pottam, and Gordon Zheng (Team Charizar) for completing their project entitled "Biorobotic Hand".
June 2013. Congratulations to Ilya Lederman for being one of 12 UCR undergraduate students to receive a Chancellor's Research Fellowship for 2012-2013.
April 2013, Professor Morikis received the 2013 Carolyn K. McGillvray Memorial Award for Macular Degeneration Research by the BrightFocus Foundation.
April 2013, A research grant was awarded to Dr. Morikis by the BrightFocus Foundation for research on drug discovery for macular disease. This is a collaborative project with Drs. Monte Radeke and Linc Johnson of University of California, Santa Barbara.
February 2013, A cancer-related research project led by Dr. Morikis and Dr. WenYong Chen of the Beckman Institute of the City of Hope is funded by CUBRI (City of Hope - UCR Biomedical Research Initiative).
February 2013, Welcome to Ilya Lederman, new undergraduate lab member.
February 2013, Welcome to Michael Haduong, new undergraduate lab member.
January 2013. Welcome to Nehemiah Zewde, new undergraduate lab member.
2012
New publication. Kieslich CA, Morikis D (2012) The two sides of complement C3d: evolution of electrostatics in a link between innate and adaptive immunity, PLoS Computational Biology 8:e1002840. Link. Suppl.
New publication. López de Victoria A, Tamamis P, Kieslich CA, Morikis D (2012) Insights into the Structure, Correlated Motions, and Electrostatic Properties of Two HIV-1 gp120 V3 Loops, PLOS ONE 7:e49925. Link. Suppl.
November 2012. Undergraduate lab member Wilson Rodriguez will serve a member of the Student Editorial Board for volume VII of the UCR Undergr