News
2024
Reyhaneh Nouri was a guest speaker in BIOL-3231L (Invertebrate Zoology)
Dr. Aline Costa invited Reyhaneh Nouri to talk about her Ph.D. research in class Reyhaneh Nouri giving her presentation to undergrads Reyhaneh Nouri was a guest speaker in UNC Charlotte’s undergraduate class BIOL-3231L (Invertebrate Zoology) on April 4, 2024. She gave a talk on “How can we reversibly control collagen pliability? An investigation of mutable collagenous tissue in the brittle star Ophiomastix wendtii” (originally presented at the presented at UNC Charlotte’s 9th An...
UNC Charlotte STEAM Expo and Charlotte Kids Fest 2024
UNC Charlotte STEAM Expo and Charlotte Kids Fest 2024 Join us! The UNC Charlotte STEAM Expo and Charlotte Kids Fest return to Charlotte Sunday, April 14, from 11 a.m. to 4 p.m. These two free events offer unique experiences for children, encouraging them to engage in fun, creative, interactive and informative activities and live performances. Help the Scientist! Untangle the Tree Mystery to Save The Day The Phyloinformatics Lab will be there with an activity named “Help the Sc...
Ramadan Kareem Iftar Party on April 8
Ramadan Kareem: Iftar Party Join us in SAC Salons on April 8 at 7 PM. The CCI’s Equity and Inclusion committee together with 49er student organizations invites the 49er community for a cultural event of sharing and support during the National Arab American Heritage Month. Where: SAC Salons (on the 3rd floor). When: Monday, April 8, 2024, at 7:00 PM (ET). Who: Everyone is invited, including those who are not Arab American and those who are not celebrating Ramadan How Mu...
Open gig position Where? The Phyloinformatics lab is led by Dr. Denis Jacob Machado, an assistant professor of bioinformatics. Dr. Machado is a faculty member of UNC Charlotte’s Department of Bioinformatics and part of our Computational Intelligence to Predict Health and Environmental Risks (CIPHER)center. CIPHER is a university-wide research center that focuses on genomics and computing technologies as applied to microbiology, biological and human diversity, and health. What? The phylo...
Girls Who Code's Axe Hacks event
Axe Hacks: A Girls Who Code event Denis Jacob Machado and Rick White at Axe Hacks 2024 It was a pleasure being a host at Axe Hacks. Girls Who Code at Charlotte hosted the 2024 Axe Hacks Hackathon on Saturday, March 16, 2024. Axe Hacks aimed (and succeeded) to increase hackathon participation, specifically among women and beginner-level students. Their mission is to uplift and maintain a strong community for women in computer science, as well as develop technical and professiona...
Rose Larson talks about technical advisory on patents
Rose Larson and the patent world Rose Larson (rose [at] freshwatercounsel [dot] com) is the Director of Patent Professionals at Freshwater Counsel, a legal recruiting firm. She will explain to our grad students what it means to be a technical advisor and the prospects of a career advising on patent matters. we will talk to her on this hybrid event. You can join us in CIPHER’s seminar room, BINF 402, or via Zoom. Details for the Zoom meeting: You are invited to a Zoom meeting on Friday, ...
New preprint available Our new preprint on “Predicting Antibody and ACE2 Affinity for SARS-CoV-2 BA.2.86 and JN.1 with In Silico Protein Modeling and Docking” is available on bioRxiv. The emergence of SARS-CoV-2 lineages derived from Omicron, including BA.2.86 (nicknamed “Pirola”) and its relative, JN.1, has raised concerns about their potential impact on public and personal health due to numerous novel mutations. Despite this, predicting their implications based solely on mutation counts p...
2023
Denis is Green Dot Trainer of the Month this December 2023
Green Dot Trainer of the Month The Green Dot’s newsletter (December 2023, Vol. 3) announced that Dr. Denis Jacob Machado is the Green Dot Trainer of the Month. Below, we past a copy of that announcement. Copy of the original announcement “Denis is an assistant professor inthe Department of Bioinformaticsand Genomics. He has beenworking at UNC Charlotte’sCIPHER center since August2022, but has been a part of thecommunity in various roles since2016. As a faculty member, Deniscreated the Phyl...
New Preprint on in silico analyses of the SAR-CoV-2 Pirola variant
New Preprint: Predicting Antibody and ACE2 Affinity for SARS-CoV-2 BA.2.86 with In Silico Protein Modeling and Docking The emergence of the Omicron sublineage of SARS-CoV-2 virus BA.2.86 (nicknamed “Pirola”) has raised concerns about its potential impact on public health and personal health as it has many mutations with respect to previous variants. We conducted an in silico analysis of neutralizing antibody binding to BA.2.86. Selected antibodies came from patients who were vaccinated and/...
The Phyloinformatics Lab will be in ICICPE 2023
The Phyloinformatics Lab at the 7th International Conference on Interdisciplinary Research on Computer Science, Psychology, and Education (ICICPE’ 2023) Undergraduate students Hannah Zeru (UNC Charlotte) and Cameron Jones (Eastern Michigan University) are presenting their summer 2023 reserach virtually at the International Conference on Interdisciplinary Research on Computer Science, Psychology, and Education (ICICPE’ 2023), to be hosted in Bali, Indonesia, December 27–29, 2023. Their work ...
9th Annual Biological Sciences Research Symposium
The Phyloinformatics Lab at the 9th Annual Biological Sciences Research Symposium Our representatives at the symposium. From the left: Omkar Marne, Denis Jacob Machado, Anastasiia Duchenko, Reyhaneh Nouri, and Philippe Vieira Alves. On November 17, 2023, our Ph.D. students, Reyhaneh Nouri and Omkar Marne, delivered oral presentation of their work at UNC Charlotte’s 9th Annual Biological Sciences Research Symposium. These are the presentation details and the links to download the...
A large-scale virtual screen of compounds database against viral drug targets Dr. Denis Jacob Machado received a pilot award for the project “A large-scale virtual screen of compounds database against viral drug targets” (proposal number: IPF2023-0761, BANNER fund number: 570500, period: 01-May-2023 to 30-Apr-2025, total costs: $462,000 USD). This is a mentored award submitted in response to a request from the parent award “Antiviral Drug Discovery (AViDD) Centers for Pathogens of Pandemic ...
Phylogenetics in the one health context
Phylogenetics in the one health context Stydying One Health, by DALL-E 2 Our new research topic is out on Frontiers in Microbiology, and it is all about phylogenetics and its different applications in One Health. “Omics” technologies (e.g., genomics, transcriptomics, proteomics, and metabolomics) have revolutionized human health. For example, during the COVID-19 pandemic, genomic epidemiology consolidated as an essential tool to study emerging infectious diseases (EIDs) in huma...
DALE at the Bioinformatics building DALE in Bioinformaticsm The Phyloinformatics Lab worked together with CCI’s Diversity and Inclusion Committee to organize events during Hispanic Heritage Month. One of the events involved inviting a student group called DALE to have one of their events in our spaces. Any individuals, regardless of their background or skill level in dance, were welcomed to join us. The primary focus of this DALE event revolve around Samba. We were the Bioinfor...
We’re Building STEAM In Kannapolis Join us for a variety of fun family events on October 7, as we celebrate (STEAM) - Science, Technology, Engineering, Arts and Math. The Building STEAM Festival will be held from 10 a.m. to 2 p.m. at the North Carolina Research Campus Horseshoe (401 Laureate Way, Kannapolis). The event is free and will include activities for children, teenagers, and parents – both indoors and outdoors on the campus. Bring your lab coats and get your hands dirty with hands-...
New paper on echinoderm radial glia
Echinoderm radial glia in adult cell renewal, indeterminate growth, and regeneration Anatomical organization of the central nervous system in echinoderms (see Mashanov et al. 2023; Figure 2). A new review paper published in the journal Frontiers in Neural Circuits sheds light on the role of radial glia in adult cell renewal, indeterminate growth, and regeneration in echinoderms. Radial glia are a type of glial cell that plays a critical role in the development of the nervous sy...
Dr. Cathy Moore at the Larry Mays Seminars
Dr. Cathy Moore’s special presentation at the Larry Mays Seminars in Bioinformatics At 2:30 p.m. today, Dr. Cathy Moore (Biosafety Officer at UNC Charlotte’s Division of Research) will give a special presentation at the Larry Mays Seminars in Bioinformatics. Dr. Moore will provide Biosafety Training for Graduate Students. Dr. Moore is the University contact for: Handling and working with biological agents on campus Institutional Biosafety Committee protocol review and approval process...
The Hispanic Potluck 2023 in CIPHER’s seminar room Hispanic potluck This event was be a potluck to honor the Hispanic Heritage Month (September 15 to October 15, 2023) organized by SACNAS (Society for Advancement of Chicanos/Hispanics & Native Americans in Science) in collaboration with CCI’s Diversity and Equity Committee. We encouraged students to bring their favorite national dish for everyone to share and have opportunities for socialization and community. We were very ...
Ifest 2023 and the Brazilian Trivia
The Brazilian stand in the Ifest 2023 Brazilian Trivia We are thrilled to share the fantastic news of an electrifying event that took place on September 23, 2023! The Phyloinformatics Lab proudly sponsored the vibrant Brazilian table at UNC Charlotte’s 2023 Ifest, and what an adventure it was! We extended an enthusiastic invitation to all to join us in an exhilarating trivia game, testing their knowledge of the beautiful land of Brazil. Laughter and learning echoed through the ...
Susana Cisneros is the Higher Education Teacher of the Year
Excelente Awards Congratulations Susana Cisneros! The Excelent Awards is a wonderful event to recognize the outstanding achievements of Latino leaders and their supporters. Excelente Awards will be presented to Latin American business and service people. Also, one special award recognizes a non-Latin person who has strongly supported the Latino community and another special award will recognize outstanding Latino students. Teacher of the Year This award recognizes an exceptio...
Hispanic Heritage Month Olá! Denis here. I am part of CCI’s committee of diversity and inclusion. I am also a member of the Hispanic/Latinx Staff/Faculty Caucus. In those capacities, it is my pleasure to announce: the Hispanic Heritage Month has started! What is the Hispanic Heritage Month The Hispanic Heritage Month is a month-long celebration of the history, culture, and contributions of Hispanic and Latine people. It is observed annually from September 15 to October 15. The dates were c...
Larry Mays Seminars in Bioinformatics
Larry Mays Seminars in Bioinformatics: Fall 2023 UNC Charlotte’s Department of Bioinformatics and Genomics (BiG) hosts a weekly seminar series named after Dr. Lawrence Mays (Emeritus Faculty). The Larry Mays Seminars in Bioinformatics covers research within Bioinformatics, Genomics, and Computational Biology. Seminars are free and open to the public. Seminars take place on Fridays at 2:30- 3:30 PM. All seminars are hosted from the Bioinformatics building, room 105. Please contact Dr. Denis J...
New Events with Dr. Kary Ocaña
The Phyloinformatics Lab is receiving the visit of Dr. Kary Ocaña from July 9 to July 25, 2023. Dr. Ocaña is a researcher at the Brazilian National Laboratory of Scientific Computing (LNCC), which is a part of Brazilian The Ministry of Science, Technology and Innovation (MCTI). Her main interests are phylogenomics, high-performance computing, data analytics in bioinformatics, and machine learning. We want to make the most of Dr. Ocaña’s time with us. To helpo with that, we are putting togeth...
Postdoc wanted in CIPHER (CLOSED)
Postdoctoral Fellow for One Health Research in UNC Charlotte’s CIPHER center (CLOSED) UPDATE (6/16/2023): WE ARE NO LONGER ACCEPTING APPLICATIONS FOR THIS POSITION. General Information Position Number: POST40 (all post-doc positions have the same number) Working Title: Postdoctoral Fellow for One Health Research in UNC Charlotte’s CIPHER center College: CCI Supervisor: Professor Dr. Daniel A. Janies Work Location: CIPHER center (Dept. of Bioinformatics, 4th floor) Vacancy Open...
This position was closed. Postdoctoral Fellow for ZVBD Lab (position closed) General Information Position Number: POST40 (all postdoc positions have the same number) Working Title: Postdoctoral Fellow for Zoonotic and Vector-Borne Diseases (ZVBD) Lab; College of Health and Human Services College: College of Health and Human Services (CHHS) Supervisor: Assistant Professor Dr. Rafael Felipe da Costa Vieira Work Location: CIPHER center Vacancy Open To: All Candidates Employment...
All of our grad students got summer scholarship awards
Congratulations Congratulations to Reyhaneh Nouri and Omkar Marne. They both wrote summer research projects and will received a summer fellowship to support master’s or early-stage doctoral students’ research, paid in June, $5,000 USD per student. Nouri will work on “identifying differentially expressed genes associated with mutable collagenous tissue (MCT) in the brittle star Ophiomastix wendtii.” Marne will work on a “phylogenomics and machine learning framework for discriminating SARS-Co...
New temporary part-time work position (position closed)
ATTENTION: THIS POSITION HAS BEEN FILLED AND THE JOB POST HAS BEEN CLOSED. We are hiring a Phylogenetics and Artificial Intelligence Specialist General Information Position Number: STMP15 Working Title: Phylogenetics and Artificial Intelligence Specialist Work Unit: CIPHER Vacancy: Open To All Candidates Position Designation: Non-Student Temporary Employment Type: Temporary - Part-time Hours per week: 20 Work Schedule: M-F 4hrs per day Pay Rate: $20 to $25 per hour Min...
A new HPC training module for UNC Charlotte's URC
I have been talking to the people from UNC Charlotte’s Office of One IT and students from our graduate program in bioinformatics about potentially creating a training module to help users of our University Research Cluster (URC; see https://oneit.charlotte.edu/urc/research-clusters). We are just brainstorming at this stage, and your opinion could really help us while we are trying to think about how this could work. Please use the “CONTRIBUTE” button (below) to submit ideas of topics, proble...
SMART AND SECURE FUTURE COMPUTING General Information What: Summer REU in Computing When: from May 30 to August 04, 2023 Priority date: March 20 (applications will be accepeted while positions last) Website: (reu.charlotte.edu)[https://reu.charlotte.edu/] Funding: National Science Foundation (NSF) Details The CCI’s REU site (funded by NSF) will return to an in-person program this summer. Join the Phyloinformatics Lab or other labs in the UNC Charlotte’s campus for a 9-week res...
Our Work is a Top Cited Article Cladistics has announced that our article is one of the most cited in 2021-22. The paper title is “Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2,” and the abstract is below. Abstract The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SAR...
Tucana is our New High-Memory Computer Node
Tucana is now online Tucana is a new large memory machine acquired by the Phyloinformatics Lab and added to UNC Charlotte’s University Research Cluster (URC). Tucana has 64 cores (2 x AMD EPYC 7513 2.6GHz, 32C/64T, 128M Cache, 200W, DDR4-3200), 4,096GB RAM (32 x 128GB LRDIMM, 3200MT/s, Quad Rank 480GB SSD SATA Mix Use 6Gbps 512 2.5in Hot-plug AG Drive,3.5in HYB CARR, 3 DWPD), a 480GB SSD (SATA Mix Use 6Gbps 512 2.5in Hot-plug AG Drive,3.5in HYB CARR, 3 DWPDand), and a CONNECTX 6 VPI ADAPT C...
2022
Postdoc wanted (position closed)
ATTENTION: THIS POSITION HAS BEEN FILLED AND THE JOB POST HAS BEEN CLOSED. We are hiring a Postdoctoral Fellow in Bioinformatics and Genomics General Information Position Number: POST40 (all postdoc positions have the same number) Working Title: Postdoctoral Fellow: Bioinformatics and Genomics College: College of Computing and Informatics (CCI) Department: Department of Bioinformatics and Genomics (BiG) Work Location: CCI, BiG, CIPHER center Vacancy Open To: All Candidates E...
AI Software Nearly Predicted Omicron’s Tricky Structure Our research on the protein structure of the SARS-CoV-2 Omicron spike protein and how it is predicted to interact with neutralizing antibodies was mentioned written by Tom Simonite and published in WIRED. The peer-reviewed publication was published by Frontiers in Virology on February 7, 2022. Read original article Read the paper
2021
Our research was featured in the cover of Cladistics On September 27, 2022, the cover of Volume 37, Issue 5 of Cladistics was designed by Dr. Denis Jacob Machado and inspired on a paper publised in that same issue. The paper entitled “Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2” was co-authored by Rachel Scott, Sayal Guirales, and Daniel A. Janies. Check the co...
Listen to our interview with Finding Genious
Viral Genome Annotation and Comparative Genomics Through Evolutionary Processes Richard Jacobs interviewed Dr. Denis Jacob Machado for the Finding Genius podcast. See the full description of that episode and its link below. Episode description How can we view evolution through comparative genomics? By understanding how viruses and various organisms have evolved, new views of world issues can be gained. Listen up to learn: How long have specific viruses been known to us Why complex r...
Our research in the largest Brazilian newspaper
Largest evolutionary study of coronavirus confirms origin of Sars-CoV-2 from bats to humans Ana Botallo interviewed Dr. Denis Jacob Machado for Folha de São Paulo, the largest Brazilian newspaper. This special scientific article discusses Dr. Jacob Machado’s phylogenetic analysis of all coronaviruses and lessons learned from it. Click here for a digital version of this article, written in Portuguse (last accessed: Aug. 9, 2021). Read original article online