Molecular scaffolds are special and useful guides to discovery, poster (36x54"). Presented at ACS National Meeting SciMix in Indianapolis, Sep 9, 2013.
The Who in Collections: Revealing the Network of Collectors and Determiners o...David Shorthouse
Workshop Invite:
We invite you to bring your extensive knowledge of bats and historic and present-day bat collectors to a special two-hour workshop designed to enable building a master list of the world’s bat collectors.
We will explore the digitally accessible bat specimen records in the Families Hipposideridae and Rhinolophidae and actively link these to the people who collected and/or identified them. This will be a state of the art, new approach in which you will also receive brief training on the use of ORCID, Wikidata, and a new online resource called Bionomia. No technical skills are required, just your unique, insider knowledge of chiropterologists and bat collections across the world.
You will be helping to create links in the biodiversity knowledge network that will aid in the uncovering of what is known, but currently hidden, and enable future digitization efforts. Through your work and Bionomia, you may also discover the research in which your specimens may have played a part, and just where your specimens are now and who else has looked at them. You’ll be participating in a pilot run for this new kind of community data enhancement campaign helping us discover the potential for doing this in the future for other taxa (e.g., Revealing the Who in Bird Collecting).
GigaScience Editor-in-Chief Laurie Goodman's talk at the International Conference on Genomics pre-conference press-session on the release of new unpublished datasets, and a new look beta version of their database: GigaDB.org
The Who in Collections: Revealing the Network of Collectors and Determiners o...David Shorthouse
Workshop Invite:
We invite you to bring your extensive knowledge of bats and historic and present-day bat collectors to a special two-hour workshop designed to enable building a master list of the world’s bat collectors.
We will explore the digitally accessible bat specimen records in the Families Hipposideridae and Rhinolophidae and actively link these to the people who collected and/or identified them. This will be a state of the art, new approach in which you will also receive brief training on the use of ORCID, Wikidata, and a new online resource called Bionomia. No technical skills are required, just your unique, insider knowledge of chiropterologists and bat collections across the world.
You will be helping to create links in the biodiversity knowledge network that will aid in the uncovering of what is known, but currently hidden, and enable future digitization efforts. Through your work and Bionomia, you may also discover the research in which your specimens may have played a part, and just where your specimens are now and who else has looked at them. You’ll be participating in a pilot run for this new kind of community data enhancement campaign helping us discover the potential for doing this in the future for other taxa (e.g., Revealing the Who in Bird Collecting).
GigaScience Editor-in-Chief Laurie Goodman's talk at the International Conference on Genomics pre-conference press-session on the release of new unpublished datasets, and a new look beta version of their database: GigaDB.org
In the era of computers life sciences databases are still understated. Here is my presentation on biological databases. Complete classification of different databases.
For more presentations and work come and visit
https://www.linkedin.com/in/shradheya-r-r-gupta-54492984/
Using Public Access Clinical Databases to Interpret NGS VariantsGolden Helix Inc
In this webcast on February 19th, Gabe Rudy, Vice President of Product Development, will showcase publicly available databases and resources available for interpreting rare and novel mutations in the context of his own personal exome obtained through a limited 23andMe pilot in 2012.
The last couple years have seen many changes in well-established resources such as OMIM and dbSNP, while motivating new efforts such as ClinVar and PhenoDB to bring NGS interpretation to clinical grade through a global data sharing effort.
In this webcast, Gabe will cover:
The changing landscape of public annotations: Then, Now, and Soon.
Will the new human reference (GRCh38) released in December be a game changer?
Specific examples of improvements in annotation and algorithms that result in more accurate analysis of his own exome.
The utility and progress of NGS to different clinical applications in terms of public resources: carrier screening, hereditary cancer risk, pharmacogenomics, oncology care, and genetic disorder diagnosis.
Sharing of new clinical data: How both variation and phenotype level data is currently being shared and what will be the way forward to match rare and undiagnosed cases at a global scale.
Scott Edmunds talk in the "Policies and Standards for Reproducible Research" session on Revolutionizing Data Dissemination: GigaScience, at the Genomic Standards Consortium meeting at Shenzhen. 6th March 2012
Published on Feb 07, 2016 by PMR
Use of ContentMine tools on the Open Access subset of EuropePubMedCentral to discover new knowledge about the Zika virus. Includes clips of the software in action
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
Various lists of “jobs, likely to be replaced by robots” usually place scientists into “later or never” section. But is this profession really safe?
We'll try to answer this question by looking at some "probability to be replaced” criteria, current AI development challenges, and their solutions, including examples of what is happening right now.
Data analysis & integration challenges in genomicsmikaelhuss
Presentation given at the Genomics Today and Tomorrow event in Uppsala, Sweden, 19 March 2015. (http://connectuppsala.se/events/genomics-today-and-tomorrow/) Topics include APIs, "querying by data set", machine learning.
In the era of computers life sciences databases are still understated. Here is my presentation on biological databases. Complete classification of different databases.
For more presentations and work come and visit
https://www.linkedin.com/in/shradheya-r-r-gupta-54492984/
Using Public Access Clinical Databases to Interpret NGS VariantsGolden Helix Inc
In this webcast on February 19th, Gabe Rudy, Vice President of Product Development, will showcase publicly available databases and resources available for interpreting rare and novel mutations in the context of his own personal exome obtained through a limited 23andMe pilot in 2012.
The last couple years have seen many changes in well-established resources such as OMIM and dbSNP, while motivating new efforts such as ClinVar and PhenoDB to bring NGS interpretation to clinical grade through a global data sharing effort.
In this webcast, Gabe will cover:
The changing landscape of public annotations: Then, Now, and Soon.
Will the new human reference (GRCh38) released in December be a game changer?
Specific examples of improvements in annotation and algorithms that result in more accurate analysis of his own exome.
The utility and progress of NGS to different clinical applications in terms of public resources: carrier screening, hereditary cancer risk, pharmacogenomics, oncology care, and genetic disorder diagnosis.
Sharing of new clinical data: How both variation and phenotype level data is currently being shared and what will be the way forward to match rare and undiagnosed cases at a global scale.
Scott Edmunds talk in the "Policies and Standards for Reproducible Research" session on Revolutionizing Data Dissemination: GigaScience, at the Genomic Standards Consortium meeting at Shenzhen. 6th March 2012
Published on Feb 07, 2016 by PMR
Use of ContentMine tools on the Open Access subset of EuropePubMedCentral to discover new knowledge about the Zika virus. Includes clips of the software in action
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
Various lists of “jobs, likely to be replaced by robots” usually place scientists into “later or never” section. But is this profession really safe?
We'll try to answer this question by looking at some "probability to be replaced” criteria, current AI development challenges, and their solutions, including examples of what is happening right now.
Data analysis & integration challenges in genomicsmikaelhuss
Presentation given at the Genomics Today and Tomorrow event in Uppsala, Sweden, 19 March 2015. (http://connectuppsala.se/events/genomics-today-and-tomorrow/) Topics include APIs, "querying by data set", machine learning.
Understanding Information Processing in Human Brain by Interpreting Machine L...Ilya Kuzovkin
The thesis explores the role machine learning methods play in creating intuitive computational models of neural processing. Combined with interpretability techniques, machine learning could replace human modeler and shift the focus of human effort to extracting the knowledge from the ready-made models and articulating that knowledge into intuitive descriptions of reality. This perspective makes the case in favor of the larger role that exploratory and data-driven approach to computational neuroscience could play while coexisting alongside the traditional hypothesis-driven approach.
We exemplify the proposed approach in the context of the knowledge representation taxonomy with three research projects that employ interpretability techniques on top of machine learning methods at three different levels of neural organization. The first study (Chapter 3) explores feature importance analysis of a random forest decoder trained on intracerebral recordings from 100 human subjects to identify spectrotemporal signatures that characterize local neural activity during the task of visual categorization. The second study (Chapter 4) employs representation similarity analysis to compare the neural responses of the areas along the ventral stream with the activations of the layers of a deep convolutional neural network. The third study (Chapter 5) proposes a method that allows test subjects to visually explore the state representation of their neural signal in real time. This is achieved by using a topology-preserving dimensionality reduction technique that allows to transform the neural data from the multidimensional representation used by the computer into a two-dimensional representation a human can grasp.
The approach, the taxonomy, and the examples, present a strong case for the applicability of machine learning methods to automatic knowledge discovery in neuroscience.
91918, 4(12 PMThread DB #7 – BIO-101-1-Fall-2018-CRN-20168.docxsleeperharwell
9/19/18, 4(12 PMThread: DB #7 – BIO-101-1-Fall-2018-CRN-20168
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Anonymous
DB #7
1 month ago
ReplyReply
Select and summarize two of the short articles linked under
“Broad News” on the CRISPR Research News page.
(https://www.broadinstitute.org/project-spotlight/crispr-news-
and-press-releases)
RE: DB #7
1 day agoSara Smith
The first article I chose to read was titled, "Reading the rule of
gene regulation with CRISPR". This article started off by
discussing the rules that go into genome protien-coding
components. For instance, we know where it begins, it ends, and
the pieces of it's geography. However, the part where that dictates
which genes the cell reads, we do not know this much about. This
is where CRISPR could come in and help. CRISPR in correlation
to gene editing, could lend a helping hand in grasping these
unknown rules. In two different approaches, using CRISPR to
locate these unkown rules, led to finding and locating several
genetic regulators. From locating these genetic regulators lend,
??
My Institution My Courses My ContentHamad Alzahid
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Security Concerns of Future Technology Arriving Today - Gregory CarpenterEC-Council
Because of the advancements in prosthetics after the last decade of wars, technology has made advancements beyond those of security. We are using yesterdays security with tomorrow’s technology, and it is not working. New technology allows for in vivo bioanorobotic technology to assist in reestablishing neurological functional continuity, minimizing peripheral neuropathy or establishing the neuro-human-machine interface after an avulsive trauma. The inherent vulnerability within the nano technology allows for exploitation and remote access or even real-time control of a prosthetic or even a persons neurological functioning. Neurostatic controls in these devices are also vulnerable causing malfunctions or unwanted actions out of the control of the user. Nanotechnology can also come equipped with processors, storage and the ability to communicate wirelessly. Some have embedded 3D printers producing segments of DNA or axons to be used as surrogates for malfunctioning or missing ones, can we allow these networks to go unregulated and open in a situation where security must never be compromised?
TIGA: Target Illumination GWAS AnalyticsJeremy Yang
Aggregating and assessing experimental evidence for interpretable, explainable, accountable gene-trait associations. Presentation for NIH IDG Annual Meeting, Feb 9-11, 2021.
DrugCentralDb and BioClients: Dockerized PostgreSql with Python API-tizerJeremy Yang
DrugCentralDb, a biomedical research database developed at UNM and widely used by drug discovery scientists, has been Dockerized and deployed via AWS EC2. Additionally, we have developed a Python package BioClients, with module 'drugcentral' API for DrugCentral. Source code and Docker image are available via GitHub and DockerHub, respectively. These tools are new and in testing, with full release planned for later in 2020.
TIN-X v2: modernized architecture with REST APIJeremy Yang
TIN-X v2: modernized architecture with REST API for sustainability and interoperability. Presented at the IDG Face2Face meeting in Arlington, VA, Feb 26-27, 2019.
Ex-files: Sex-Specific Gene Expression Profiles ExplorerJeremy Yang
Poster prepared for NIH Data Commons Pilot Project Consortium (DCPPC) scientific use case, developed in 2018, with GTEx gene expression data and deployed as online application.
Illuminating the Druggable Genome with Knowledge Engineering and Machine Lear...Jeremy Yang
Talk given at 14th Annual New Mexico BioInformatics, Science and Technology (NMBIST) Symposium, entitled Integrative Omics, on March 14-15, 2019. Most slides c/o IDG KMC PI Tudor Oprea, MD, PhD.
Badapple: promiscuity patterns from noisy evidence (poster)Jeremy Yang
Badapple: promiscuity patterns from noisy evidence. Bioassay data analysis using scaffold associations. Presented at the UNM Staff Research Expo, Jan 27, 2017. Adapted from "Badapple: promiscuity patterns from noisy evidence", Yang JJ, Ursu O, Lipinski CA, Sklar LA, Oprea TI Bologa CG, J. Cheminfo. 8:29 (2016), DOI: 10.1186/s13321-016-0137-3.
Bibliological data science and drug discoveryJeremy Yang
Presented at the 2016 ACS Fall Meeting in Philadelpha, session "Effectively Harnessing the World's Literature to Inform Rational Compound Design", on 8/21/16.
BioMISS: Language Diversity of ComputingJeremy Yang
Talk given at the UNM BioMedical Informatics Seminar Series, Oct 15, 2015. Because the languages of computing are numerous and diverse, it can be challenging to choose an appropriate language for a given task. Yet data are of little value unless represented by semantic systems of languages with appropriate levels of abstraction. We consider the analogy between object-oriented programming and abstraction in biomedical vocabulary and the Sapir-Whorf Hypothesis (that an individual’s thoughts and actions are determined by the language he or she speaks). As an example, we consider the differences between ICD-10 and disease ontology.
Cyberinfrastructure Day 2010: Applications in BiocomputingJeremy Yang
UNM Cyberinfrastructure Day 2010 presentation: Applications in Biocomputing, biomedical and cheminformatics research computing cyberinfrastructure issues.
Promiscuous patterns and perils in PubChem and the MLSCN
Molecular scaffolds poster
1. Molecular scaffolds are special and useful guides for discovery
Jeremy Yang1,2, Cristian Bologa1,David Wild2, and Tudor Oprea1
1UNM Translational Informatics Division, Dept. of Internal Medicine, Albuquerque, NM
2IU Cheminformatics & Chemogenomics Research Group, School of Informatics & Computing, Bloomington, IN
Some famous scaffolds
beta – lactam
(penicillins,
cephalosporins )
Millions saved,
billions earned
steroid
(testosterone,
hydrocortisone, etc. )
Wonder drugs and
hormones
diazepam
(Valium, flurazepam,
etc. )
“Mother’s little
helper”
What is a scaffold?
"Ring-system", "Ring", "Core", "Framework"
Estradiol
docked into
ER-alpha
(using
OpenEye
Fred and
Vida)
• Clustering, indexing databases.
• Navigation of chemical space.
• Data reduction, visualization.
Scaffold Applications
What can be done with scaffolds?
Scaffold Hunter CARLSBAD
CARLSBAD:
The Power to Explore Biological
Networks via Chemical Patterns
Badapple Promiscuity Plugin
(BioActivity Data Associative Promiscuity Pattern Learning Engine)
Badapple
Promiscuity Plugin
for BARD,
http://bard.nih.gov
Related ACS talk: "The Badapple Promiscuity Plugin for BARD: Evidence-based promiscuity scores", in CINF
session "Integrative Chemogenomics Knowledge Mining Using NIH Open Access Resources", Mon, Sept. 9,
10:45am, Rm. 140.
Scaffold analysis algorithm
• Remove non-linking chains
• Keep multiply-bonded atoms
• Special case: ignore solo-benzene.
quinine
Bemis-Murcko
framework
scaffolds
Scaffolds & drug-scaffolds, the privileged few
explaining a lot of activity...
Dataset:
BARD,
MLSMR,
MLP HTS
Totals: compounds:
373,802 ; scaffolds:
146,024 ; assays: 528
; wells/results:
30,612,714;
drugs: 283;
drugscafs: 1958
“activity of DB” ~ # active scaffold-instances
Scaffold Hopper
• R-group / SAR analyses.
• Bioactivity prediction.
• Promiscuity prediction.
Privileged Scaffolds Concept
Nature favors a few privileged scaffolds, a.k.a. "privileged structures", for multiple receptors.
"What is clear is that certain “privileged structures” are capable of providing useful ligands for more than one receptor and that
judicious modification of such structures could be a viable alternative in the search for new receptor agonists and antagonists."[1]
Problems with scaffolds
• Definition of "scaffold" not consistent & rigorous
among chemists & cheminformaticians.
Testosterone
Estradiol
Danazol
Cyproterone
acetate
"We think in generalities, but we live in detail." - Alfred North Whitehead
"The only rules that really matter are these: what a man can do and what a man can't do." - Jack Sparrow
Scaffold software: UNM-Biocomp-HScaf
(Google Code project)
http://code.google.com/p/unm-biocomp-hscaf/
http://en.wikipedia.org/wiki/Steroids
Steroidogenesis
[#8]~[#6;R1]~1~[#6;R1]~[#6;R1]~[#6;R2]~2~[#6;R2]~1
~[#6;R2]~[#6;R1]~[#6;R2]~1~[#6;R2]~2~[#6;R1]~[#6;R
1]~[#6;R2]~2~[#6;R1]~[#6;R1](~[#8])~[#6;R1]~[#6;R1]
~[#6;R2]~1~2
Steroid pattern
definition via
SMARTS
Problems solved by cheminformatics
News: antibiotic scaffold:
Anthracimycin
Acknowledgements
• Cristian Bologa, UNM
• Tudor Oprea, UNM
• Oleg Ursu, UNM
• David Wild, IU
• Gary Wiggins, IU
References:
1. "Methods for drug discovery: development of potent, selective,
orally effective cholecystokinin antagonists", Evans et al., J. Med.
Chem., 1988, 31, 2235.
2. “The properties of known drugs. 1. Molecular frameworks”, G Bemis
& M Murcko, J Med Chem, 39, 2887-2893, 1996.
3. “Drug rings database with web interface. A tool for identifying
alternative chemical rings in lead discovery programs”, X Lewell, A
Jones, C Bruce, G Harper, M Jones, I McLay, J Bradshaw, J Med Chem,
46, 3257-3274, 2003.
4. “HierS: hierarchical scaffold clustering using topological chemical
graphs”, S Wilkens, J Janes, A Su, J Med Chem, 48, 182-193, 2005.
5. P Ertl, S Jelfs, J Muhlbacher, A Schuffenhauer, & P Selzer, “Quest for
the Rings”, J Med Chem, 49, 4568-4573, 2006.
6. "Interactive exploration of chemical space with Scaffold Hunter", S
Wetzel, K Klein, S Renner, D Rauh, T Oprea, P Mutzel, H Waldmann,
Nat Chem Bio, 5, 2009, 581-583.
7. Scaffold Hopper, NCATS/NCGC, http://tripod.nih.gov,
http://tripod.nih.gov/files/ACS_apr8_2013.pdf.
8. "The CARLSBAD Database: A Confederated Database of Chemical
Bioactivities", S Mathias, J Hines-Kay, J Yang, G Zahoransky-Kohalmi,
C Bologa, O Ursu & T Oprea, Database, 2013, bat044.
9. "Anthracimycin, a Potent Anthrax Antibiotic from a Marine-Derived
Actinomycete", K Jang et al., Ang Chemie, 52 (30), 2013, 7822–7824.
More scaffold charms
• Patents, Markush, $$$.
• Lead discovery ~ scaffold discovery.
• Organic chemists like scaffolds.
• Scaffolds can be "privileged".
Happy Explorations!
Scaffolds are special
because: 3D shape