Lyman BioPharma Consulting LLC

Advice and Resources for the Biotech Industry

Advice and Resources for the Biotech Industry

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LInks to Additional Biotechnology and Related Resources

  • Search: Patents, Scientific Literature/Alerts, Research Projects

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    Quertle - This is a very useful search engine that combines MEDLINE/Pubmed, full text documents from BioMed Central, and News. Instructions for using Quertle and how it differs from PubMed can be found here.
    goPubMed - Another PubMed alternative, this one features semantic search technology that make your results more useful.
    Patent Storm - Offers full text US patents and patent applications form the US Patent Office for free.
    EnGrant Scientific - Searchable database of research projects and funding, with analytics tools and it’s own search engine.

    These links are focused on finding papers via search and/or alerts:
    Google Scholar Alerts - Set queries and have notification of newly published papers emailed to you.
    JournalTOCS - Tables of contents from some 23,436 journals produced by 2155 publishers.
    Mendeley Suggest - A part of Mendeley that allows you to search for papers within the program.
    Nowomics - A personalized newsfeed of publications.
    PubChase - One more way to find papers of interest.
    PubCrawler - Another alerting service that trolls through PubMed and GenBank databases.
    PubMed Alerts - Search for papers through your NCBI account.
    Read by QxMD - Service that is specifically aimed at finding papers for those in clinical practice i.e. doctors.
    ScienceScape - Yet another way to organize your research and find new papers.
  • Trade Associations

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    AdvaMed - Trade group for the medical device industry/medical technology industry.
    Alliance for Regenerative Medicine - This is the lobbying group for stem cell (regenerative medicine) proponents, consisting of biotech, patient, and academic organizations.
    Alliance for Safe Biologic Medicines - Lobbying group for producing safe biosimilar drugs that will compete with branded biologics
    ACRO - Association of Clinical Research Organizations; the lobbying group for CROs.
    BIO - Biotechnology Industry Organization. This is the lobbying organization for the biotechnology industry.
    GphA - Generic Pharmaceutical Association. This is the lobbying group for companies that make generic medicines.
    PhRMA - Pharmaceutical Research and Manufacturers of America. This is the lobbying group for the pharmaceutical industry.
    Pharmaceutical Security Institute - Not-for-profit trade group that assesses, tracks, and fights the flow of counterfeit medicines around the world.
  • Accessing the Biomedical Literature (Science Journals)

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    Pubget - Find and purchase papers available on PubMed and many other journals
    DeepDyve - Rental service for access to scientific research articles
    Get It Now - Full text articles from the Copyright Clearance Center for academic users
    bioRxiv - Preprint sever for biology articles (set up by Cold Spring Harbor Laboratory)
    FreeFullPDF - Provides access to open access scientific journals, theses, posters and patents
    ReadCube Access – 48 hr rental, Cloud article, or pdf of articles from Nature journals
    iPubSci - This is a concept for next-generation access to the scientific literature using an iTunes type of interface. Details and a link to the original article describing the rationale for the proposal can be found here.
    PatientINFORM is a collaboration between medical publishers and health organizations where patients and their families can get access to research articles.
    PatientACCESS is a similar service for providing access to papers published in the Journal of Clinical Oncology for patients and caregivers.
  • Collaborative BioPharma and Academic Initiatives

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    NOTE: the Faster-Cures Project has put together a very comprehensive catalog of research and medical consortia, with over 400 listings. Click here to go to this terrific resource!

    Academic Drug Discovery Consortium - Non-profit created to enhance drug discovery efforts at academic institutions.
    Accelerating Medicines Partnership - Collaborative effort between NIH, 10 pharma companies, and several non-profits to identify and validate targets in three different disease research areas (Alzheimers, diabetes, autoimmune disease).
    Alzheimer’s Disease Neuroimaging Initiative - Designed to find more sensitive and accurate methods to detect Alzheimer’s disease at earlier stages and mark its progress through biomarkers.
    Biomanufacturing Research Program - Focus on making drugs and delivering them globally.
    Biomarkers Consortium - Discover, develop, and qualify biomarkers to support new drug development.
    Cancer Commons - Develop treatments for cancer patients via patients centered Rapid Learning Communities.
    CancerLinq - The American Society of Clinical Oncology is putting together this health information technology (HIT) initiative to achieve higher quality, higher value cancer care with better outcomes for patients.
    Cancer MoonShot 2020 - Launched in 2016, combined effort of biotech, pharma, insurance, and technology companies. Also known as the National Immunotherapy Coalition.
    Centre for Therapeutic Target Validation (CTTV) - Will focus on a wide range of human diseases and will share its data openly in the interests of accelerating drug discovery.
    Clinical Data Interchange Standards Consortium - Mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare.
    Clinical Pharmacogenetics Implementation Consortium (CPIC) - Goal is to address some of the barriers to implementation of pharmacogenetic tests into clinical practice.
    Center for Medical Technology Policy - Making health care more effective and affordable by improving the quality, relevance, and efficiency of clinical research.
    Clinical Trials Transformation Initiative - A public-private partnership to identify and promote practices that will increase the quality and efficiency of clinical trials.
    Coalition Against Major Disease - A public-private-partnership aimed at creating new tools and methods that can be applied to increase the efficiency of the development process of new treatments for Alzheimer’s disease (AD) and Parkinson’s disease (PD).
    DERP (Drug Effectiveness Review Project) - A collaborative project out of the University of Oregon that is conducting systematic, evidence-based reviews of the comparative effectiveness and safety of drugs.
    Drugs for Neglected Disease Initiative - This is a collaborative, non profit drug research and development organization that is developing new treatments for malaria, visceral leishmaniasis, sleeping sickness, and Chagas disease. Works in partnership with industry, academia, and non-government organizations.
    Dundee Kinase Consortium - World's largest collaboration between the academic community and the pharmaceutical industry focused on signal transduction.
    European Federation for Pharmaceutical Sciences (EUFEPS) - Consists of industry, academia, government and other institutions engaged in drug research, development, regulation and policymaking through Europe.
    Exome Aggregation Consortium - Publicly available database of the Broad Institute containing at least 60,000 human exomic sequences.
    Faster Cures - Mission is to accelerate the progress of discovery and development of new medical solutions for deadly and debilitating diseases.
    Global Alliance for Genomics and Health - International coalition to facilitate sharing of genomic info includes over 150 organizations including healthcare providers, research funders, research institutions, disease advocacy organizations, and life science and information technology companies.
    GPCR Consortium - A non-profit entity formed to bring together industry and academic scientists to advance GPCR research for drug development. The goal of the GPCR Consortium is to generate high-resolution pictures of hundreds of medically important GPCRs.
    International Cancer Genome Consortium - Goal is to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe
    Innovative Medicines Initiative - Europe’s largest public-private program supports collaborative research projects; a joint undertaking of the EU and the pharma industry association EFPIA.
    International Mouse Phenotyping Consortium - Systematically make and test phenotypes of "knockout"mice.
    International Serious Adverse Event Consortium - The mission of the iSAEC is to identify DNA-variants useful in understanding the risk of drug-related serious adverse events.
    International Rare Disease Research Consortium - Working to put together a framework to facilitate research activities and develop treatments for rare diseases.
    Institute for Safe Medication Practices - Non-profit that educates consumers and the healthcare community on best practices for safely giving medications.
    National Biomarker Development Alliance (NBDA) - A collaborative network-based, non-profit organization focused on creating standards to develop biomarkers needed for precision (personalized) medicine.
    National Consortium for Data Science - Figuring out ways to expedite the handling and analysis of Big Data.
    National Immunotherapy Coalition - Launched in 2016, combined effort of biotech, pharma, insurance, and technology companies. Also known as the Cancer MoonShot 2020.
    NEW Drug Development ParaDIGmS - Goal is to create new prediction models, new ways to share information about the biology of diseases, and a new inclusiveness involving earlier participation of regulators, health insurers, health care providers and patients.
    Patient-Centered Outcomes Research Institute - Goal is to give patients a better understanding of the prevention, treatment and care options available, and the science that supports those options.
    Patient to Trials Consortium - Novartis, Pfizer and Eli Lilly and Company are partnering in the U.S. to provide a new platform to improve access to information about clinical trials.
    Project Data Sphere - Initiative provides a platform to share, integrate, and analyze comparator arms of historical cancer trial data sets so we can learn from them and accelerate research.
    PROTECT - Pharmaco-epidemiological research on outcomes of therapeutics by a European consortium.
    SAFE-T - Developing improved tools for prediction, detection, and monitoring of drug-induced injuries to the kidney, the liver, and the vascular system, using markers in patients’ blood and/or urine.
    Sage Bionetworks - Creates technology platforms that facilitate collaboration on data, governance platforms that enable data sharing and reuse, and run challenges to solve complex biomedical problems.
    Transcelerate BioPharma - To collaborate across the global research and development community to identify, prioritize, design and implement solutions designed to drive the efficient, effective and high quality delivery of innovative new therapies.
    tranSmart - A repository of open-access, open-source data designed to enable collaboration across disciplines, specialties and geography.
    Universities Allied for Essential Medicines - Non-profit organization promoting the development of medicines in the public interest by focusing on how universities handle their intellectual property and the effects of the Bayh-Dole amendment and analogous legislation.
  • Science Societies and Associations

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    American Association for the Advancement of Science - Primary organization in the US whose mission is to "advance science and serve society"; publishes the journal Science weekly. Founded in 1848, it operates as an international non-profit organization.
    American Association for Cancer Research - Mission is to prevent and cure cancer through research, education, communication, and collaboration.
    American Society of Clinical Oncology - Professional organization for doctors who treat cancer.
    FASEB - The Federation of American Societies for Experimental Biology - A coalition of societies that serve the interests of biomedical and life scientists, with a focus on public policy issues.
    National Postdoctoral Association - Organization that provides career and professional resources for post doctoral fellows, with information for graduate students and faculty as well.
    Principal Investigators Association - Advice and information for PI’s on grants, publishing, lab management, intellectual property, research compliance, and more.
  • Government Resources

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    Bayh-Dole Legislation - Website highlights the role the 1980 Bayh-Dole amendment had on enabling academic institutions to retain title to their inventions developed using federal funds.
    The Biomarkers Consortium - A public-private partnership that endeavors to develop, validate, and qualify biological markers (biomarkers) in an effort to enable the detection, prevention, diagnosis, and treatment of various diseases.
    Biotechnology Resources for Researchers - Databases, registries, clinical research, basic research networks, reagents, services, standardization programs, resources for tissues, cells, and animals.
    Cancer Biomedical Informatics Grid (caBIG) - Collection of biological cancer data along with tools for analyzing this data; supported by the National Cancer Institutes Center for Biomedical Informatics.
    The Cancer Genome Atlas - A project aimed at understanding the molecular basis of cancer using genome analysis and related technologies.
    Centers for Disease Control and Prevention (CDC) - Covers a variety of health information including disease information, healthy living, etc.
    Clinical Trials - A registry of on ongoing and completed federal and privately supported clinical trials; the site is sponsored by the National Institutes of Health. Allows searching by condition, drug, sponsor, and location.
    ClinVar - Public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.
    Critical Path Initiative - A strategic plan enacted by the FDA to drive innovation in the way that drugs are developed, evaluated, manufactured, and used.
    Food and Drug Administration (FDA) - Information on drugs, drug approvals, medical devices, vaccines, biologics, cosmetics, food, tobacco, and public health.
    FDA Basics for Industry - Website to provide information to industry to facilitate an understanding of the drug approval process.
    Genetic Testing Registry - Repository of genetic test information voluntarily submitted by testing companies. Information is not verified by the NIH, and they do not endorse the tests. Simply a collection of what tests are available.
    Golden Goose Awards - Recognizes scientists and engineers whose federally funded research has had significant human and economic benefits.
    Informatics for Integrating Biology and the Bedside (i2b2) - NIH funded National Center for Biomedical Computing. It is developing tools to allow researchers to use existing clinical data for discovery research.
    The International HapMap Project - Overseen by the National Human Genome Research Institute, this project is focused on identifying genetic variations between various individuals and using this information to understand how these differences contribute to health and disease.
    Knockout Mouse Project at the National Human Genome Research Institute - Goal is to knock out some 8500 mouse genes using gene targeting, and to establish a repository of knockout mice. This effort is tied to the International Knockout Mouse Consortium.
    Library of Integrated Network-based Cellular Signatures (LINCS) - NIH funded effort to created a database of human cellular responses.
    National Comprehensive Cancer Network - Comprehensive collection of resources for fighting cancer for both patients and doctors.
    National Center for Advancing Translational Sciences - New 2010 NIH initiative designed to “do some of the dirty work that pharmaceutical companies cannot or will not do”. Will work on drug development and be run out of the NIH budget.
    National Center for Biotechnology Information (NCBI) - Hosts numerous databases that can be queried for free.
    National Institute of Allergy and Infectious Diseases - Offers advice on putting together presentations for small business innovation research (SBIR) and small business technology transfer research (STTR) grants. The grants sites themselves can also be reached directed at SBIR and STTR.
    National Institutes of Health (NIH) - The nation's medical research agency. Health information for consumers in addition to info on grants, research, and health news.
    National Science Foundation (NSF) - Information on funding opportunities, awards, discoveries, news, publications, statistics, classroom resources, speeches and lectures etc.
    PCORI - Patient-Centered Outcomes Research Institute - Established as part of the 2010 Patient Protection and Affordable Care Act, the group is charged with is charged with examining the "relative health outcomes, clinical effectiveness, and appropriateness" of different medical treatments.
    Pubmed - A service of the US National Library of Medicine that allows searching of Medline as well as a large number of life science journals.
    Pubmed Central - A free digital archive of biomedical and life sciences information that is part of the national library of medicine. How current and how far back the collection goes varies with each journal in the archive. Some journals are not part of the collection.
    Rare Diseases Clinical Research Network (RDCRN) - Led by NIH’s National Center for Advancing Translational Sciences (NCATS0, they work on setting up clinical trails for rare diseases in concert with patient advocacy groups.
    Reagan-Udall Foundation for the Food and Drug Administration - Independent non-profit organization created by Congress to advance the FDA's mission through regulatory science and research.
    Therapeutics for Rare and Neglected Diseases (TRND Project) - Program run out of the National Center for Advancing Translational Sciences and whose focus in on new drugs for rare diseases.
    United States Patent and Trademark Office (USPTO) - Information on applying for patents and searching the US patent database. Also includes info on trademarks and intellectual property law and policy.
  • Other Biomedical/Pharma/Biotech Websites of Interest

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    12andMe Sarcoma Community - Effort to understand the biology of sarcoma by studying the genes of sarcoma patients and sarcoma survivors - Practical advice from working researchers to up and coming scientists on the ins and outs of funding, research design, collaboration, publishing, giving talks, and career advancement.
    Access to Medicine Index - This is an international non-profit organization based in the Netherlands. It ranks pharmaceutical companies with respect to their efforts to provide drugs and other resources for neglected diseases that primarily afflict people in impoverished parts of the world.
    Addgene - A non-profit repository that makes it easier to share and obtain plasmids.
    Adverse Events - Critical drug safety and outcome information on all FDA approved medications.
    Allen Human Brain Atlas - Maps the anatomical location and activity of genes within the human and mouse brain.
    American Society of Heath-System Pharmacists Drug Product Shortages - List of drugs and vaccines that are currently in short supply in the US due to manufacturing problems or other issues
    American Type Culture Collection - A private, non-profit biological resource center and resource organization focused on the acquisition, authentication, production, preservation, development, and distribution of standard reference microorganisms, cell lines, and other research materials.
    Asian Cancer Research Group - An independent, not-for-profit company established by Eli Lilly, Merck, and Pfizer to accelerate research on commonly diagnosed cancers in Asia; data to be shared via an open-source community.
    Assay Depot - The world's largest online marketplace for pharmaceutical research services.
    Bioethics International - Mission is to empower professionals and organizations in healthcare, life science and biotechnology to make responsible decisions. Focus is on the ethics and governance of how medicines are researched, developed, marketed and made accessible to patients around the world.
    Biotechnology Institute - Institute with a mission to promote biotechnology and its medicinal, agricultural, and environmental applications.
    BioModels Database - A repository of peer-reviewed, published, computational models, primarily from the field of systems biology
    Cancer Commons - An open science initiative that provides patients with personalized, actionable information that can save lives. It’s utility is focused through CollabRx web based applications and services.
    CANDO - Computational Analysis of Novel Drug Opportunities at the U. Washington
    canSar - Cancer drug discovery database based at the UK’s Centre for Cancer Therapeutics at the Institute of Cancer Research. The site seeks to meld chemical, biological, and eventually clinical information on drug targets, genes, chemicals and is a freely available resource for researchers.
    CollabRx - Patient driven approach for developing treatments for various diseases.
    Creative Commons - Expanding the use of licenses to scientific and technical research to facilitate open access.
    Crimson Project - Enables high-throughput, IRB compliant specimen acquisition for medical centers and research enterprises.
    DNA Learning Center - Educational project of the Cold Spring Harbor Laboratory.
    Drug Gene Interaction Database - Lists all known interactions between drugs and genes.
    DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures) is the most comprehensive Biological Resource Centre in Europe.
    EGAPP - Evaluation of Genomic Applications in Practice and Prevention supports the development of a systematic process for assessing the available evidence regarding the validity and utility of rapidly emerging genetic tests for clinical practice.
    ENCODE: The Encyclopedia of DNA Elements - An international research consortium that is building a comprehensive parts list of functional genomic elements in both humans and mice.
    Faster Cures - A non-profit think tank that works to improve the effectiveness and efficiency of medical research; associated with the Milken Institute.
    GAPP KB - An online resource providing access to information on applications of genomic research for use in public health and health care.
    Genetic Alliance - Nonprofit health advocacy group; network includes more than 1000 disease specific organizations as well as companies, universities, government agencies, and public policy organizations.
    Genomes Unzipped - Information on developments in genetic testing of individuals and genome sequencing.
    Global Alliance of Leading Drug Discovery and Development Centres - An association of international peer organizations dedicated to translating health research into new medicines.
    Human Genome Variation Society - Promotes collection, documentation, and distribution of genomic variation information with links to many databases.
    iSymposia - Free online science conferences.
    Life Sciences Foundation - Non-profit foundation focused on recording and preserving the history of biotechnology.
    Masters in Biotechnology - Site with information on academic institutions that grant masters degrees in biotechnology.
    Medical Technology & Practice Patterns Institute is a nonprofit organization established in 1986 to conduct research on the clinical and economic implications of health care technologies.
    Medicines for Malaria Venture - This is a not-for-profit public-private partnership established as a foundation in Switzerland in 1999. As the name indicates, it is focused on developing new medicines to treat malaria.
    Medicines Patent Pool Initiative - Program aims to improve access to affordable HIV medications in low and middle income companies.
    mutaDATABASE - free online database of human disease genes, variants, genes, and features of patients with monogenic disease.
    National Foundation for Medical Research and Innovation - Australian organization whose mission is to support innovative areas of research to help benefit mankind through the prevention or eradication of diseases.
    National Institute for Pharmaceutical Technology and Education - Not-for-profit organization focused on research and education in pharmaceutical product development and manufacturing.
    National Science Communication Institute - Non-profit that aims to improve science collaboration, discovery, education and public policy by reforming the communication culture inside science.
    One Mind for Research - Organization that seeks to develop treatments for brain diseases by pooling academic and industry efforts.
    Pharmacogenomics Knowledge Base - A searchable database illustrating how genetics effects the activity of various drugs.
    PharmedOut - A university-based project that empowers physicians to identify and counter inappropriate pharmaceutical promotion practices.
    PLoS One - An interactive open-access journal for the communication of peer-reviewed scientific and medical research.
    Program for Breakthrough Biomedical Research at University of California - San Francisco. Innovative grant funding program to support research at this branch campus that is considered too risky for the NIH.
    Public Citizen Health Research Group - Division of Public Citizen that is focused on promoting safer drugs and public health.
    Rare Disease Challenge: Be HEARD (Helping Empower and Accelerate Research Discoveries) to accelerate rare disease research. Prizes include $10,000 cash and more than $400,000 of donated research services.
    Rare Genomics - Non-profit focused on crowdsourcing to fund DNA sequencing of individuals with rare diseases
    RARE Project - Focused on rare disease advocacy, research, and education.
    Registry of Standard Biological Parts - Collection of genetic elements that can be mixed and matched to build synthetic biology devices and systems.
    Research!America - The nation's largest not-for-profit public education and advocacy alliance working to make research to improve health a higher national priority.
    ResearchGate - Social network for scientists to promote collaboration and open science
    Scientific American World View - A global biotechnology perspective, focused on IP, intensity, enterprise support, education and workforce, and foundations that support biotechnology.
    Science Commons - Creates strategies and tools that are designed to make web enabled scientific research more efficient. Their stated ultimate goal is to speed the translation of data into discoveries. One specific project is focused on improving the Material Transfer Agreement process.
    Science Exchange - A marketplace where you can outsource an experiment, take advantage of extra capacity to handle the experiments of others. A way to get experiments done more quickly and easily.
    Sense About Science - An organization that equips people to make sense of science claims that are put in front of them by asking for evidence; maintains a database of experts in various areas to help answer questions
    Therapeutic Targets Database - Searchable database of drugs, drug targets, and specific pathways, including information on clinical trials, approved drugs, and experimental drugs made against targets (61 protein classes and 140 drug therapeutic classes).
    TRAIN Central Station - A platform facilitating venture philanthropy in medical research; associated with the Faster Cures think tank.
    Transparency Life Sciences - Drug company based on open innovation; designs studies via crowdsourcing.
    Tufts University Institute for Biopharmaceutical Partnerships - Model program through which Tufts University seeks to establish collaborations and explore commercialization strategies to partner with faculty research programs.
    Undiagnosed Diseases Program - This is a special program of the NIH set up to diagnose and understand extremely rare diseases where no medical explanations have been forthcoming. The resulting information has generated new biological understandings.
  • Public Data Repositories

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    National Center for Biotechnology Information’s Gene Expression Omnibus.
    The gene-expression
    database at the European Bioinformatics Institute.
    Sage BioNetworks
    Synapse Commons Repository.
    tranSmart - A repository of open-access, open-source data designed to enable collaboration across disciplines, specialties and geography.