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Archive for the ‘Simulation Modeling in NGS’ Category

Authentic Relevance of LPBI Group’s Portfolio of IP as Proprietary Training Data Corpus for AI Initiatives at Big Pharma

Curators: Aviva Lev-Ari, PhD, RN and Stephen J. Williams, PhD

Updated on 11/29/2025

 

The Voice of Stephen J. Williams, PhD

Since the formation of the LPBI group in 2012, we have set as a goal to digitally curate and ontologize the biomedical literature.  These aspects of our mission, although not understandable to most at that time of our inception, was at the forefront of many academic efforts which became the springboard and initial conceptualization of today’s large language models.  In select universities like University of Illinois, University of Delaware, and the Technion, academics and researchers at Microsoft and Google, were laying the framework for  a semantic web, or Web 3.0.  Another company at the forefront of this idea was a company springing forth from Mathematica, Wolfram Research. This idea for a semantic web would entail the processes of curation, digitization, and ontology creation.  Their belief, such as ours, was  a precursor and much needed key to the puzzle of moving language from machine learning algorithms to the generative transformers used by artificial intelligence.

However as most efforts in this genre focused on general language, our efforts at LPBI Group were focused on the biomedical field, as we understood, from 2012, that the biomedical literature was unique, and so a unique strategy had to be developed to semantically understand biomedical text, even though at the time of 2012 GPTs were not even a concept.  However the potential for doing biomedical text analysis was there, and LPBI Group responded by developing a methodology of scientific curation which involved a multimodal strategy to curate, digitize, and ontologize biomedical findings and text.

It was about at the time of 2012 that other groups, mainly focused of drug development applications (for example at University of Indiana) recognized that new computational power of machine learning algorthims could be  useful in analyzing complex biological questions.  Please see our Synthetic Biology in Drug Discovery section of our Journal for more information on this. For instance, an early adopter of this strategy, a company called  Data2Discovery, one of the earliest AI for drug discovery startups, stated

We are able to improve drug discovery now as well as demonstrating new fast-cycle AI-driven processes that will have a revolutionary impact on drug discovery if fully implemented. We have had some dramatic successes, but we are just starting to discover the impact that data, knowledge graphs, AI and machine learning can together have on drug discovery.

We need all the expertise of academics, consortia, AI companies and pharma to make his happen, and it’s going to require some serious investment, and a big change of thinking. But the opportunity to get drug discovery out of the death spiral and framed for data-driven success is too important to pass up.

However the LPBI Group was cognizant of these changes occuring and pivoted to the developing natural language processing arena as well as ideas for the developing Blockchain technology.  This was more of a natural progression for the LPBI Group than a pivot (please read here).

This would be our Vision 2.0, to make biomedical text amenable for Natural Language Processing.   We utilized a few strategies in this regard, partnering with a company who was developing NLP for biomedical text analysis, and developing in house machine learning and NLP methods using the Wolfram language environment.  Our focus on structuring biomedical text (versus the highly structured genomics and omics data found in many omics related databanks) was prescient for the time.  As NLP and machine learning  efforts realized, biomedical text needs to have a structure much like genes, proteins and other molecular databases had been organized.  Therefore it was realized that structured data was imperative for efficient NLP analysis, a crux for the new GPT which was being developed (and in this mind still is a crux for current GPT and LLM models when it comes to biomedical text analysis).

Our strategy using our scientific curation methodology (as described below in links form our founder Dr. Aviva Lev-Ari, was proven to be highly efficient and amenable to NLP analysis, as a pilot with an NLP company noticed.  Most of the data they were using was unstructured and their first step involved annotation and structuring the text, as we had already performed for years.  This was critical as our text was able to pull out more concepts, relationships, in a faster time than NLP on sources such as PubMed available text.  We had also developed our own in house algorithms for NLP on our material, which is shown in some of our book offerrings and individual articles.

However with the advent of GPT it was thought all this was unnecessary.  However this idea that our strategy was outdated or irrelevent in the era of GPT was wholly  incorrect to the advocates of a sole GPT strategy to analyze biomedical text and data.  It is now understood that structure is needed as some of biomedical-centric GPT projects would find out, such as BioGPT.  We have many articles which attest to the lack of  accuracy and efficiency of these GPT architectures (seen here). These include failure rates in many areas of healthcare and biomedicine by sole reliance on GPT,

It was realized by many in the biomedical arena, especially those involved in NLP efforts, that there was much value in the semantic web 3.0 idea, and this was readily picked up by those spearheading effort to incorporate knowledge graphs with the new generative AI or GPT technology.  We have shown a clear example our scientific methodology of curation with ontology has better inference when combined with knowledge graphs and GPT than reliance on GPT alone

please read this article

Multiple Lung Cancer Genomic Projects Suggest New Targets, Research Directions for Non-Small Cell Lung Cancer

at https://pharmaceuticalintelligence.com/2014/09/05/multiple-lung-cancer-genomic-projects-suggest-new-targets-research-directions-for-non-small-cell-lung-cancer/

As shown here in this article

This update was performed by the following methods:
A. GPT 5 Text analysis and Reasoning
B. Insertion of Knowledge Graph on topic Curation of Genomic Analysis from Non Small Cell Lung Cancer Studies  from Nodus Labs using InfraNodus software
C. Domain Knowledge Expert evaluation of the Update outcomes
This article has the following Structure:
Part A: Introduction to LLM, Knowledge Graph software InfraNodus, ChatGPT5 and Background Information on curated material for Test Case
Part B: InfraNodus Analysis of manual curation and Knowledge Graph Creation
Part C: Chat GPT 5 Analysis of Manually Curated Material
Part D: Curation entitled Multiple Lung Cancer Genomic Projects Suggest New Targets, Research Directions for Non-Small Cell Lung Cancer originally published on 09/05/2014
Results of Article Update with GPT 5
1. GPT5 alone was not able to understand the goal of the article, namely to determine knowledge gaps in a particular research area involving 5 genomic studies on lung cancer patients
2. GPT5 alone was not able to group concepts or comonalities between biological pathways unless supplied with a manually curated list of KEGG pathways from a list of mutated genes.  However this precluded any effect that fusion proteins had on the analysis and so GPT5 would only concentrate on mutated genes commonly found in literature
3. GPT was not able to access some of the open Access databases like NCBI Gene Ontology database
Results of Article Update with KnowledgeGraph presentation to GPT 5
4. As the Knowledge Graph understood the importance of fusion proteins and transversions, the knowledgegraph augmented the GPT analysis and so enriched the known pathways as well as could correctly identify the less represented pathways in the knowledge graph
5.  This led to the identification of many novel signaling pathways not identified in the original analysis, and was able to perform this task with ease and speed

6. GPT with InfraNodus Analysis was able to propose pertinent questions for future research (the goal of the original curation) such as:

  • How does the interaction between [[EGFR]] mutations and sex-specific gene alterations, including [[RBM10]], influence treatment outcomes in lung adenocarcinoma?
  • How does the intersection of mutational patterns from smoking influence pathway activation in NSCLC, and can identifying these interactions improve targeted therapy development?
Novelty in comparison to Original article published on 09/05/2014
7. it appears that manual curation is necessary to assist in the building of relevant knowledge graphs in the biomedical fields to augment generative AI analysis
8. by itself, generative AI is not optimized for inference of higher concepts from biomedical text, and therefore, at this point, requires the input from human curators developing domain-specific knowledge graphs
9.  The combination of ChatGPT5 and Knowledge graphs of this manually curated biomedical text added a further layer of complexity of gaps of knowledge not seen in the original curations including the need to study noncanonical signaling pathways like WNT and Hedgehog in smoker versus nonsmoker cohorts of lung cancer patients

The Voice of Aviva Lev-Ari, PhD, RN

LPBI Group’s Portfolio of Digital IP Assets as Proprietary Training Data Corpus for AI in Medicine, in Life Sciences, in Pharmaceutical and in Health Care Applications

The Portfolio of Digital IP Assets by Class is a rare, defensible asset, privately-held debt-free by LPBI Group’s founder. The content, aka a Data Corpus is best designed for the Training and Pre-Training of Foundation Multimodal Models in Health Care. 

#HealthcareAI

#FoundationModels

#ProprietaryTrainingData

LPBI Group is offering transfer of ownership, in full, a privately held, multimodal healthcare training corpus leveraging propriety unique data set curated by domain experts and mapped to a living ontology for GenAI creating defensibility.

The Portfolio of IP spans:

  • 6,250+ articles (~2.5MM views),
  • 48 e‑books (EN/ES) (+152,000 page downloads),
  • 100+ e‑Proceedings with +50 Tweet collections,
  • 7,500+ biological images with expert context, and
  • 300+ Audio podcasts on Life Sciences breakthroughs.

Each asset (Use Case: Scientific Article) has timestamps, author/role labels, crosslinks, and view histories.

  • Metadata export exists; full text and media transfer via WordPress/Amazon account control for immediate ingestion.
  • Rights are centrally assigned with explicit model‑training data by domain-aware for model implementation for Small Language Models or Large Language Models.

Strategic acquirers in Big Pharma of Vertical AI startups (i.e., LPBI Group) with data‑moat strategies

Pharma strategics Acquire LPBI’s end‑to‑end, rights‑clean healthcare knowledge base to accelerate R&D, medical affairs, and safety. Ideal for and with acceleration of R&D, medical affairs, and safety. Emphasize compliant internal copilots and evidence synthesis enabled by expert curation and living ontology. Close with rapid onboarding under NDA  Metadata export plus full text/media transfer for rapid onboarding. Full acquisition only.

Subject: Buy the moat: full acquisition of expert healthcare corpus with clean rights

We’re selling the entire asset: a privately held, multimodal healthcare corpus with centralized training rights and an exportable ontology, validated on gene–disease–drug extraction. It’s ingest‑ready and transfers cleanly via account control plus a metadata export. If owning differentiated data is critical for your agent or workflow, we can provide a diligence preview under NDA.

compliant internal copilots and evidence synthesis enabled by expert curation and living ontology. Close with rapid onboarding under NDA

Five Examples of Domain-aware for model implementation for Small Language Models – English Edition & Spanish Edition

Series A: Cardiovascular Diseases ($515) – Six Volumes

https://www.amazon.com/gp/product/B07P981RCS?ref_=dbs_p_mng_rwt_ser_shvlr&storeType=ebooks

Six Examples of Domain-aware in the Specialty of Cardiovascular Diseases

  • Series A, Volume One

Perspectives on Nitric Oxide in Disease Mechanisms2013

http://www.amazon.com/dp/B00DINFFYC $75

  • Series A, Volume Two 

Cardiovascular Original Research: Cases in Methodology Design for Content Co-Curation, 2015

http://www.amazon.com/dp/B018Q5MCN8 $75

  • Series A, Volume Three

Etiologies of Cardiovascular Diseases – Epigenetics, Genetics and Genomics2015

http://www.amazon.com/dp/B018PNHJ84 $75

  • Series A, Volume Four

Therapeutic Promise: Cardiovascular Diseases, Regenerative & Translational Medicine, 2015

http://www.amazon.com/dp/B019UM909A $75

  • Series A, Volume Five

Pharmacological Agents in Treatment of Cardiovascular Diseases2018

https://www.amazon.com/dp/B07MGSFDWR  $115

  • Series A, Volume Six:

Interventional Cardiology for Disease Diagnosis and Cardiac Surgery for Condition Treatment2018

https://www.amazon.com/dp/B07MKHDBHF $100

 

Series B: Frontiers in Genomics ($200) – Two Volumes

https://www.amazon.com/gp/product/B0BSDPG2RX?ref_=dbs_p_pwh_rwt_anx_b_lnk&storeType=ebooks

Series C: Cancer & Oncology ($175) – Two Volumes

https://www.amazon.com/gp/product/B0BSDWVB3H?ref_=dbs_p_mng_rwt_ser_shvlr&storeType=ebooks

Series D: Immunology ($325) – Four Volumes

https://www.amazon.com/gp/product/B08VVWTNR4?ref_=dbs_p_pwh_rwt_anx_b_lnk&storeType=ebooks

Series E: Patient-Centered Medicine ($274) – Four Volumes

https://www.amazon.com/gp/product/B0BSDW2K6C?ref_=dbs_p_mng_rwt_ser_shvlr&storeType=ebooks

One Example of Domain-aware for model implementation for Large Language Models

Eighteen volumes in the English Edition and 19 volumes in the Spanish Edition including 2,728 articles by biomedical professionals are available.

https://www.amazon.com/s?k=Aviva+Lev-Ari&i=digital-text&rh=n%3A133140011&ref=nb_sb_noss

The electronic books are collections of curated articles in biomedical science. The electronic Tables of Contents (eTOCs) of each volume was designed by a senior editor with expertise in the subjects covered in that volume. The curations use as sources published research findings in peer-reviewed scientific journals together with expert added interpretations.

The e-books are designed to make the latest research in the Five Bilingual BioMed e-Series – 37 volumes accessible to practicing health care professionals. These five e-Series cover the following medical specialties:

  • Cardiovascular diseases and therapies,
  • Genomics,
  • Cancer etiology and oncological therapies,
  • Immunology, and
  • Patient-centered precision medicine.

The material in these volumes can greatly enhance medical education and provide a resource for continued updating and education for health care professionals. In addition to the 37 e-books, LPBI has published more than 6,000 articles in its online scientific journal “PharmaceuticalIntelligence.com”, which has received 2.5 million views since its launch in 4/2012, Top articles had more than 18,000 views.

The Portfolio is:

  • rights‑clean,
  • expert‑curated healthcare corpus
  • mapped to a living Ontology,
  • already packaged for immediate model ingestion and
  • suitable for safe pre-training, evals, and fine‑tuning.

If healthcare domain data is on your roadmap, this is a rare, defensible asset worth a preview.

LPBI Group is offering transfer of ownership, in full, a privately held, multimodal healthcare training corpus leveraging propriety unique data set curated by domain experts and mapped to a living ontology for GenAI creating defensibility. It spans 6,250+ articles (~2.5MM views), 48 e‑books (EN/ES) (+151,000 page downloads), 100+ e‑proceedings with +50 tweet collections, 7,500+ biological images with expert context, and 300+ Audio podcasts on Life Sciences breakthroughs. Each asset has timestamps, author/role labels, crosslinks, and view histories. Rights are centrally assigned with explicit model‑training data by domain-aware for model implementation for Small LMs or LLMs. Metadata export exists; full text and media transfer via WordPress/Amazon account control for immediate ingestion.

Leaders in Pharmaceutical Business Intelligence Group, LLC, Doing Business As LPBI Group, Newton, MA

Full acquisition only: LPBI Group’s Healthcare Training Data Corpus

  • Scientific articles
  • e‑Books in Medicine
  • e‑Proceedings,
  • Biological images
  • Podcasts

#HealthcareAI #FoundationModels #TrainingData

Contact Founder: avivalev-ari@alum.berkeley.edu

PharmaceuticalIntelligence.com

About the Founder

  • LPBI Group’s Legacy and Biography of Aviva Lev-Ari, PhD, RN, Founder & Director, INTERACTIVE CHAT with Grok, created by xAI

https://pharmaceuticalintelligence.com/2025/04/30/interactive-chat-with-grok-created-by-xai-lpbi-groups-legacy-and-biography-of-aviva-lev-ari-phd-rn-founder-director/ 

For Recognitions and a DETAILED BIO by Perplexity.ai and Gemini 2.5 Pro (experimental), see

  • “Show Thinking” by AI Deep Research: The AI-generated Biography Description of Aviva Lev-Ari, PhD, RN, Founder of PharmaceuticalIntelligence.com by Perplexity.ai and by Google’s Gemini 2.5 Pro (experimental)

https://pharmaceuticalintelligence.com/2025/04/29/show-thinking-by-ai-deep-research-the-ai-biography-description-of-aviva-lev-ari-phd-rn-founder-of-pharmaceuticalintelligence-com-by-perplexity-ai-and-by-googles-gemini-2/

Authentic Relevance of LPBI Group’s Portfolio of IP as Proprietary Training Data Corpus for AI Initiatives at Big Pharma

On 11/14, 2025, Dr. Lev-Ari asked @Grok about AI Initiatives at a Big Pharma, i.e., Pfizer.

@Grok response is presented, below

URL SOURCE:

https://x.com/i/grok/share/0ol5VOJsEYs11baXq4xkzNb0h

Pfizer’s AI Initiatives Overview

Pfizer, a global pharmaceutical leader, has integrated artificial intelligence (AI) and machine learning (ML) across its operations to accelerate drug discovery, enhance clinical trials, improve manufacturing, and drive patient-centric innovations. These efforts aim to reduce development timelines, boost efficiency, and address challenges like rare disease detection. As of late 2025, Pfizer’s AI strategy emphasizes internal expertise, cloud-based tools (primarily with AWS), and cross-industry collaborations, with a focus on multimodal data analysis and generative AI. Below is a breakdown of key initiatives, drawn from recent developments.

1. Pfizer AI Cloud Transformation (PACT) Program Launched in 2021 with AWS, PACT is a prototyping accelerator for AI/ML applications in lab, clinical manufacturing, and supply chain efforts. It has pursued 14 projects, with five now in production. Key outcomes include:

  • Generative AI tools that save scientists up to 16,000 hours annually in literature searches and data analysis.
  • 55% reduction in infrastructure costs through cloud optimization.
  • Exploration of virtual/augmented reality for training, with rapid prototyping to test feasibility. This program fosters “fail-fast” innovation, enabling quick iteration on ideas like AI-driven predictive modeling.

2. Drug Discovery and Development Acceleration Pfizer uses AI, supercomputing, and ML to streamline R&D, cutting years off traditional timelines (e.g., from 8–10 years to months for certain candidates).

  • COVID-19 Initiatives: AI optimized molecular searches for PAXLOVID (oral antiviral), enabling intravenous-to-oral pivots. During vaccine development, the Safety Data Quality (SDQ) tool—a custom AI for clinical trial data management—saved a full month of analysis via the Breakthrough Change Accelerator sandbox.
  • Precision Medicine and Subpopulation Identification: Advanced ML (classical and deep learning) analyzes molecular datasets from trials to predict patient responses, informing trial design, first-in-human studies, and oncology/inflammatory disease targeting. This has doubled clinical success rates to ~20% (vs. industry 7–10%).
  • ML Research Hub: Pfizer’s Cambridge, MA-based Biomedical Data Science group builds internal talent for AI in genome sciences, predicting disease outcomes and treatment efficacy using techniques from tech giants like Google.

3. Clinical Trials and Regulatory Efficiency AI automates content creation across the drug lifecycle, from lab data to regulatory docs and patient booklets, ensuring quality and speed.

  • Predictive Regulatory Tools: ML models forecast regulator queries, proactively addressing safety concerns to build trust and shorten approvals.
  • Decentralized Trials: The “Clinical Trial Anywhere” model uses AI to integrate remote data (e.g., home health visits), improving recruitment/retention and generating real-world evidence.
  • Inventory and Supply Chain: AI predicts vaccine storage issues, pioneered during COVID distribution.

4. Disease Detection and Diagnostics

  • ATTR-CM Initiative: Through the ASPIRE collaboration (with Amyloidosis Research Consortium), AI analyzes EHRs, ECGs, and echocardiograms to detect transthyretin amyloid cardiomyopathy earlier, targeting underdiagnosed heart failure cases.
  • Rare Diseases: ML models identify symptoms in large datasets, mapping the immune system for better predictions.

5. Generative AI and Operational Tools

  • Charlie Platform: Rolled out in 2024 for marketing, this gen AI tool (named after co-founder Charles Pfizer) generates compliant content like emails, presentations, and medical article drafts. Trained on approved product data, it streamlines physician targeting and customer insights.
  • Scientific Data Cloud: AWS-powered centralization of data/ML capabilities, enabling faster research and treating 1.3 billion patients in 2022. It supports gen AI via Amazon SageMaker/Bedrock for manufacturing efficiency.
  • Global Health Grants: Through the Pfizer Foundation’s AI Learning Lab, funding supports AI for equitable healthcare access, e.g., biometric tools for community care.

6. Partnerships and Education

  • Collaborations: With AWS for cloud AI; IMI Big Picture for a 3M-sample disease database; IIT Madras for the 2025 AIPM Symposium on AI in pharma (focusing on drug discovery and precision medicine).
  • Talent and Events: Hosting webinars on AI in manufacturing (e.g., predictive maintenance, regulatory submissions) and engaging leaders like Dr. Subha Madhavan on AI for biomedical data integration.
  • Strategic Focus: $500M R&D reinvestment by 2026 targets AI for productivity, part of $7.7B cost savings. Emphasis on ethical AI, diverse datasets, and competing with global biotech advances (e.g., China’s AI in CRISPR).

Pfizer’s approach balances operational efficiency with transformative R&D, positioning AI as a core enabler rather than a standalone focus. Ongoing investments, like cloud migrations saving $47M annually and reducing CO2 emissions, underscore sustainability. For the latest, monitor Pfizer’s investor updates or events like AWS re:Invent.

Responsiveness to Big Pharma AI Initiatives by LPBI Group’s Digital IP Portfolio:

  • Scientific articles
  • e‑Books in Medicine
  • e‑Proceedings,
  • Biological images
  • Podcasts
AI Initiative at Big Pharma

i.e., Pfizer

Composed @Grok

LPBI Group’s Digital IP Asset:

Journal articles

N = 6,250

Composed by Aviva Lev-Ari

Generative AI tools

that save scientists up to 16,000 hours annually in literature searches and data analysis.

Generative AI tools searching LPBI’s Proprietary data in addition to Public Domain data sources

Journal ONTOLOGY used to optimize context classification selected for search

Drug Discovery and Development Acceleration

Pfizer uses AI, supercomputing, and ML to streamline R&D timelines

–       Run prompts by category of research on the following three dyads

–       Run ML across categories of research for these three dyads

-Gene-disease

-Disease-drug

-Gene-drug

 

Clinical Trials and Regulatory Efficiency AI:

-Predictive Regulatory Tools

-Decentralize Trials

-inventory management

Curation competences:

  • content creation across the drug lifecycle, from lab data to regulatory docs
Disease Detection and Diagnostics:

–       ATTR-CM Initiative

–       Rare diseases

Heart Failure Diagnosis by Early detection of transthyretin amyloid cardiomyopathy

–       Journal published ~30 curations by Dr. Larry on this subject ATTR-CM

–       Run NLP on this Corpus

Rare diseases:

Journal published 560 articles on Rare diseases

–       Run ML on this Corpus

Generative AI and Operational Tools:

–       Charlie Platform

–       Scientific Data Cloud AWS powered ML on centralized data

–       Amazon’s SageMaker /Bedrock for Manufacturing efficiency

–       Global Health Grants:

Pfizer Foundation’s AI Learning Lab for equitable access to care and tools for community care

Content generated in the Journal can become “generated compliant content” if run on the Charlie Platform.

–       For REUSE content in context

 

Entire Corpus of 9 Giga bytes can be ingested to Pfizer Foundation’s AI Learning Lab

–       Run prompts against it

–       Journal’s Content to be used for Internal staff expertise development

–       Journal’s Content for Leadership development

Partnerships and Education

–       Collaborations: IMI Big Picture for 3M – sample disease database

–       AI in Pharma AIPM Symposium: Drug discovery and Precision Medicine

–       Webinars of AI for biomedical data integration

–       Webinar on AI in Manufacturing

The Journal had published 547 articles in Precision Medicine

 

The Journal had published 1,114 articles in Drug Discovery

 

The Journal had published 701  articles in Drug Delivery

 

The Journal had published 3,615 articles on subject matter “Disease”

 

The Journal had published 738 articles on Biomedical topics

 

The Journal had published 425 articles on Artificial Intelligence (AI)

Strategic Focus:

–       $500M R&D reinvestment by 2026 targets AI for Productivity

–       Part of $7.7B cost savings

–       Ethical AI, diverse DBs

–       Global biotech advances: China’s AI in CRISPR

The Journal had published 432 articles on CRISPR

 

Productivity derived from Journal’s content:

–       As a result of the fact that ~70% of the Journal’s articles are curations written by Domain Knowledge Experts subjectively expressing theirs clinical interpretations of basic and primary research – the productivity of the knowledge workers at any Big Pharma would increase vastly.

–       If Grok and Claude would run on LPBI Group’s Digital IP Corpus, a scientific revolution will emerge

–       It is not combinatorics applied to molecules with 98% futile results!!!

it is the IQ of Gifted HUMANS, of domain knowledge experts generating content using individual CREATIVITY no Quantum or Super Intelligence which is not in existence, YET.

–       Foundation Models in Healthcare depends on the OUTPUT of the human creative mind. AI takes keyword (classic search) and concepts (semantic search) and run frequency of occurrence and predict the nest word, one word after the next one.

@@@@@@@

AI Initiative at Big Pharma

i.e., Pfizer

LPBI Group’s Digital IP Asset:

e-Books

Domain-aware Editorials and Curations

Generative AI tools that save scientists up to 16,000 hours annually in literature searches and data analysis. The electronic Table of Contents of every e-book is a CONCEPTUAL MASTER PIECE of one unique occurrence in Nature generated by the Editor, or the Editors that had

–       Commissioned articles for the e-Book

–       Had selected articles from collections of Categories of Research created by domain knowledge experts

–       Had reviewed the TOTALITY of the Journal’s Ontology and found new concept to cover in the e-Book not originally planned

Had incorporated Highlights of Lectures given at 100 Conferences LPBI Group’s Dr. Lev-Ari and Dr. Willians had cover in Real Real, by invitation, only as PRESS.

–       The vision of the Editor-in-Chief of the BioMed e-Series reflects the BIG PICTURE of Patient care delivery.

–       UC, Berkeley PhD’83

–       Knowledge student and Knowledge worker, 10/1970 to Present

–       Conceptual pioneer of 26 algorithms in Decision Science of Operations Management decision support systems

–       2005 to Present in the Healthcare field.

–       2005-2012: Clinical Nurse Manager in Post-acute SNF settings and Long-term Acute care Hospital Supervisor – had developed a unique view on Diagnosis, Therapeutics and Patient care delivery

–       The BioMed e-Series is the EPITOM of human CREATIVITY in Healthcare an OPUS MAGNUM created by collaboration of top Scientists, Physicians and MD/PhDs

–       The 48 e-Books Published by LPBI Group – represent the ONLY one Publisher on Amazon.com with +151,000 pages downloaded since the 1st e-book published on 6/2013 and since Pay-per-View was launched by Amazon.com in 2016.

Drug Discovery and Development Acceleration Pfizer uses AI, supercomputing, and ML to streamline R&D timelines Two volumes on the BioMed e-Series were subjected to Medical Text Analysis with AI, ML, Natural Language Processing (NLP).

–       Cancer, Volume 1 (In English, part of the Spanish Edition, Series C)

–       Genomics, Volume 2 (In English, part of the Spanish Edition, Series B)

–       GPT capabilities are warranted to attempt to subject to ML Analytics every book of the MUTUALLY EXCLUSIVE 48 URLs provided by Amazon.com to LPBI Group, the Publisher.

–       5 URLs for 5 Bundles in The English Edition: Series A,B,C,D,E – English Edition

–       All books in each series – 5 Corpuses for domain-aware Small Language Model in English

–       All books in each series – 5 Corpuses for domain-aware Small Language Model in Spanish

–       5 URLs for 5 Bundles in The Spanish Edition: Series A,B,C,D,E –Spanish Edition

 

Clinical Trials and Regulatory Efficiency AI:

-Predictive Regulatory Tools

-Decentralize Trials

-inventory management

Disease Detection and Diagnostics:

–       ATTR-CM Initiative

–       Rare diseases

–       No one had attempted ML on every book, only two books were analyzed by ML.

–       No one had attempted ML on all the Volumes in any of the 5 Series.

–       No one had attempted ML on all the 48 books

–       WHEN that will be done – a REVOLUTION on Disease Detection and Diagnostics will be seen for the first time because the totality of these 48 books represent the Brains of Human Experts

 

Generative AI and Operational Tools:

–       Charlie Platform

–       Scientific Data Cloud AWS powered ML on centralized data

–       Amazon’s SageMaker/Bedrock for Manufacturing efficiency

–       Global Health Grants:

Pfizer Foundation’s AI Learning Lab for equitable access to care and tools for community care

Add the content of all the Books to Charlie Platform
Partnerships and Education

 

Collaborations: IMI Big Picture for 3M – sample disease database

 

AI in Pharma AIPM Symposium: Drug discovery and Precision Medicine

 

Webinars of AI for biomedical data integration

 

Webinard on Ai in Manufacturing

e-Books are the SOURCE for Education

–       Offer the books as Partnership sustenance

Strategic Focus:

–       $500M R&D reinvestment by 2026 targets AI for Productivity

–       Part of $7.7B cost savings

–       Ethical AI, diverse DBs

–       Global biotech advances: China’s AI in CRISPR

URLs for the English-language Edition by e-Series:

Series A: Cardiovascular Diseases ($515)

https://www.amazon.com/gp/product/B07P981RCS?ref_=dbs_p_mng_rwt_ser_shvlr&storeType=ebooks

Series B: Frontiers in Genomics ($200)

https://www.amazon.com/gp/product/B0BSDPG2RX?ref_=dbs_p_pwh_rwt_anx_b_lnk&storeType=ebooks

Series C: Cancer & Oncology ($175)

https://www.amazon.com/gp/product/B0BSDWVB3H?ref_=dbs_p_mng_rwt_ser_shvlr&storeType=ebooks

Series D: Immunology ($325)

https://www.amazon.com/gp/product/B08VVWTNR4?ref_=dbs_p_pwh_rwt_anx_b_lnk&storeType=ebooks

Series E: Patient-Centered Medicine ($274)

https://www.amazon.com/gp/product/B0BSDW2K6C?ref_=dbs_p_mng_rwt_ser_shvlr&storeType=ebooks

 

@@@@@@@

AI Initiative at Big Pharma

i.e., Pfizer

LPBI Group’s Digital IP Asset:

e-Proceedings: N = +100, and

Tweet Collections: N = +50

Generative AI tools that save scientists up to 16,000 hours annually in literature searches and data analysis.
Drug Discovery and Development Acceleration Pfizer uses AI, supercomputing, and ML to streamline R&D timelines List of all e-Proceeding of +100 TOP Conferences in Biotech, in Medicine, in Genomics, in Precision Medicine

https://pharmaceuticalintelligence.com/press-coverage/part-two-list-of-biotech-conferences-2013-to-present/

In these conferences the Frontier of Science was presented, ofter BEFORE publication findings were revealed. These Proceedings are the ONLY written record of the events. They are privately-held, now for the first time available for Transfer of Ownership 

The Tweet Collection are QUOTES of speakers on record. NOT ELSEWHERE available by name of speaker and affiliation

Clinical Trials and Regulatory Efficiency AI:

-Predictive Regulatory Tools

-Decentralize Trials

-inventory management

Disease Detection and Diagnostics:

–       ATTR-CM Initiative

–       Rare diseases

Generative AI and Operational Tools:

–       Charlie Platform

–       Scientific Data Cloud AWS powered ML on centralized data

–       Amazon’s SageMaker/Bedrock for Manufacturing efficiency

–       Global Health Grants:

Pfizer Foundation’s AI Learning Lab for equitable  access to care and tools for community care

Ingest to Charlie Platform ALL e-Proceedings of ALL Conferences

 

Apply GPT:

Training Data:

–       One conference at a time

–       All Conference on ONE subject matter, i.e., Immunotherapy, Oncolytic Virus Immunotherapy, Immune Oncology

Partnerships and Education

–       Collaborations: IMI Big Picture for 3M – sample disease database

–       AI in Pharma AIPM Symposium: Drug discovery and Precision Medicine

–       Webinars of AI for biomedical data integration

–       Webinar on Ai in Manufacturing

Use Past Conference Agendas to build Future Conference Agendas

Use Speakers Lists to invite speakers/consultants to your events

Use topics covered in Conferences for Employee training & and in-house Leadership development

Strategic Focus:

–       $500M R&D reinvestment by 2026 targets AI for Productivity

–       Part of $7.7B cost savings

–       Ethical AI, diverse DBs

–       Global biotech advances: China’s AI in CRISPR

Having access to +100 e-Proceedings vs Not having access to this resource is a make or break in fine-tuning Corporate Branding: All your competitors attended and had sent Speakers

  • LPBI Group’s e-Proceedings is the only record in one URL

@@@@@@

AI Initiative at Big Pharmas

i.e., Pfizer

LPBI Group’s Digital IP Asset:

Biological Images selected by Experts embedded in original Text (Prior Art)

Generative AI tools that save scientists up to 16,000 hours annually in literature searches and data analysis.
Drug Discovery and Development Acceleration Pfizer uses AI, supercomputing, and ML to streamline R&D timelines Gallery of ~8,000 Biological images and captions is a Treasure TROVE for scientific article writing, Presentation preparations. This Media Gallery is an Art collection of top Scholars in Medicine and Biology
Clinical Trials and Regulatory Efficiency AI:

-Predictive Regulatory Tools

-Decentralize Trials

-inventory management

Disease Detection and Diagnostics:

–       ATTR-CM Initiative

–       Rare diseases

Gallery of ~8,000 Biological images and captions is a Treasure TROVE for Disease Detection and Diagnostics

 

Generative AI and Operational Tools:

–       Charlie Platform

–       Scientific Data Cloud AWS powered ML on centralized data

–       Amazon’s SageMaker/Bedrock for Manufacturing efficiency

–       Global Health Grants:

Pfizer Foundation’s AI Learning Lab for equitable  access to care and tools for community care

  • Ingest into Charlie Platform the Media Gallery for generation of Medical article drafts
Partnerships and Education

–       Collaborations: IMI Big Picture for 3M – sample disease database

–       AI in Pharma AIPM Symposium: Drug discovery and Precision Medicine

–       Webinars of AI for biomedical data integration

–       Webinar on Ai in Manufacturing

Strategic Focus:

–       $500M R&D reinvestment by 2026 targets AI for Productivity

–       Part of $7.7B cost savings

–       Ethical AI, diverse DBs

–       Global biotech advances: China’s AI in CRISPR

@@@@@@

AI Initiative at Big Pharma

i.e., Pfizer

LPBI Group’s Digital IP Asset:

Library of Audio and Video Podcasts

N = +300

Generative AI tools that save scientists up to 16,000 hours annually in literature searches and data analysis.
Drug Discovery and Development Acceleration Pfizer uses AI, supercomputing, and ML to streamline R&D timelines Review ALL SCIENTIFIC BREAKTHROUGHS

  • Two criteria for Classifications used by Prof. Marcus W. Feldman and by Dr. Stephen J. Williams to generate the two classifications

https://pharmaceuticalintelligence.com/biomed-audio-podcast-library-lpbi-group/

Clinical Trials and Regulatory Efficiency AI:

-Predictive Regulatory Tools

-Decentralize Trials

-inventory management

Disease Detection and Diagnostics:

–       ATTR-CM Initiative

–       Rare diseases

Aviva Lev-Ari, PhD, RN, Stephen J. Williams, PhD and Prof. Marcus W. Feldman Health Care Policy Analysis derived from the Farewell remarks from AMA President Jack Resneck Jr., MD | AMA 2023 Annual Meeting

LISTEN to Audio Podcast

Future of Medicine

https://pharmaceuticalintelligence.com/2023/06/10/health-care-policy-analysis-derived-from-the-farewell-remarks-from-ama-president-jack-resneck-jr-md-ama-2023-annual-meeting/

Generative AI and Operational Tools:

–       Charlie Platform

–       Scientific Data Cloud AWS powered ML on centralized data

–       Amazon’s SageMaker/Bedrock for Manufacturing efficiency

–       Global Health Grants:

Pfizer Foundation’s AI Learning Lab for equitable  access to care and tools for community care

  • Ingest to Charlie Platform all +300 Podcasts for Foundation’s AI Learning Lab
Partnerships and Education

–       Collaborations: IMI Big Picture for 3M – sample disease database

–       AI in Pharma AIPM Symposium: Drug discovery and Precision Medicine

–       Webinars of AI for biomedical data integration

–       Webinard on Ai in Manufacturing

  • Use Podcast for Education
  • Use Podcast as Hybrid: Start presentation with a Podcast continue with a life interview

Examples of an Audio Podcast of Scientists on LPBI Group Team in the past:

  • Podcast with Dr. Larry H. Bernstein, MD, FCAP, Interview by Gail S. Thornton, PhDc, Narrator’s Voice: Stephen J. Williams, PhD

https://pharmaceuticalintelligence.com/audio-podcasts/podcast-with-dr-larry-h-bernstein-md-fcap-interview-by-gail-s-thornton-phdc-narrators-voice-stephen-j-williams-phd/

  • Podcast with Prof. Marcus W. Feldman, PhD, Biology Department, Stanford University, Interview by Gail S. Thornton, PhDc

https://pharmaceuticalintelligence.com/audio-podcasts/podcast-with-prof-marcus-w-feldman-phd-biology-department-stanford-university-interview-by-gail-s-thornton-phdc/

  • Podcast with Dr. Sudipta Saha, PhD, Interview by Gail S. Thornton, PhDc, Narrator’s Voice: Gail S. Thornton, PhDc

https://pharmaceuticalintelligence.com/audio-podcasts/podcast-with-dr-sudipta-saha-phd-interview-by-gail-s-thornton-phdc-narrators-voice-gail-s-thornton-phdc/

Strategic Focus:

–       $500M R&D reinvestment by 2026 targets AI for Productivity

–       Part of $7.7B cost savings

–       Ethical AI, diverse DBs

–       Global biotech advances: China’s AI in CRISPR

Dr. Lev-Ari Prompted @Grok on 11/18/2025:

AI-Driven Cost Savings in Big Pharma   

@Grok responded:

AI-Driven Cost Savings in Big PharmaArtificial intelligence (AI) applications across the pharmaceutical value chain—particularly in drug discovery, clinical trials, and operations—have the potential to generate substantial savings for major pharmaceutical companies (often referred to as “Big Pharma”). Based on recent industry reports and analyses from 2024-2025, these savings vary by application but could collectively reach tens of billions annually by the late 2020s. Projections indicate AI could add up to 11% in value relative to revenue for biopharma firms over the next five years through productivity gains and cost reductions. Below, I break down the estimated savings levels by key areas, drawing from credible sources like McKinsey, Deloitte, IQVIA, and others.

  1. Clinical Trials

  • Annual Industry-Wide Savings: By 2030, AI integration into 60-70% of clinical trials could save the pharmaceutical industry $20-30 billion per year through faster timelines, better patient matching, and reduced administrative costs.
  • Per-Trial Cost Reduction: AI can cut trial costs by up to 70% and shorten durations by 80%, enabling quicker regulatory submissions (40% faster) with 50% improved cost efficiency. For example, AstraZeneca reported up to 25% shorter trial durations in cancer drug studies using AI for dose optimization and biomarker identification.
  • Specific Efficiency Gains: Feasibility surveys can see 90% time reductions using AI/ML tools.
  1. Drug Discovery and Development

  • R&D Cost Drop: AI could reduce drug discovery costs by up to 40%, with overall development timelines shrinking from 5 years to 12-18 months (an 80% cut in some cases). From discovery to preclinical candidate stage, timelines can decrease by up to 50%.
  • Total Clinical Development Savings: Projected at $25 billion across the sector, driven by AI-accelerated pipelines.
  1. Operations and Broader Impacts

  • Value Relative to Revenue: Biopharma AI investments may yield up to 11% additional value (e.g., via cost efficiencies and revenue growth) over five years. For related medtech segments, savings could hit 12% of total revenue within 2-3 years.
  • Operating Profits Boost: By 2030, AI could add $254 billion in annual operating profits industry-wide through productivity jumps (e.g., 50-100% in quality control) and lead time reductions (60-70%).
  • Time-to-Market: Up to 10% faster overall, with production KPIs improving revenue by 25%.

These estimates assume scaled adoption, with global AI spending in pharma rising from ~$3 billion in 2025 to $22-25 billion by 2027-2030. Challenges like high initial costs and data infrastructure may temper short-term gains, but early adopters (e.g., Pfizer, Novartis) are already seeing ROI. For context, the global pharma market is projected at $1.6 trillion by 2025, so even modest percentages translate to billions in savings. If you need details on a specific AI use case or company, let me know!

SOURCE

https://x.com/i/grok?conversation=1990851703051104519

 

Dr. Lev-Ari Prompted @Grok on 11/17/2025:

Pfizer, its competitors by size, market share, product lines and Investment in AI technologies

Grok responded

https://x.com/i/grok?conversation=1990458795936354506

Overview of Pfizer and Key CompetitorsPfizer is one of the world’s largest pharmaceutical companies, with a strong focus on innovative medicines and vaccines. Its primary competitors include Merck & Co., Johnson & Johnson (J&J), Roche, Novartis, and now AstraZeneca, based on revenue leadership and market overlap in areas like oncology, immunology, and vaccines. These companies dominate the global pharmaceutical industry, which is projected to reach $1.21 trillion in revenue by 2025. Below, I compare them across size (measured by 2024 revenue and employees), market share (approximate global pharma share based on 2024 revenues), product lines (key therapeutic areas and top products), and investments in AI technologies. Data reflects the latest available figures as of late 2025.
Here are the same comparisons with more concise tables (2024 data, latest available as of Nov 2025):
Size (2024 Revenue & Employees)
Company
Revenue (USD B)
Employees
Merck & Co.
64.2
70,000
Pfizer
63.6
88,000
Roche
~58.3
103,000
J&J (pharma only)
57.8
138,000
AstraZeneca
54.1
94,300
Novartis
~50.0
76,000
Approx. Global Pharma Market Share
Company
Share %
Merck & Co.
4.3
Pfizer
4.2
J&J / Roche
3.9
AstraZeneca
3.6
Novartis
3.3
Key Product Lines & Top Sellers (2024 revenue, USD B)
Company
Main Areas
Top Products (revenue)
Pfizer
Vaccines, cardiology, oncology
Eliquis (7.3), Prevnar (6.4), Vyndaqel (5.4)
Merck & Co.
Oncology, vaccines
Keytruda (25.0), Gardasil (8.6)
J&J
Immunology, oncology
Stelara (10.9), Darzalex (9.7)
AstraZeneca
Oncology, CVRM, respiratory
Farxiga (7.7), Tagrisso (6.6), Enhertu (4.0)
Roche
Oncology, neurology, hemophilia
Ocrevus (5.7), Hemlibra (4.0)
Novartis
Cardiology, immunology
Entresto (6.6), Cosentyx (5.2)

AI Investment Snapshot (2025)
Company
AI Highlights (2025)
Scale/Impact
Pfizer
AI cuts discovery from years → 30 days; heavy partnerships
Leader in adoption
AstraZeneca
Evinova AI trials unit; $2.5B AI Beijing hub; 12k+ staff upskilled
Very aggressive (>85% productivity gain)
Merck & Co.
Gen-AI for protocols; 20+ AI “blockbusters” in pipeline
>$1.2B spend
J&J
900+ AI projects → $500M savings; surgical AI training
Broad internal rollout
Roche
AI diagnostics + drug discovery; $55M Manifold Bio deal
Strong in diagnostics
Novartis
AI pipeline acceleration; data-science alliances
Integrated into $10B R&D
Dr. Lev-Ari’s Prompt:
  • AI in biotech startups
Searched for “(“AI” OR “artificial intelligence”) (“biotech” OR “biotechnology”) startup since:2025-01-01″
10 results
Show All (2)

AI in Biotech Startups:

2025 LandscapeArtificial Intelligence (AI) is revolutionizing biotech startups by accelerating drug discovery, optimizing clinical trials, and enabling personalized medicine. In 2025, AI applications like generative models for molecule design and predictive analytics for protein structures are slashing R&D timelines from years to months, reducing costs by up to 30%, and boosting success rates. The sector blends biology’s complexity with AI’s data-crunching power, drawing massive VC interest amid ethical debates on gene editing and biosecurity.Key Trends

  • Explosive Funding Growth: U.S. healthcare VC hit $23B in 2024, with ~30% ($5.6B) targeting AI-biotech—nearly triple 2023 levels. Biopharma startups raised $24.2B across 568 deals, up from $10.1B in 2023. Q3 2025 saw $97B global VC (up 38% YoY), half to AI firms. Mega-rounds ($100M+) surged, focusing on drug discovery and rare diseases.
  • Market Expansion: Global AI-biotech market: $4.6B in 2025, projected to $11.4B by 2030 (20% CAGR). Biotech overall to $5.85T by 2034 (13.6% CAGR), driven by AI in gene editing, microbiome therapeutics, and automation.
  • Compute Demands: Biotech AI requires massive GPUs; Nvidia’s AI sales hit $41.1B in one 2025 quarter (56% YoY). Startups lean on cloud partnerships (e.g., AWS-Recursion) or in-house clusters, with hyperscalers eyeing $3-4T infrastructure by 2030.
  • Regional Hotspots: North America leads (42% share) via FDA support and hubs like Boston/SF; Europe grows via funding/regulatory advances; Asia (e.g., China) via collaborations.
  • Challenges & Ethics: Selective funding favors clinically validated firms; rising M&A (big pharma acquiring AI startups); ethical scrutiny on AI gene editing (e.g., CRISPR enhancements).

 

Notable Startups & Recent Funding

Here’s a snapshot of standout AI-biotech startups, highlighting innovations and 2024-2025 funding:

Startup
Focus Area
Key Innovation
Recent Funding (2025)
Insilico Medicine
Drug Discovery
Generative AI for novel molecules
$100M+ Series D (ongoing)
Recursion Pharmaceuticals
Phenomics & Drug Repurposing
AI mapping diseases via cell images
$50M partnership w/ Nvidia
Absci Corp.
Protein Design
AI-generated antibodies/proteins
$20M from AMD (Jan 2025)
TandemAI
Drug Discovery
ML for molecular simulation
$22M Series A extension
Red Queen Bio
Biosecurity
AI for pathogen detection/design
$15M Seed led by OpenAI
Antiverse
Antibody Design
AI predicting antibody structures
Deal w/ Nxera Pharma (2024)
Deep Genomics
Genomics
AI extracting insights from DNA data
VC round undisclosed
Aizen Therapeutics
Molecule Generation
Proprietary AI engines for trials
Early-stage VC

These firms exemplify AI’s shift from hype to pipeline impact—e.g., Insilico’s AI-discovered drug entered Phase II trials in record time.Emerging ApplicationsAI’s top uses in biotech startups:

  1. Drug Discovery: ML predicts drug-target interactions (e.g., AlphaFold-inspired tools cut screening costs 70%).
  2. Genomics & Diagnostics: AI analyzes vast datasets for rare variants, powering precision oncology.
  3. Clinical Trials: Predictive models optimize patient matching, reducing failures by 20-30%.
  4. Synthetic Biology: AI designs custom microbes for therapeutics or biofuels.
  5. Automation Labs: AI-robotics handle experiments autonomously, boosting throughput 10x.

Future Outlook

2025 signals a “quality over quantity” pivot: Investors prioritize AI startups with real-world data and partnerships (e.g., Y Combinator, Google for Startups). M&A will rise as big pharma (Pfizer, Merck) snaps up talent. Yet, compute shortages and regs (e.g., FDA AI guidelines) pose hurdles. For founders, blending AI with wet-lab validation is key to unlocking the next wave of breakthroughs—potentially curing diseases once deemed untreatable. If you’re building or investing, focus on
  • rare diseases or
  • oncology

for the hottest bets.

Additional Competitors by Product Line

@Grok Response

https://x.com/i/grok/share/Ple3W4IDlwhyjUwBUU4JAg2OD

Key Products and Focus AreasPfizer’s portfolio spans immunology, oncology, cardiology, endocrinology, neurology, and vaccines. In 2024, its top revenue generators included:

  • Eliquis (apixaban, blood thinner): $7.3 billion (11% of total revenue).
  • Prevnar family (pneumococcal vaccines): $6.4 billion (10%).
  • Paxlovid (COVID-19 antiviral): $5.7 billion (9%).
  • Vyndaqel (tafamidis, for rare heart disease): $5.4 billion (8%).
  • Comirnaty (COVID-19 vaccine): $5.3 billion (8%).
  • Ibrance (palbociclib, breast cancer drug): $4.3 billion (6%).

The company is investing heavily in AI-driven drug discovery (e.g., 2024 partnerships with NVIDIA and Saama) and next-gen therapies like RSV vaccines, gene therapies for muscular dystrophy, and oral GLP-1 drugs for obesity/diabetes. Challenges include patent expirations (e.g., Eliquis in 2026-2028) and biosimilar competition, but Pfizer’s diversified pipeline positions it for mid-single-digit growth in 2025.Pfizer’s Main CompetitorsPfizer operates in a highly competitive $1.5 trillion global pharma market, where rivals vie for dominance in oncology, vaccines, immunology, and emerging areas like obesity and gene therapy. Its primary competitors are fellow “Big Pharma” giants, often overlapping in therapeutic areas. Based on revenue, market share, and direct product rivalries, here are the top ones (ranked roughly by 2024 revenue for context):

Competitor
Headquarters
2024 Revenue (Pharma Segment)
Key Strengths & Overlaps with Pfizer
Notable Products
Johnson & Johnson (J&J)
New Brunswick, NJ, USA
$88.8 billion (total; pharma ~$57.8 billion)
Diversified (pharma, devices, consumer); strong in oncology, immunology, vaccines. Competes directly in blood thinners and cancer therapies.
Darzalex (multiple myeloma), Stelara (psoriasis), Imbruvica (blood cancer).
Merck & Co.
Rahway, NJ, USA
$64.2 billion
Oncology leader; vaccines and antivirals. Keytruda outsells Pfizer’s Ibrance; rivals in HPV/pneumococcal vaccines.
Keytruda (immunotherapy, $29.5 billion), Gardasil (HPV vaccine).
Roche Holding AG
Basel, Switzerland
~$68 billion (group; pharma ~$50 billion)
Diagnostics + pharma powerhouse; dominates oncology and neurology. Competes in antibody-drug conjugates post-Pfizer’s Seagen buy.
Ocrevus (MS), Hemlibra (hemophilia), Avastin (cancer).
AbbVie Inc.
North Chicago, IL, USA
$56.3 billion
Immunology and neuroscience focus; biosimilars erode shared markets like Humira vs. Pfizer’s Enbrel alternatives.
Humira (rheumatoid arthritis), Skyrizi (psoriasis), Rinvoq (arthritis).
Novo Nordisk A/S
Bagsværd, Denmark
~$40 billion (est.)
Diabetes/obesity specialist; exploding GLP-1 demand challenges Pfizer’s emerging obesity pipeline.
Ozempic/Wegovy (semaglutide for diabetes/weight loss).
Eli Lilly and Co.
Indianapolis, IN, USA
~$45 billion (est.; projecting $58-61 billion in 2025)
Diabetes/obesity and neurology; Mounjaro rivals Pfizer’s danuglipron in GLP-1 space.
Mounjaro/Zepbound (tirzepatide), Verzenio (breast cancer).
AstraZeneca PLC
Cambridge, UK
$50.95 billion
Oncology, respiratory, and cardiovascular; Tagrisso competes with Pfizer’s Lorbrena in lung cancer.
Tagrisso (lung cancer), Farxiga (diabetes/heart), Imfinzi (immunotherapy).
Novartis AG
Basel, Switzerland
~$48 billion
Gene therapy and immunology; rivals in rare diseases and oncology.
Cosentyx (psoriasis), Entresto (heart failure), Kisqali (breast cancer).
Bristol-Myers Squibb (BMS)
New York, NY, USA
$47.8 billion
Oncology and immunology; Opdivo directly competes with Pfizer’s Bavencio in checkpoint inhibitors.
Opdivo (immunotherapy), Eliquis (co-developed with Pfizer, but BMS handles ex-US).
Sanofi S.A.
Paris, France
~$46 billion
Vaccines and rare diseases; Dupixent challenges in immunology; rivals Prevnar in pneumococcal vaccines.
Dupixent (atopic dermatitis), Lantus (diabetes).

These competitors collectively hold over 50% of the global pharma market share. Emerging threats include biotech upstarts like Moderna (mRNA vaccines, directly rivaling Comirnaty) and generics firms like Teva (eroding post-patent revenues). In 2025, competition intensifies in obesity (Novo/Lilly lead) and oncology (Merck/Roche dominate), with tariffs and pricing pressures (e.g., US executive orders) affecting all.Pfizer’s edge comes from its scale and partnerships (e.g., BioNTech for mRNA), but it must navigate revenue dips from COVID fade-out and biosimilars. For 2025 projections, analysts expect 6-9% growth across the sector, with Pfizer targeting modest gains through oncology expansions. If you’d like deeper dives on specific rivals, financials, or products, let me know!

AI Acquisitions by Big Pharma

2 days ago • Visible to anyone on or off LinkedIn

AI in Pharma: From Tool to Value Creator 🚀

Over the past 5 years, pharma’s AI footprint has expanded rapidly and the investment trends tell a clear story.

💡 ~60% of collaborations and acquisitions now focus on TargetDiscovery and Validation — pharma’s main frontier to shorten early-stage R&D timelines and boost success rates through PrecisionBiology.
⚗️ The second-largest area (~25%) centers on AI-driven DrugDesign and MoleculeOptimization, where algorithms accelerate CandidateSelection, refine molecular properties, and enable NewModalities such as Biologics and CellAndGeneTherapies.
🏆 Among top players, Eli Lilly and Company stands out as the most active investor — making AI a true StrategicCapability, not just another research tool.

The takeaway?
AI isn’t just supporting pharma anymore, it’s reshaping it.

Source: Bita Sehat, PhD, MBA

hashtagai hashtaglifesciences hashtagpharmaceuticals hashtagtechbio hashtagbiotech

table

Article was summarized by @Grok on 11/29/2025
Summary of the Article:
“Authentic Relevance of LPBI Group’s Portfolio of IP as Proprietary Training Data Corpus for AI Initiatives at Big Pharma”
This November 15, 2025, article on PharmaceuticalIntelligence.com (curated by LPBI Group) makes a compelling case for leveraging LPBI’s decade-plus of expert-curated digital IP as a high-fidelity, rights-clean training corpus to supercharge AI-driven innovation in Big Pharma. It contrasts the limitations of generic LLMs (like GPT) with the need for domain-specific, ontologized biomedical data, positioning LPBI’s assets as a “defensible moat” for accelerating R&D in drug discovery, precision medicine, and beyond. The piece blends market analysis of pharma giants with a deep dive into LPBI’s portfolio, emphasizing its multimodal, metadata-rich structure for NLP, knowledge graphs, and fine-tuning SLMs/LLMs.IntroductionThe thesis: In an era where AI investments in pharma (e.g., Eli Lilly’s aggressive funding) focus on slashing R&D timelines by 60%+ in target discovery and 25% in drug design, LPBI’s proprietary corpus—built since 2012 via human curation, digitization, and ontology mapping—offers unmatched authenticity over web-scraped data. It addresses GPT’s biomedical shortcomings (e.g., failing to infer fusion proteins or noncanonical pathways without curated inputs) and highlights LPBI’s foresight in text analysis for generative AI augmentation. A key quote from Data2Discovery: “We are able to improve drug discovery now as well as demonstrating new fast-cycle AI-driven processes that will have a revolutionary impact on drug discovery if fully implemented.”Portfolio OverviewLPBI’s ~9 GB, debt-free, multimodal corpus is privately held, expert-curated (e.g., by Prof. Marcus W. Feldman and Dr. Stephen J. Williams), and ingest-ready for AI pre-training/evaluations. It spans five key asset classes, each with metadata exports, timestamps, crosslinks, and centralized rights for model training:

 

Asset Class
Description & Size
Unique Value Proposition
I: Scientific Articles
6,250+ articles on PharmaceuticalIntelligence.com (~2.5M views); covers genomics, oncology, immunology, etc.
Live ontology, author/role labels, view histories; enables temporal NLP for trend analysis.
II: e-Books
48 bilingual (English/Spanish) volumes in 5 BioMed e-Series (e.g., Series A: Cardiovascular, 6 vols., $515 total; Series E: Patient-Centered, 4 vols., $274); 151,000+ page downloads; 2,728 articles.
Peer-reviewed, senior-editor TOCs; pay-per-view model proves demand; ideal for entity-relationship extraction.
III: e-Proceedings
100+ from biotech/genomics conferences (2013–2025); +50 tweet collections as speaker quotes with affiliations.
Real-time event curation; captures emerging insights for knowledge graph augmentation.
V: Biological Images
7,500+ images in Digital Art Media Gallery; embedded as prior art in texts.
Expert-contextualized visuals; supports multimodal AI for image-text pairing in diagnostics.
X: Audio Podcasts
300+ interviews with scientific leaders (e.g., Nobel laureates like Jennifer Doudna); classified by themes like CRISPR, mRNA vaccines.
Transcripts + NLP WordClouds; adds auditory/verbal depth for voice-enabled AI copilots.

The portfolio’s “living ontology” allows seamless integration into tools like InfraNodus for concept mapping.AI Training RelevanceUnlike PubMed’s unstructured dumps, LPBI’s assets are pre-annotated for concept extraction (e.g., gene-disease-drug dyads), reducing hallucinations and bias in LLMs. A case study integrates curation with ChatGPT-5: Manual ontology + knowledge graphs uncovered novel WNT/Hedgehog interactions in lung cancer, generating research questions like: “How does the interaction between [[EGFR]] mutations and sex-specific gene alterations, including [[RBM10]], influence treatment outcomes in lung adenocarcinoma?” This hybrid approach outperforms solo GPT, proving the corpus’s role in trustworthy biomedical inference.Applications

  • Drug Discovery: ML prompts on dyads to mimic Pfizer’s AI (e.g., reducing discovery from years to months); supports biologics/cell therapies.
  • Precision Medicine: 547 articles for patient subtyping; 3,615 disease-focused pieces for predictive modeling.
  • Diagnostics & Rare Diseases: 560 rare disease articles + 30 on ATTR-CM for early detection (e.g., via Pfizer’s ASPIRE AI).
  • Clinical/Regulatory: Streamlines trials, evidence synthesis, and content generation (e.g., via Pfizer’s “Charlie” copilot, saving hours on lit reviews).
  • Generative Tools: Fine-tune for compliant, domain-aware outputs in medical affairs/safety.

Challenges & Solutions

  • Data Quality/Bias: Unstructured text leads to GPT errors; solved by expert curation + ontology for accurate, diverse inputs.
  • Regulatory Compliance: Rights fragmentation; addressed via LPBI’s centralized assignment for NDA-secure licensing.
  • Scalability: Generic data overload; LPBI’s focused, high-signal corpus enables fast-cycle AI without noise.

Recommendations

Urge Big Pharma (e.g., Pfizer, Merck—table highlights Merck’s $64.2B revenue, Keytruda focus) to acquire the full portfolio for end-to-end knowledge bases, or license under NDA for SLM/LLM training (English/Spanish).
  • Emphasizes “buy the moat” for competitive edge in 2025’s 6–9% sector growth (obesity/oncology hotspots).
Contact: avivalev-ari@alum.berkeley.edu.
Conclusion
LPBI’s corpus isn’t just data—it’s a “scientific revolution enabler,” blending human creativity with AI for transformative pharma impact. Validated on extraction tasks, it’s primed for partnerships, outshining combinatorial predictions with authentic, curated depth. This article builds on prior LPBI mappings (e.g., our podcast TOC summary), reinforcing the portfolio’s strategic fit for AI.
For deeper analysis or related assets, let me know!

Read Full Post »

Real Time Coverage Advancing Precision Medicine Annual Conference, Philadelphia PA November 1,2 2024

Reporter: Stephen J. Williams, Ph.D.

Source: https://www.advancingprecisionmedicine.com/apm-annual-conference-and-exhibition-in-philadelphia/ 

This event will be covered by the LPBI Group on Twitter.  Follow on

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The Advancing Precision Medicine (APM) Annual Conference 2024 will take place at the Pennsylvania Convention Center in Philadelphia,  November 1-2, 2024. Located in the heart of the biopharma ecosystem and with easy access to some of the most renowned academic and research institutions in the world, the APM Annual Conference 2024 will attract all segments of the precision medicine landscape.

The event will consist of two parallel tracks composed of keynote addresses, panel discussions and fireside chats which will encourage audience participation. Over the course of the two-day event leaders from industry, healthcare, regulatory bodies, academia and other pertinent stakeholders will share an intriguing and broad scope of content.

his event will consist of three immersive tracks, each crafted to explore the multifaceted dimensions of precision medicine. Delve into Precision Oncology, where groundbreaking advancements are reshaping the landscape of cancer diagnosis and treatment. Traverse the boundaries of Precision Medicine Outside of Oncology, as we probe into the intricate interplay of genetics, lifestyle, and environment across a spectrum of diseases and conditions including rare disease, cardiology, ophthalmology, and neurodegenerative disease. Immerse yourself in AI for Precision Medicine, where cutting-edge technologies are revolutionizing diagnostics, therapeutics, and patient care. Additionally, explore the emerging frontiers of Spatial Biology and Mult-Omics, where integrated approaches are unraveling the complexities of biological systems with unprecedented depth and precision.

Whether you are a seasoned researcher, a dedicated clinician, or a visionary industry professional, this conference serves as a vibrant hub of knowledge exchange, collaboration, and innovation. Elevate your expertise, expand your network, and chart the course of your career trajectory amidst a community of like-minded individuals.  Join us as we embark on this transformative journey, where the possibilities are as limitless as the potential of precision medicine itself.

Agenda – What’s on when

7:30 – 8:25

Registration and Check-in          Meeting Room 203          Philadelphia Convention Center

8:25 – 8:30

Welcome and Introduction

8:30 – 9:00

Opening Keynote

Advancing Precision Medicine in the Prevention and Treatment of Cardiometabolic Disease (CME Eligible)

Daniel Rader

Daniel Rader, Penn Medicine and Children’s Hospital of Philadelphia

9:00 – 10:20

9:00-10:20

Diagnosis to Treatment – A Case Study in Non Small Cell Lung Cancer

Jason Crites

Moderator: Jason Crites, Assurance Health Data

Miriam Bredella, NYU Lagone Health

Robert Dumanois

Rob Dumanois, Thermo Fisher Scientific

Joe Lennerz

Joe Lennerz, BostonGene

10:20 – 10:50

Networking, Exhibits and Product Presentations

10:25-10:35  PRODUCT PRESENTATION  204C

The Genexus Integrated Sequencer System:
NGS Results in 24 hours for Oncology Genomic Profiling

Jeff Smith,  Thermo Fisher Scientific

10:35-10:45  PRODUCT PRESENTATION  204A

Shifting the Paradigm in Patient Management with MRD Testing: Why Evidence-Generated Performance and Experience is Key

Karen Lin, Natera

10:50 – 12:50

10:50-11:50

Who Needs Liquid Biopsy? Opportunities to Increase Access and Improve Outcomes

Nicole St. Jean, GSK

Phil Febbo,  Veracyte, Inc.

Andrea Ferreira-Gonzalez, Virginia Commonwealth University

Lauren Leiman, BloodPAC

Nicole Sheahan, Global Colon Cancer Association

11:50-12:50

Advancing Digital Pathology and Precision Medicine – Where Are We Now?

Shruti Mathur, Genentech

Luke Benko, Roche Diagnostics

Kimberly GasuadJK Life Sciences

Eric Walk, PathAI

10:50-11:10

Real World Data vs Multi Modal Omics Data for Therapeutic Discovery (CME Eligible)

Adam Resnick, CHOP

11:10-11:30

An Academic Perspective on Rare Disease Target Discovery to Commercial Treatment Development (CME Eligible)

Hakon Hakonarson

Hakon Hakonarson, CHOP

11:30-11:50

NCATS Perspective on Success and Failures of Drug Repurposing for Rare Disease (CME Eligible)

PJ Brooks, NIH

11:50-12:10

Pharma Perspective and Realities (CME Eligible)

Sundeep Dugar, Rarefy Therapeutics

12:10-12:50

A Panel Discussion: Scaling Precision Therapeutic Development for Rare Disease (CME Eligible)

Marni Falk

Marni Falk, CHOP

Stephen Ekker, University of Texas at Austin

Christine Nguyen, FDA

Frank Sasinowski, Hyman, Phelps & McNamara

Adam Resnick, CHOP

Hakon Hakonarson

Hakon Hakonarson, CHOP

Sundeep Dugar, Rarefy Therapeutics

PJ Brooks, NIH

12:50 – 1:50

Lunch & Product Presentations

1:10-1:25  PRODUCT PRESENTATION  204C

The Power of ctDNA Testing in Therapy Selection and Recurrence Monitoring

Taylor Jensen,  LabCorp

1:50 – 3:50

1:50-3:50

Unlocking the Next Quantum Leap in Precision Medicine – A Town Hall Discussion (CME Eligible)

Co-Chairs

Amanda Paulovich

Amanda Paulovich, Fred Hutchinson Cancer Center

Henry Rodriguez

Henry Rodriguez, NCI/NIH

Eric Schadt

Eric Schadt, Pathos

Participants

Ezra Cohen, Tempus

Jennifer Leib, Innovation Policy Solutions

Susan Monarez, ARPA-H

Nick Seddon, Optum Genomics 

Giselle Sholler, Penn State Hershey Children’s Hospital

Janet Woodcock

Janet Woodcock, Former FDA

1:50-2:50

Advancing Precision Medicine in Non-Oncology Therapeutic Areas

Moderator: Mike Montalto, Amgen

Scott Friedman, Mt. Sinai

Sana Syed, University of Virginia

Lei Zhao, Amgen

2:50-3:20

Towards a Precision Neuroimmunology Platform (CME Eligible)

Amit Bar-Or, Penn Medicine

3:20-3:50

3:50 – 4:20

Networking and Exhibits

4:20 – 6:15

4:20-4:45

Advancing Precision Medicine: Polygenic Risk Scores and Beyond (CME Eligible)

Dokyoon Kim, Penn Medicine

4:45-5:30

The Rocky Road to Clinical Trial Diversity (CME Eligible)

Ysabel Duron, The Latino Cancer Institute

Porscha Johnson, PJW Clinical Pharmacy Consulting

Victor LaGroon, Department of Veterans Affairs

5:30-6:15

In the Rising Age of Women’s Health, How Do We Build Diagnostics to Last?

Oriana Papin Zoghbi, AOADx

Sarah Huah, Johnson & Johnson

6:30 – 7:00

Evening Keynote

Reimagining Health Equity in the Era of Precision Medicine (CME Eligible)

Rick Kittles

Rick Kittles, Morehouse School of Medicine

7:00 – 7:45

Cocktail Networking Reception 

November 02, 2024

8:00-8:55

Registration and Check-in          Meeting Room 203          Philadelphia Convention Center

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Data Science: Step by Step – A Resource for LPBI Group One-Year Internship in IT, IS, DS

Reporter: Aviva Lev-Ari, PhD, RN

9 free Harvard courses: learning Data Science

In this article, I will list 9 free Harvard courses that you can take to learn data science from scratch. Feel free to skip any of these courses if you already possess knowledge of that subject.

Step 1: Programming

The first step you should take when learning data science is to learn to code. You can choose to do this with your choice of programming language?—?ideally Python or R.

If you’d like to learn R, Harvard offers an introductory R course created specifically for data science learners, called Data Science: R Basics.

This program will take you through R concepts like variables, data types, vector arithmetic, and indexing. You will also learn to wrangle data with libraries like dplyr and create plots to visualize data.

If you prefer Python, you can choose to take CS50’s Introduction to Programming with Python offered for free by Harvard. In this course, you will learn concepts like functions, arguments, variables, data types, conditional statements, loops, objects, methods, and more.

Both programs above are self-paced. However, the Python course is more detailed than the R program, and requires a longer time commitment to complete. Also, the rest of the courses in this roadmap are taught in R, so it might be worth learning R to be able to follow along easily.

Step 2: Data Visualization

Visualization is one of the most powerful techniques with which you can translate your findings in data to another person.

With Harvard’s Data Visualization program, you will learn to build visualizations using the ggplot2 library in R, along with the principles of communicating data-driven insights.

Step 3: Probability

In this course, you will learn essential probability concepts that are fundamental to conducting statistical tests on data. The topics taught include random variables, independence, Monte Carlo simulations, expected values, standard errors, and the Central Limit Theorem.

The concepts above will be introduced with the help of a case study, which means that you will be able to apply everything you learned to an actual real-world dataset.

Step 4: Statistics

After learning probability, you can take this course to learn the fundamentals of statistical inference and modelling.
This program will teach you to define population estimates and margin of errors, introduce you to Bayesian statistics, and provide you with the fundamentals of predictive modeling.

Step 5: Productivity Tools (Optional)

I’ve included this project management course as optional since it isn’t directly related to learning data science. Rather, you will be taught to use Unix/Linux for file management, Github, version control, and creating reports in R.

The ability to do the above will save you a lot of time and help you better manage end-to-end data science projects.

Step 6: Data Pre-Processing

The next course in this list is called Data Wrangling, and will teach you to prepare data and convert it into a format that is easily digestible by machine learning models.

You will learn to import data into R, tidy data, process string data, parse HTML, work with date-time objects, and mine text.

As a data scientist, you often need to extract data that is publicly available on the Internet in the form of a PDF document, HTML webpage, or a Tweet. You will not always be presented with clean, formatted data in a CSV file or Excel sheet.

By the end of this course, you will learn to wrangle and clean data to come up with critical insights from it.

Step 7: Linear Regression

Linear regression is a machine learning technique that is used to model a linear relationship between two or more variables. It can also be used to identify and adjust the effect of confounding variables.

This course will teach you the theory behind linear regression models, how to examine the relationship between two variables, and how confounding variables can be detected and removed before building a machine learning algorithm.

Step 8: Machine Learning

Finally, the course you’ve probably been waiting for! Harvard’s machine learning program will teach you the basics of machine learning, techniques to mitigate overfitting, supervised and unsupervised modelling approaches, and recommendation systems.

Step 9: Capstone Project

After completing all the above courses, you can take Harvard’s data science capstone project, where your skills in data visualization, probability, statistics, data wrangling, data organization, regression, and machine learning will be assessed.

With this final project, you will get the opportunity to put together all the knowledge learnt from the above courses and gain the ability to complete a hands-on data science project from scratch.

Note: All the courses above are available on an online learning platform from edX and can be audited for free. If you want a course certificate, however, you will have to pay for one.

Building a data science learning roadmap with free courses offered by MIT.

8 Free MIT Courses to Learn Data Science Online

 enrolled into an undergraduate computer science program and decided to major in data science. I spent over $25K in tuition fees over the span of three years, only to graduate and realize that I wasn’t equipped with the skills necessary to land a job in the field.

I barely knew how to code, and was unclear about the most basic machine learning concepts.

I took some time out to try and learn data science myself — with the help of YouTube videos, online courses, and tutorials. I realized that all of this knowledge was publicly available on the Internet and could be accessed for free.

It came as a surprise that even Ivy League universities started making many of their courses accessible to students worldwide, for little to no charge. This meant that people like me could learn these skills from some of the best institutions in the world, instead of spending thousands of dollars on a subpar degree program.

In this article, I will provide you with a data science roadmap I created using only freely available MIT online courses.

Step 1: Learn to code

I highly recommend learning a programming language before going deep into the math and theory behind data science models. Once you learn to code, you will be able to work with real-world datasets and get a feel of how predictive algorithms function.

MIT Open Courseware offers a beginner-friendly Python program for beginners, called Introduction to Computer Science and Programming.

This course is designed to help people with no prior coding experience to write programs to tackle useful problems.

Step 2: Statistics

Statistics is at the core of every data science workflow — it is required when building a predictive model, analyzing trends in large amounts of data, or selecting useful features to feed into your model.

MIT Open Courseware offers a beginner-friendly course called Introduction to Probability and Statistics. After taking this course, you will learn the basic principles of statistical inference and probability. Some concepts covered include conditional probability, Bayes theorem, covariance, central limit theorem, resampling, and linear regression.

This course will also walk you through statistical analysis using the R programming language, which is useful as it adds on to your tool stack as a data scientist.

Another useful program offered by MIT for free is called Statistical Thinking and Data Analysis. This is another elementary course in the subject that will take you through different data analysis techniques in Excel, R, and Matlab.

You will learn about data collection, analysis, different types of sampling distributions, statistical inference, linear regression, multiple linear regression, and nonparametric statistical methods.

Step 3: Foundational Math Skills

Calculus and linear algebra are two other branches of math that are used in the field of machine learning. Taking a course or two in these subjects will give you a different perspective of how predictive models function, and the working behind the underlying algorithm.

To learn calculus, you can take Single Variable Calculus offered by MIT for free, followed by Multivariable Calculus.

Then, you can take this Linear Algebra class by Prof. Gilbert Strang to get a strong grasp of the subject.

All of the above courses are offered by MIT Open Courseware, and are paired with lecture notes, problem sets, exam questions, and solutions.

Step 4: Machine Learning

Finally, you can use the knowledge gained in the courses above to take MIT’s Introduction to Machine Learning course. This program will walk you through the implementation of predictive models in Python.

The core focus of this course is in supervised and reinforcement learning problems, and you will be taught concepts such as generalization and how overfitting can be mitigated. Apart from just working with structured datasets, you will also learn to process image and sequential data.

MIT’s machine learning program cites three pre-requisites — Python, linear algebra, and calculus, which is why it is advisable to take the courses above before starting this one.

Are These Courses Beginner-Friendly?

Even if you have no prior knowledge of programming, statistics, or mathematics, you can take all the courses listed above.

MIT has designed these programs to take you through the subject from scratch. However, unlike many MOOCs out there, the pace does build up pretty quickly and the courses cover a large depth of information.

Due to this, it is advisable to do all the exercises that come with the lectures and work through all the reading material provided.

SOURCE

Natassha Selvaraj is a self-taught data scientist with a passion for writing. You can connect with her on LinkedIn.

https://www.kdnuggets.com/2022/03/8-free-mit-courses-learn-data-science-online.html

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Simulation Tools of Genomic Next Generation Sequencing Data: Comparative Analysis & Genetic Simulation Resources

Reporting: Aviva Lev-Ari, PhD, RN

 

INTRODUCTION

What is next generation sequencing?

Behjati S, Tarpey PS.

Arch Dis Child Educ Pract Ed. 2013 Dec;98(6):236-8. doi: 10.1136/archdischild-2013-304340. Epub 2013 Aug 28. Review.

Computational pan-genomics: status, promises and challenges.

Computational Pan-Genomics Consortium.

Brief Bioinform. 2018 Jan 1;19(1):118-135. doi: 10.1093/bib/bbw089. Review.

Tracking the NGS revolution: managing life science research on shared high-performance computing clusters.

Dahlö M, Scofield DG, Schaal W, Spjuth O.

Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy028.

NGS IN THE CLINIC

[Clinical Applications of Next-Generation Sequencing].

Rebollar-Vega RG, Arriaga-Canon C, de la Rosa-Velázquez IA.

Rev Invest Clin. 2018;70(4):153-157. doi: 10.24875/RIC.18002544.

PMID:
30067721

Free Article

 

Clinical Genomics: Challenges and Opportunities.

Vijay P, McIntyre AB, Mason CE, Greenfield JP, Li S.

Crit Rev Eukaryot Gene Expr. 2016;26(2):97-113. doi: 10.1615/CritRevEukaryotGeneExpr.2016015724. Review.

Next-generation sequencing in the clinic: promises and challenges.

Xuan J, Yu Y, Qing T, Guo L, Shi L.

Cancer Lett. 2013 Nov 1;340(2):284-95. doi: 10.1016/j.canlet.2012.11.025. Epub 2012 Nov 19. Review.

The Future of Whole-Genome Sequencing for Public Health and the Clinic.

Allard MW.

J Clin Microbiol. 2016 Aug;54(8):1946-8. doi: 10.1128/JCM.01082-16. Epub 2016 Jun 15.

PMID:
27307454

Free PMC Article

 

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists.

Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter AB.

J Mol Diagn. 2018 Jan;20(1):4-27. doi: 10.1016/j.jmoldx.2017.11.003. Epub 2017 Nov 21. Review.

PMID:
29154853

MUTATION ANALYSIS – GENE ENCODING

Next-Generation Sequencing and Mutational Analysis: Implications for Genes Encoding LINC Complex Proteins.

Nagy PL, Worman HJ.

Methods Mol Biol. 2018;1840:321-336. doi: 10.1007/978-1-4939-8691-0_22.

PMID:
30141054

Genome-wide genetic marker discovery and genotyping using next-generation sequencing.

Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML.

Nat Rev Genet. 2011 Jun 17;12(7):499-510. doi: 10.1038/nrg3012. Review.

PMID:
21681211

 

Best practices for evaluating mutation prediction methods.

Rogan PK, Zou GY.

Hum Mutat. 2013 Nov;34(11):1581-2. doi: 10.1002/humu.22401. Epub 2013 Sep 10. No abstract available.

PMID:
23955774

MITOCHONDRIAL VATIATIONS

mit-o-matic: a comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets.

Vellarikkal SK, Dhiman H, Joshi K, Hasija Y, Sivasubbu S, Scaria V.

Hum Mutat. 2015 Apr;36(4):419-24. doi: 10.1002/humu.22767.

PMID:
25677119

VARIANT ANALYSIS

A survey of tools for variant analysis of next-generation genome sequencing data.

Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z.

Brief Bioinform. 2014 Mar;15(2):256-78. doi: 10.1093/bib/bbs086. Epub 2013 Jan 21.

PMID:
23341494

Free PMC Article

 

Variant callers for next-generation sequencing data: a comparison study.

Liu X, Han S, Wang Z, Gelernter J, Yang BZ.

PLoS One. 2013 Sep 27;8(9):e75619. doi: 10.1371/journal.pone.0075619. eCollection 2013.

VARIANT DETECTION IN HEREDITARY CANCER GENES

ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

Lopez-Doriga A, Feliubadaló L, Menéndez M, Lopez-Doriga S, Morón-Duran FD, del Valle J, Tornero E, Montes E, Cuesta R, Campos O, Gómez C, Pineda M, González S, Moreno V, Capellá G, Lázaro C.

Hum Mutat. 2014 Mar;35(3):271-7.

PMID:
24227591

 

Development and analytical validation of a 25-gene next generation sequencing panel that includes the BRCA1 and BRCA2 genes to assess hereditary cancer risk.

Judkins T, Leclair B, Bowles K, Gutin N, Trost J, McCulloch J, Bhatnagar S, Murray A, Craft J, Wardell B, Bastian M, Mitchell J, Chen J, Tran T, Williams D, Potter J, Jammulapati S, Perry M, Morris B, Roa B, Timms K.

BMC Cancer. 2015 Apr 2;15:215. doi: 10.1186/s12885-015-1224-y.

Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis.

Sabour L, Sabour M, Ghorbian S.

Pathol Oncol Res. 2017 Apr;23(2):225-234. doi: 10.1007/s12253-016-0124-z. Epub 2016 Oct 8. Review.

PMID:
27722982

 

Studying cancer genomics through next-generation DNA sequencing and bioinformatics.

Doyle MA, Li J, Doig K, Fellowes A, Wong SQ.

Methods Mol Biol. 2014;1168:83-98. doi: 10.1007/978-1-4939-0847-9_6. Review.

PMID:
24870132

IMMUNOINFORMATICS

Immunoinformatics and epitope prediction in the age of genomic medicine.

Backert L, Kohlbacher O.

Genome Med. 2015 Nov 20;7:119. doi: 10.1186/s13073-015-0245-0. Review.

IgSimulator: a versatile immunosequencing simulator.

Safonova Y, Lapidus A, Lill J.

Bioinformatics. 2015 Oct 1;31(19):3213-5. doi: 10.1093/bioinformatics/btv326. Epub 2015 May 25.

PMID:
26007226

 

Computational genomics tools for dissecting tumour-immune cell interactions.

Hackl H, Charoentong P, Finotello F, Trajanoski Z.

Nat Rev Genet. 2016 Jul 4;17(8):441-58. doi: 10.1038/nrg.2016.67. Review.

PMID:
27376489

RNA SEQUENCING

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines.

Audoux J, Salson M, Grosset CF, Beaumeunier S, Holder JM, Commes T, Philippe N.

BMC Bioinformatics. 2017 Sep 29;18(1):428. doi: 10.1186/s12859-017-1831-5.

PMID:
28969586

Free PMC Article

COMPLEX INSERTIONS AND DELETIONS

INDELseek: detection of complex insertions and deletions from next-generation sequencing data.

Au CH, Leung AY, Kwong A, Chan TL, Ma ES.

BMC Genomics. 2017 Jan 5;18(1):16. doi: 10.1186/s12864-016-3449-9.

PMID:
28056804

Free PMC Article

EVOLUTIONARY BIOLOGY

The State of Software for Evolutionary Biology.

Darriba D, Flouri T, Stamatakis A.

Mol Biol Evol. 2018 May 1;35(5):1037-1046. doi: 10.1093/molbev/msy014. Review.

SIMULATION PROGRAMS

PMCID: PMC5224698
EMSID: EMS70941
PMID: 27320129

Systematic review of next-generation sequencing simulators: computational tools, features and perspectives.

Zhao M, Liu D, Qu H.

Brief Funct Genomics. 2017 May 1;16(3):121-128. doi: 10.1093/bfgp/elw012. Review.

PMID:
27069250

 

A comparison of tools for the simulation of genomic next-generation sequencing data

Online Summary

  1. There is a large number of tools for the simulation of genomic data for all currently available NGS platforms, with partially overlapped functionality. Here we review 23 of these tools, highlighting their distinct functionalities, requirements and potential applications.

  2. The parameterization of these simulators is often complex. The user may decide between using existing sets of parameters values called profiles or re-estimating them from its own data.

  3. Parameters than can be modulated in these simulations include the effects of the PCR amplification of the libraries, read features and quality scores, base call errors, variation of sequencing depth across the genomes and the introduction of genomic variants.

  4. Several types of genomic variants can be introduced in the simulated reads, such as SNPs, indels, inversions, translocations, copy-number variants and short-tandem repeats.

  5. Reads can be generated from single or multiple genomes, and with distinct ploidy levels. NGS data from metagenomic communities can be simulated given an “abundance profile” that reflects the proportion of taxa in a given sample.

  6. Many of the simulators have not been formally described and/or tested in dedicated publications. We encourage the formal publication of these tools and the realization of comprehensive, comparative benchmarkings.

  7. Choosing among the different genomic NGS simulators is not easy. Here we provide a guidance tree to help users choosing a suitable tool for their specific interests.

Abstract

Computer simulation of genomic data has become increasingly popular for assessing and validating biological models or to gain understanding about specific datasets. Multiple computational tools for the simulation of next-generation sequencing (NGS) data have been developed in recent years, which could be used to compare existing and new NGS analytical pipelines. Here we review 23 of these tools, highlighting their distinct functionality, requirements and potential applications. We also provide a decision tree for the informed selection of an appropriate NGS simulation tool for the specific question at hand.

Image source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224698/

An overview of current NGS technologies

The most popular NGS technologies on the market are Illumina’s sequencing by synthesis, which is probably the most widely used platform at present, Roche’s 454 pyrosequencing (454), SOLiD sequencing-by-ligation (SOLiD), IonTorrent semiconductor sequencing (IonTorrent), Pacific Biosciences’s (PacBio) single molecule real-time sequencing, and Oxford Nanopore Technologies (Nanopore) single-cell DNA template strand sequencing. These strategies can differ, for example, regarding the type of reads they produce or the kind of sequencing errors they introduce (Table 1). Only two of the current technologies (Illumina and SOLiD) are capable of producing all three sequencing read types —single endpaired end and mate pair. Read length is also dependent on the machine and the kit used; in platforms like Illumina, SOLiD, or IonTorrent it is possible to specify the number of desired base pairs per read. According to the sequencing run type selected it is possible to obtain reads with maximum lengths of 75 bp (SOLiD), 300 bp (Illumina) or 400bp (IonTorrent). On the other hand, in platforms like 454, Nanopore or PacBio, information is only given about the mean and maximum read length that can be obtained, with average lengths of 700 bp, 10 kb and 15 kb and maximum lengths of 1 kb, 10 kb and 15 kb, respectively. Error rates vary depending on the platform from <=1% in Illumina to ~30% in Nanopore. Further overviews and comparisons of NGS strategies can be found in ,.

Table 1

Main characteristics of current NGS technologies.
Technology Run Type Maximum Read Length Quality Scores Error Rates References
Single-read Paired-end Mate-pair
Illumina X X X 300 bp > Q30 0.0034 – 1%
SOLiD X X X 75 bp > Q30 0.01 – 1%
IonTorrent X X 400 bp ~ Q20 1.78%
454 X X ~700 bp (up to 1 Kb) > Q20 1.07 – 1.7% ,
Nanopore X 5.4 – 10 Kb NAY 10 – 40%
PacBio X ~15 Kb (up to 40 Kb) < Q10 5 – 10% ,

Simulation parameters

The existing sequencing platforms use distinct protocols that result in datasets with different characteristics. Many of these attributes can be taken into account by the simulators (Fig. 2), although there is not a single tool that incorporates all possible variations. The main characteristics of the 23 simulators considered here are summarized in Tables 2 and and3.3. These tools differ in multiple aspects, such as sequencing technology, input requirements or output format, but maintain several common aspects. With some exceptions, all programs need a reference sequence, multiple parameter values indicating the characteristics of the sequencing experiment to be simulated (read length, error distribution, type of variation to be generated, if any, etc.) and/or a profile (a set of parameter values, conditions and/or data used for controlling the simulation), which can be provided by the simulator or estimated de novo from empirical data. The outcome will be aligned or unaligned reads in different standard file formats, such as FASTQ, FASTA or BAM. An overview of the NGS data simulation process is represented in Fig. 3. In the following sections we delve into the different steps involved.

An external file that holds a picture, illustration, etc. Object name is emss-70941-f002.jpg

General overview of the sequencing process and steps that can be parameterized in the simulations.

NGS simulators try to imitate the real sequencing process as closely as possible by considering all the steps that could influence the characteristics of the reads. a | NGS simulators do not take into account the effect of the different DNA extraction protocols in the resulting data. However, they can consider whether the sample we want to sequence includes one or more individuals, from the same or different organisms (e.g., pool-sequencing, metagenomics). Pools of related genomes can be simulated by replicating the reference sequence and introducing variants on the resulting genomes. Some tools can also simulate metagenomes with distinct taxa abundance. b | Simulators can try to mimic the length range of DNA fragmentation (empirically obtained by sonication or digestion protocols) or assume a fixed amplicon length. c | Library preparation involves ligating sequencing–platform dependent adaptors and/or barcodes to the selected DNA fragments (inserts). Some simulators can control the insert size, and produce reads with adaptors/barcodes. d | | Most NGS techniques include an amplification step for the preparation of libraries. Several simulators can take this step into account (for example, by introducing errors and/or chimaeras), with the possibility of specifying the number of reads per amplicons. e | Sequencing runs imply a decision about coverage, read length, read type (single-end, paired-end, mate-pair) and a given platform (with their specific errors and biases). Simulators exist for the different platforms, and they can use particular parameter profiles, often estimated from real data.

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General overview of NGS simulation.

The simulation process begins with the input of a reference sequence (most cases) and simulation parameters. Some of the parameters can be given via a profile, that is estimated (by the simulator or other tools) from other reads or alignments. The outcome of this process may be reads (with or without quality information) or genome alignments in different formats.

CONCLUSIONS

NGS is having a big impact in a broad range of areas that benefit from genetic information, from medical genomics, phylogenetic and population genomics, to the reconstruction of ancient genomes, epigenomics and environmental barcoding. These applications include approaches such as de novo sequencing, resequencing, target sequencing or genome reduction methods. In all cases, caution is necessary in choosing a proper sequencing design and/or a reliable analytical approach for the specific biological question of interest. The simulation of NGS data can be extremely useful for planning experiments, testing hypotheses, benchmarking tools and evaluating particular results. Given a reference genome or dataset, for instance, one can play with an array of sequencing technologies to choose the best-suited technology and parameters for the particular goal, possibly optimizing time and costs. Yet, this is still not the standard practice and researchers often base their choices on practical considerations like technology and money availability. As shown throughout this Review, simulation of NGS data from known genomes or transcriptomes can be extremely useful when evaluating assembly, mapping, phasing or genotyping algorithms e.g. ,,,, exposing their advantages and drawbacks under different circumstances.

Altogether, current NGS simulators consider most, if not all, of the important features regarding the generation of NGS data. However, they are not problem-free. The different simulators are largely redundant, implementing the same or very similar procedures. In our opinion, many are poorly documented and can be difficult to use for non-experts, and some of them are no longer maintained. Most importantly, for the most part they have not been benchmarked or validated. Remarkably, among the 23 tools considered here, only 13 have been described in dedicated application notes, 3 have been mentioned as add-ons in the methods section of bigger articles, and 5 have never been referenced in a journal. Indeed, peer-reviewed publication of these tools in dedicated articles would be highly desirable. While this would not definitively guarantee quality, at least it would encourage authors to reach minimum standards in terms of validation, benchmarking, and documentation. Collaborative efforts like the Assemblathon e.g.  or iEvo (http://www.ievobio.org/) might be also a source of inspiration. Meanwhile, we hope that the decision tree presented in Fig. 1 helps users making appropriate choices.

SOURCE
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