Apr 22, 2020

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Dmitry Korkin is a professor of bioinformatics and computational biology at Worcester Polytechnic Institute, where he specializes in bioinformatics of complex disease, computational genomics, systems biology, and biomedical data analytics. I came across Dmitry’s work when in February his group used the viral genome of the COVID-19 to reconstruct the 3D structure of its major viral proteins and their interactions with human proteins, in effect creating a structural genomics map of the coronavirus and making this data open and available to researchers everywhere. We talked about the biology of COVID-19, SARS, and viruses in general, and how computational methods can help us understand their structure and function in order to develop antiviral drugs and vaccines.
This conversation is part of the Artificial Intelligence podcast.
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OUTLINE: 0:00 – Introduction 2:33 – Viruses are terrifying and fascinating 6:02 – How hard is it to engineer a virus? 10:48 – What makes a virus contagious? 29:52 – Figuring out the function of a protein 53:27 – Functional regions of viral proteins 1:19:09 – Biology of a coronavirus treatment 1:34:46 – Is a virus alive? 1:37:05 – Epidemiological modeling 1:55:27 – Russia 2:02:31 – Science bobbleheads 2:06:31 – Meaning of life
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Recent Grim COVID-19 Statistics in U.S. and Explanation from Dr. John Campbell: Why We Need to be More Proactive

Reporter: Stephen J. Williams, Ph.D.

In case you have not been following the excellent daily YouTube sessions on COVID-19 by Dr. John Campbell I am posting his latest video on how grim the statistics have become and the importance of using proactive measures (like consistent use of facial masks, proper social distancing) instead of relying on reactive measures (e.g. lockdowns after infection spikes).  In addition, below the video are some notes from his presentation and some links to sites discussed within the video.


Notes from the video:

  • approaching 5 million confirmed cases in US however is probably an underestimation
  • 160,00 deaths as of 8/08/2020

From the University of Washington Institute for Health Metrics and Evaluation in Seattle WA

  • 295,000 US COVID-19 related deaths estimated by December 1, 2020
  • however if 95% of people in US consistently and properly wear masks could save 66,000 lives
  • however this will mean a remaining 228,271 deaths which is a depressing statistic
  • Dr. John Campbell agrees with Dr. Christopher Murray, director of the Institute for Health Metrics that “people’s inconsistent use of these measures (face masks, social distancing) is a serious problem”
  • States with increasing transmission like Colorado, Idaho, Kansas, Kentucky, Mississippi, Missouri, Ohio, Oklahoma, Oregon, and Virginia are suggested to have a lockdown when death rate reaches 8 deaths per million population however it seems we should be also focusing on population densities rather than geographic states
  • Dr. Campbell and Dr. Murray stress more proactive measures than reactive ones like lockdowns
  • if mask usage were to increase to 95% usage reimposition to shutdown could be delayed 6 to 8 weeks


New IHME COVID-19 Forecasts See Nearly 300,000 Deaths by December 1

SEATTLE (August 6, 2020) – America’s COVID-19 death toll is expected to reach nearly 300,000 by December 1; however, consistent mask-wearing beginning today could save about 70,000 lives, according to new data from the Institute for Health Metrics and Evaluation (IHME) at the University of Washington’s School of Medicine.The US forecast totals 295,011 deaths by December. As of today, when, thus far, 158,000 have died, IHME is projecting approximately 137,000 more deaths. However, starting today, if 95% of the people in the US were to wear masks when leaving their homes, that total number would decrease to 228,271 deaths, a drop of 49%. And more than 66,000 lives would be saved.Masks and other protective measures against transmission of the virus are essential to staying COVID-free, but people’s inconsistent use of those measures is a serious problem, said IHME Director Dr. Christopher Murray.

“We’re seeing a rollercoaster in the United States,” Murray said. “It appears that people are wearing masks and socially distancing more frequently as infections increase, then after a while as infections drop, people let their guard down and stop taking these measures to protect themselves and others – which, of course, leads to more infections. And the potentially deadly cycle starts over again.”

Murray noted that there appear to be fewer transmissions of the virus in Arizona, California, Florida, and Texas, but deaths are rising and will continue to rise for the next week or two. The drop in infections appears to be driven by the combination of local mandates for mask use, bar and restaurant closures, and more responsible behavior by the public.

“The public’s behavior had a direct correlation to the transmission of the virus and, in turn, the numbers of deaths,” Murray said. “Such efforts to act more cautiously and responsibly will be an important aspect of COVID-19 forecasting and the up-and-down patterns in individual states throughout the coming months and into next year.”

Murray said that based on cases, hospitalizations, and deaths, several states are seeing increases in the transmission of COVID-19, including Colorado, Idaho, Kansas, Kentucky, Mississippi, Missouri, Ohio, Oklahoma, Oregon, and Virginia.

“These states may experience increasing cases for several weeks and then may see a response toward more responsible behavior,” Murray said.

In addition, since July 15, several states have added mask mandates. IHME’s statistical analysis suggests that mandates with no penalties increase mask wearing by 8 percentage points. But mandates with penalties increase mask wearing by 15 percentage points.

“These efforts, along with media coverage and public information efforts by state and local health agencies and others, have led to an increase in the US rate of mask wearing by about 5 percentage points since mid-July,” Murray said. Mask-wearing increases have been larger in states with larger epidemics, he said.

IHME’s model assumes that states will reimpose a series of mandates, including non-essential business closures and stay-at-home orders, when the daily death rate reaches 8 per million. This threshold is based on data regarding when states and/or communities imposed mandates in March and April, and implies that many states will have to reimpose mandates.

As a result, the model suggests which states will need to reimpose mandates and when:

  • August – Arizona, Florida, Mississippi, and South Carolina
  • September – Georgia and Texas
  • October – Colorado, Kansas, Louisiana, Missouri, Nevada, North Carolina, and Oregon.
  • November – Alabama, Arkansas, California, Iowa, New Mexico, Oklahoma, Utah, Washington, and Wisconsin.

However, if mask use is increased to 95%, the re-imposition of stricter mandates could be delayed 6 to 8 weeks on average.

Source: http://www.healthdata.org/news-release/new-ihme-covid-19-forecasts-see-nearly-300000-deaths-december-1


The 40th Anniversary of SRI ORGANON TOASTMASTERS virtual celebration on Tuesday, August 18, 11:45 a.m.-1:00 p.m

Past Member of SRI Organon Toastmasters, 5/1985 – 9/1988: Aviva Lev-Ari, PhD, RN


I was a Competent Toastmasters working on the Distinguished Toastmasters rank.

Today, 8/7/2020 was invited to attend the SRI Organon Toastmasters 40th Anniversary. 

The picture on my Student ID Card at University of California, Berkeley, 9/1978 – 12/1983


From: NAOMI LEVENSON <na8mi@comcast.net>

Date: Friday, August 7, 2020 at 3:38 PM

Subject: SRI Organon Anniversary

SRI Organon Toastmasters turned 40 in February!

We invite you to join the virtual celebration on Tuesday, August 18, 11:45 a.m.-1:00 p.m.



More information is on the attached flyer.

Plan to come to the meeting early and stay afterwards. There will be time to reminisce and catch up.

Do you have any memories you might want to share. You can add your thoughts, anecdotes and comments on   https://tinyurl.com/yxl4nuu4.

Bring your own beverage for the TOAST!

Please plan to attend.

Naomi Levenson


40th Anniversary Flyer (1)



We are in the midst of a pandemic that is impacting people and society in ways that are hard to grasp. The most apparent impact is on physical health. It also effects our attitudes in society, our economy and our cultural life. Throughout history, humanity has had to face the challenge of understanding, managing and fighting viruses.

In the exhibition Contagious we are highlighting Nobel Prize-awarded researchers who have expanded our knowledge about viruses, mapped our immune system and developed vaccines. We also examine the perspectives from Literature and Economics Laureates about the impact of epidemics on life and society. Visit us at the museum or on these pages.

Museums have an important role to play in times of crisis, since they can help people tackle existential questions and provide a broader context. The Nobel Museum is about ideas that have changed the world. The Nobel Prize points to the ability of humans to find solutions to difficult challenges that we face time and time again. It is a source of hope, even in the midst of the crisis.


Nobel Prize Museum



On March 11 this year, the World Health Organization announced that the spread of the coronavirus should be classified as a pandemic, that is “an infectious disease that spreads to large parts of the world and affects a large proportion of the population of each country”. Today, nobody knows how many will die in this pandemic, or when, or if, we can have a vaccine against the disease.

SARS-CoV-2, or Severe acute respiratory syndrome coronavirus 2, is an RNA virus from the family coronavirus that causes the respiratory disease covid-19.

The virus was detected at the end of last year in the Wuhan sub-province of China, and in most cases causes milder disease symptoms that disappear within two weeks. But sometimes, especially in certain groups such as the elderly and people with certain other underlying illnesses, the infection becomes more severe and can in some cases lead to death.

The virus is believed to have zoonotic origin, that is, it has been transmitted to humans from another animal. Where the origin of the disease comes from, that is to say from which host animal the virus originates, is still unknown. However, the virus has close genetic similarity to a corona virus carried by some bats, which might indicate where the virus comes from.

This model shows the SARS-CoV-2 virus, which causes the illness covid-19. The globe-shaped envelope has a membrane of fat-like substances. Inside the envelope are proteins bound to RNA molecules, that contain the virus’s genes. Short spikes of proteins and longer spikes of glycoprotein stick out of the envelope and attach to receptors on the surface of attacked cells. The spikes, which are bigger at the top, give the virus its appearance reminiscent of the Sun’s corona. This where the coronavirus’s name comes from.

Testing is an important tool for tracking and preventing the spread of infection during an epidemic.

One type of test looks at if a person is infected by looking for traces of the virus’s RNA genetic material. The test is taken using a swab stick inserted into the throat. The small amounts of RNA or DNA that attach to the swab are analyzed using the PCR technique, which was invented by Kary Mullis in 1983. Ten years later he was awarded the Nobel Prize in Chemistry.

Another type of test looks for antibodies to the virus in the blood. This indicates that the person has had the disease.


The first virus ever discovered

We have understood since the 19th century that many diseases are caused by microscopic bacteria that cannot be seen by the naked eye. It turned out that there were even smaller contagions: viruses. Research on viruses has been recognized with several Nobel Prizes.


Spanish flu

The worst pandemic of the 20th century was the Spanish flu, which swept across the world 1918–1920.

The Spanish flu was caused by an influenza virus. American soldiers at military facilities at the end of World War I were likely an important source of its spread in Europe. The war had just ended, and the pandemic claimed even more lives than the war. Between 50 and 100 million people died in the pandemic.

The Red Cross, an international aid organization, which received the Nobel Peace Prize for its efforts during the war, also took part in fighting the Spanish flu. International Committee of the Red Cross received the prize in 1917, 1944 and 1963.

This photo shows personnel from the Red Cross providing transportation for people suffering from the Spanish flu in St. Louis, Missouri in the United States.



Polio is an illness that often affects children and young people and that can lead to permanent paralysis.

Polio is a highly infectious RNA virus belonging to the genus Enterovirus. The virus only infects humans and enters the body via droplets such as sneezing and coughing, or through contact with infected people’s feces. Usually, polio infects our respiratory and intestinal tract, but sometimes the virus spreads to the spinal cord and can then cause paralysis. The virus mainly affects children, but most of those infected show no or very mild symptoms.

Vaccines are a way to help our immune system fight viruses. The immune system is the body’s defence mechanism against attacks from viruses and bacteria. A number of Nobel Laureates have researched the immune system and contributed to the development of vaccines.

Hepatitis B

The virus can infect people without them becoming sick. Discoveries in the 1960s enabled both vaccines and tests to prevent the spread.

Hepatitis B can infect humans and apes, and is most common in West Africa and in sub-Saharan Africa. The disease also occurs in the rest of Africa, as well as in areas from the Caspian Sea through to China and Korea and further down to Southeast Asia.

Baruch Blumberg discovered the virus behind hepatitis B and developed a vaccine against the disease.

There are many varieties of hepatitis, or jaundice, that cause inflammation in the liver. When studying blood proteins from people from different parts of the world at the end of the 1960s, Baruch Blumberg unexpectedly discovered an infectious agent for hepatitis B. He showed that the infectious agent was linked to a virus of previously unknown type. The virus can infect people without them becoming sick. The discoveries enabled both vaccines and tests to prevent the spread through blood transfusions.

Baruch Blumberg was awarded the Nobel Prize in Physiology or Medicine 1976. He has summarized what the Nobel Prize meant to him.


Yellow fever

Each year, Yellow fever causes about 30,000 deaths. The vaccine against yellow fever was produced in the 1930s. A work awarded the Nobel Prize.

Yellow fever is a serious disease caused by a virus that is spread by mosquitos in tropical areas of Africa and South America.

Each year, Yellow fever causes about 200,000 infections and 30,000 deaths. About 90% of the cases occur in Africa. The disease is common in warm, tropical climates such as South America and Africa, but it is not found in Asia.

You may think that the number of people infected would be decreasing, but since the 1980s the number of yellow fever cases has unfortunately increased. This is believed to be due to the fact that more and more people are living in cities, that we are traveling more than before, and an increased climate impact.

Since there is no cure for the disease, preventive vaccination is a very important measure. Max Theiler successfully infected mice with a virus in the 1930s, which opened the door to more in-depth studies. When the virus was transferred between mice, a weakened form of the virus was created that gave monkeys immunity. In 1937, Theiler was able to develop an even weaker version of the virus. This version could be used as a vaccine for people.

Max Theiler was awarded the Nobel Prize in Physiology or Medicine in 1951.



In the early 1980s, reports began to emerge about young men that suffered from unusual infections and cancers that normally only affect patients with weakened immune systems. It turned out to be a previously unknown epidemic, HIV, which spread rapidly across the world.

HIV, which is an abbreviation of human immunodeficiency virus, is a sexually transmitted retrovirus that attacks our immune system. An untreated infection eventually leads to AIDS, or acquired immune deficiency syndrome. In 2008, French scientists Luc Montagnier and Françoise Barré-Sinoussi were awarded the Nobel Prize in Physiology or Medicine for the detection of human immunodeficiency virus.

Watch the interview where Françoise Barré-Sinoussi talks about what it is like to meet patients affected by the virus she discovered.



Viruses captured in photos

Viruses are incredibly small and cannot be seen in normal microscopes.

The electron microscope, which was invented by Ernst Ruska and Max Knoll in 1933, made it possible to take pictures of much smaller objects than was previously possible. Ernst Ruska’s brother, Helmut Ruska, was a doctor and biologist, and used early electron microscopes to make images of viruses and other small objects. The tobacco mosaic virus was the first virus captured on film. The development of the electron microscope has enabled increasingly better images to be taken.

Ernst Ruska was awarded the 1986 Nobel Prize in Physics together with Gerd Binnig and Heinrich Röhrer, who developed the scanning electron microscope.

Read more about Ernst Ruska – his life and research. https://www.nobelprize.org/prizes/physics/1986/ruska/facts/



Epidemics and literature

When epidemics and pandemics strike the world, it isn’t just the physical health of people that are impacted but also ways of life, thoughts and feelings. Nobel Laureates in literature have been effected by epidemics and written about life under real and fictive epidemics.

The coronavirus crisis has had a dramatic impact on our lives and our view of our lives. Olga Tokarczuk is one of the authors who has reflected on this.

Tokarczuk argues that the coronavirus has swept away the illusion that we are the masters of creation and that we can do anything since the world belongs to us. She wonders if the pandemic has forced us into a slower, more natural rhythm in life, but also worries about how it may increase distrust of strangers and worsen inequality among people.

Orhan Pamuk has worked for many years on a novel about a bubonic plague epidemic that struck primarily Asia in 1901. The coronavirus crisis has caused him to consider the similarities between the ongoing pandemic and past epidemics throughout history.

He sees several recurring behaviors when epidemics strike: denial and false information, distrust of individuals belonging to other groups, and theories about a malicious intent behind the pandemic. But epidemics also remind us that we are not alone and allow us to rediscover a sense of solidarity. He writes in The New York Times.


Economics Laureates on the current pandemic

Pandemics have wide-ranging impacts on the economy. Paul Romer and Paul Krugman are two economists who have been active in the public discourse during the coronavirus crisis.

Paul Romer has expressed concerns about the pandemic’s effects on the economy but is optimistic about the possibilities of technology. He supports widespread testing. Those who are infected have to stay home for two weeks while others can work and take part in other ways in society.

Paul Romer was awarded the prize “for integrating technological innovations into long-run macroeconomic analysis.” Paul Romer has demonstrated how knowledge can function as a driver of long-term economic growth. He showed how economic forces govern the willingness of firms to produce new ideas.

His thoughts are developed in his lecture during the Nobel Week 2018.






Is SARS-COV2 Hijacking the Complement and Coagulation Systems?

Reporter: Stephen J. Williams, PhD

In a recent Nature Medicine paper “Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection” Ramlall et al. demonstrate, in a retrospective study, that a significant number of patients presenting SARS-CoV2 complications had prior incidences of macular degeneration and coagulation disorders and these previous indications are risk factors for COVID-related complications.



Understanding the pathophysiology of SARS-CoV-2 infection is critical for therapeutic and public health strategies. Viral–host interactions can guide discovery of disease regulators, and protein structure function analysis points to several immune pathways, including complement and coagulation, as targets of coronaviruses. To determine whether conditions associated with dysregulated complement or coagulation systems impact disease, we performed a retrospective observational study and found that history of macular degeneration (a proxy for complement-activation disorders) and history of coagulation disorders (thrombocytopenia, thrombosis and hemorrhage) are risk factors for SARS-CoV-2-associated morbidity and mortality—effects that are independent of age, sex or history of smoking. Transcriptional profiling of nasopharyngeal swabs demonstrated that in addition to type-I interferon and interleukin-6-dependent inflammatory responses, infection results in robust engagement of the complement and coagulation pathways. Finally, in a candidate-driven genetic association study of severe SARS-CoV-2 disease, we identified putative complement and coagulation-associated loci including missense, eQTL and sQTL variants of critical complement and coagulation regulators. In addition to providing evidence that complement function modulates SARS-CoV-2 infection outcome, the data point to putative transcriptional genetic markers of susceptibility. The results highlight the value of using a multimodal analytical approach to reveal determinants and predictors of immunity, susceptibility and clinical outcome associated with infection.


As part of a separate study, the authors mapped over 140 cellular proteins that are structurally mimicked by coronaviruses (CoVs) and identified complement and coagulation pathways as targets of this strategy across all CoV strains4. The complement system is a critical defense against pathogens, including viruses5 and when dysregulated (by germline variants or acquired through age-related effects or excessive tissue damage) can contribute to pathologies mediated by inflammation5,6,7.

“So, virally encoded structural mimics of complement and coagulation factors may contribute to CoV-associated immune-mediated pathology and indicate sensitivities in antiviral defenses.”


Methods and Results

  • Between 1 February 2020 and 25 April 2020, 11,116 patients presented to New York-Presbyterian/Columbia University Irving Medical Center with suspected SARS-CoV-2 infection, of which 6,398 tested positive
  • Electronic health records (EHRs) were used to define sex, age and smoking history status as well as histories of macular degeneration, coagulatory disorders (thrombocytopenia, thrombosis and hemorrhage), hypertension, type 2 diabetes (T2D), coronary artery disease (CAD) and obesity (see Methods). A Python algorithm was used to analyze all confounders.
  • identified 88 patients with history of macular degeneration, 4 with complement deficiency disorders and 1,179 with coagulatory disorders).
  • observed a 35% mortality rate among patients that were put on mechanical ventilation and that 31% of deceased patients had been on mechanical respiration.
  • patients with AMD (a proxy for complement activation disorders) and coagulation disorders (thrombocytopenia, thrombosis and hemorrhage) were at significantly increased risk of adverse clinical outcomes (including mechanical respiration and death) following SARS-CoV-2 infection
  • 650 NP swabs from control and SARS-CoV-2-infected patients who presented to Weill-Cornell Medical Center were evaluated by RNA-Seq. Gene set enrichment analysis (GSEA) of Hallmark gene sets found that SARS-CoV-2 infection (as defined by presence of SARS-CoV-2 RNA and stratified into ‘positive’, ‘low’, ‘medium’ or ‘high’ based on viral load; induces genes related to pathways with known immune modulatory functions (Fig. 2a). Moreover, among the most enriched gene sets, SARS-CoV-2 infection induces robust activation of the complement cascade (false discovery rate (FDR) P < 0.001), with increasing enrichment and significance with viral load (FDR P < 0.0001).
  • KEGG Pathway Analysis revealed KEGG_Complement_and_Coagulation_Cascades’, ‘GO_Coagulation’ and ‘Reactome_initial_triggering_of_complement’ to be significantly enriched in expression profiles of SARS-CoV-2-infected samples
  • conducted a candidate-driven study to evaluate whether genetic variation within a 60-Kb window around 102 genes with known roles in regulating complement or coagulation cascades (2,888 genetic variants fulfill this criteria of the 805,426 profiled in the UK Biobank) is associated with poor SARS-CoV-2 clinical outcome
  • identified 11 loci representing seven genes with study-wide significance. A variant of coagulation factor III (F3), variant rs72729504, was found to be associated with increased risk of adverse clinical outcome associated with SARS-CoV-2 infection. The analysis also identified that four variants previously reported to be associated with AMD (rs45574833, rs61821114, rs61821041 and rs12064775)15predispose carriers to hospitalization following SARS-CoV-2 infection

As authors state:

“Among the implications, the data warrant heightened public health awareness for the most vulnerable individuals and further investigation into an existing menu of complement and coagulation targeting therapies that were recently shown to be beneficial in a small cohort of patients with SARS-CoV-2 infection.” 26,27.



Ramlall, V., Thangaraj, P.M., Meydan, C. et al. Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection. Nat Med (2020). https://doi.org/10.1038/s41591-020-1021-2



Lasso, G., Honig, B. & Shapira, S. D. A sweep of earth’s virome reveals host-guided viral protein structural mimicry; with implications for human disease. Preprint at bioRxiv https://doi.org/10.1101/2020.06.18.159467 (2020).



Viruses deploy an array of genetically encoded strategies to coopt host machinery and support viral replicative cycles. Molecular mimicry, manifested by structural similarity between viral and endogenous host proteins, allow viruses to harness or disrupt cellular functions including nucleic acid metabolism and modulation of immune responses. Here, we use protein structure similarity to scan for virally encoded structure mimics across thousands of catalogued viruses and hosts spanning broad ecological niches and taxonomic range, including bacteria, plants and fungi, invertebrates and vertebrates. Our survey identified over 6,000,000 instances of structural mimicry, the vast majority of which (>70%) cannot be discerned through protein sequence. The results point to molecular mimicry as a pervasive strategy employed by viruses and indicate that the protein structure space used by a given virus is dictated by the host proteome. Interrogation of proteins mimicked by human-infecting viruses points to broad diversification of cellular pathways targeted via structural mimicry, identifies biological processes that may underly autoimmune disorders, and reveals virally encoded mimics that may be leveraged to engineer synthetic metabolic circuits or may serve as targets for therapeutics. Moreover, the manner and degree to which viruses exploit molecular mimicry varies by genome size and nucleic acid type, with ssRNA viruses circumventing limitations of their small genomes by mimicking human proteins to a greater extent than their large dsDNA counterparts. Finally, we identified over 140 cellular proteins that are mimicked by CoV, providing clues about cellular processes driving the pathogenesis of the ongoing COVID-19 pandemic.



Risitano, A. M. Complement as a target in COVID-19?. Nat. Rev. Immunol. 20, 343–344 (2020).



Mastaglio, S. et al. The first case of COVID-19 treated with the complement C3 inhibitor AMY-101. Clin. Immunol. 215, 108450 (2020).



Polubriaginof, F. C. G. et al. Challenges with quality of race and ethnicity data in observational databases. J. Am. Med. Inf. Assoc. 26, 730–736 (2019).


From LPBI Group


Series C: e-Books on Cancer & Oncology


  • Volume 1: Cancer Biology & Genomics for Disease Diagnosis. On Amazon.com since 8/11/2015


  • Volume 2: Cancer Therapies: Metabolic, Genomics, Interventional, Immunotherapy and Nanotechnology in Therapy Delivery (Series C Book 2). On Amazon.com since 5/18/2017




From 4open-sciences.org

Current Thinking on Cancer

Guest Authors: Björn L.D.M. Brücher and Ijaz S. Jamall

New research challenges current thinking on cancer



4open special issue presents a new paradigm for cancer

Imagine if we could understand and treat the root causes of cancer, rather than struggling to remove it or mainly treating its symptoms once it has already taken hold. The authors of a new peer-reviewed Special Issue of the open access journal 4open have paved the way for this vision by challenging our understanding of how cancer begins, develops, and spreads.

Entitled “Disruption of homeostasis-induced signaling and crosstalk in the carcinogenesis paradigm “Epistemology of the origin of cancer””, the Issue reveals the robust evidence for their new hypothesis about the origin of cancer. The paradigm includes a chain of six events that together explain why the vast majority of cancers develop through complex alterations in cell signaling and communication, and why most cancers are not caused by mutations as commonly believed.

This concept will radically change how we perceive and treat cancer, and even allow us to prevent cancer in the first instance.

Genetic mutations cause cancer – or do they?

“We all learn in school that cancer is caused by genetic mutations that make our cells grow uncontrollably,” says Professor Björn Brücher, an author on the Special Issue. “This belief, although confirmed for only less than 10% of cancers, has become a dogma for the origin of all cancers.”

Clearly, something is amiss. The truth is that we know a lot less about what causes cancer than you might think. In fact, researchers don’t know what causes a massive 80% of cancers. While genetic mutations are present in many advanced cancers, there is no evidence that they caused the cancer, and likely occurred after the cancer had already begun. In most cancers, the somatic mutation hypothesis simply doesn’t stack up.

Despite this, “scientists have overwhelmingly focused on genetic mutations in their quest to understand the causes of cancer” says Dr. Ijaz Jamall and that “this has been a major hurdle to advancing cancer research, and means that we have missed opportunities to explore other possibilities.”

Current cancer treatment could be better

Our failure to understand the cause of most cancers has had real-world implications in terms of how we treat them. The most common treatment methods, including surgery, chemotherapy and radiotherapy, deal with the symptoms of cancer rather than its causes. These treatments are arguably crude and involve cutting the tumor out or attempting to kill the cancer cells using toxic drugs or radiation. This doesn’t always work, can have serious side effects, and may set the stage for secondary cancers years later.

Newer, more sophisticated treatments, such as immunotherapy can be effective in a few cancers, but still fail to address or reverse the root cause. In fact, we currently have no way to proactively prevent cancer in a targeted way, even for cancers for which we understand the cause. We are still not close to eradicating the disease, and the prevalence of many cancers is increasing.

A new cancer paradigm

However, not all researchers have focused exclusively on genetic mutations in the search to understand the origins of cancer. A small, but growing field of research has focused on exploring alternatives. Brücher and Jamall have developed an entirely new hypothesis for the origins of most cancers, which they first announced in 2014. This plausible cancer paradigm proposes a series of six events necessary for the 80% of cancers with unknown origins, and does not rely on mutations (https://www.karger.com/Article/FullText/443106).

Their hypothesis outlines a sequence of events that underlie the progression from healthy tissue to cancer. The Special Issue includes 10 papers that provide evidence to support this paradigm. One article entitled “Chronic inflammation evoked by pathogenic stimulus during carcinogenesis”, describes the biochemical and physiological signaling events involved in carcinogenesis in detail.

The process begins with a pathogenic stimulus, such as an infection, which causes inflammation in the affected tissue. Inflammation is a normal process during healing and usually resolves itself when an infection is over. This healing process is unsuccessful when the stimulus and inflammation are too great or too prolonged and the inflammation becomes chronic. Here, the disruptions that occur in biochemical and physiological homeostasis are complex, but this complexity provides many opportunities to block some of these pathways and thereby reduce the risk of developing cancer.

If chronic inflammation persists, it can cause fibrosis. Fibrosis is a process similar to scar formation where cells called fibroblasts grow and form fibrous tissue. As detailed in another article in the issue, “Precancerous niche (PCN), a product of fibrosis with remodeling by incessant chronic inflammation, fibrosis caused by chronic inflammation drastically changes the cellular environment affected by it.

This altered cellular environment and accompanying changes in the levels of biochemical signaling molecules lead to a precancerous state. If the body’s attempts to escape this situation prove ineffective, then the affected cells may transition into cancer cells.

Inflammation and cancer

While it may seem strange to think of inflammation as part of the carcinogenic process, researchers have known about the link between inflammation and cancer for a long time. For example, chronic inflammation was first reported in testicular cancer in chimney sweeps in 1755. While researchers had previously observed the link between inflammation and cancer, no one had identified the complex multi-step processes involved and assembled them into a coherent hypothesis, until recently. This includes a dysregulation in homeostasis, which is the body’s tendency to maintain complex biochemical events within a range that maintains health.

Many carcinogenic substances cause inflammation and there are numerous examples of cancers linked to it. For instance, asbestos fibers cause inflammation and lung cancer, without genetic mutations. Hepatitis C infection can cause chronic inflammation in the liver, which can progress to liver cancer with no mutations. In patients with inflammatory bowel disease, the risk of cancer is increased 20 to 30-fold. Human papilloma virus acts in a similar manner to cause cervical cancer and oropharyngeal cancers.

Brücher and Jamall are not alone in recognizing the importance of inflammation in cancer others have also drawn attention to the link between infections in early life with the later risk of colon and breast cancer, and discussed the potential of anti-inflammatory drugs to reduce this risk.

What could this new paradigm mean for cancer patients?

The interplay between pathogens, inflammation, fibrosis, and cancer cell development involves a huge range of complex biochemical signaling molecules and aberrant cell behaviors. Untangling these relationships to discover the exact mechanisms involved is an ongoing process. However, rather than being a hurdle, this complexity affords an opportunity for cancer patients in the form of new treatment options, and potentially even preventative treatments.

“This cancer paradigm offers many processes that we could target to prevent and even reverse the process of carcinogenesis before it is complete,” explains Brücher. “For example, a drug that reduces inflammation or fibrosis could potentially prevent cancer from developing” states Jamall. Developing treatments that address the root causes of cancer could be a game changer for patients.

This approach could mean that cancer goes from a lethal disease to a disease of inconvenience, such as diabetes.

Given the importance of these findings, the authors are delighted to publish their peer-reviewed Special Issue in 4open, an open access journal, making information about this new paradigm more easily available to the public and researchers alike. Open access publishing is crucial for the widespread dissemination of ground-breaking ideas and results, allowing the scientific community to freely share new information that could change the course of research and medicine.

This “Key Summaries” article is brought to you in collaboration with SciencePOD.


4open: Special issue

Disruption of homeostasis-induced signaling and crosstalk in the carcinogenesis paradigm “Epistemology of the origin of cancer”

Obul R. Bandapalli (Guest Editor)

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WordCloud Visualization of LPBI’s Top Sixteen Articles on GENOMICS by Views at All Time and their Research Categories in the Ontology of PharmaceuticalIntelligence.com

Curators: Stephen J. Williams, Aviva Lev-Ari, PhD, RN and WordCloud Producers: Daniel Menzin, Noam Steiner-Tomer, Zach Day, Ofer Markman, PhD

Now we will do the same for Genomics Volume I so for your pre class homework first read the following electronic Table of Contents

and then determine some themes around the table of contents into a mind map of what you think are the scientists/clinicians main themes on the field of Genomics

Genomics eTOC at


Content Consultant: Larry H Bernstein, MD, FCAP

Genomics Orientations for Personalized Medicine

Volume One



Image Collage by SJ Williams, PhD, Google Images in Assembly

Larry H Bernstein, MD, FCAP, Senior Editor

Triplex Medical Science, Trumbull, CT



Stephen J. Williams, PhD, Editor

Leaders in Pharmaceutical Business Intelligence, Philadelphia



Aviva Lev-Ari, PhD, RN, Editor

Editor-in-Chief BioMed E-Book Series

Leaders in Pharmaceutical Business Intelligence, Boston


Each Intern, Please insert here

Table for Article #1


Article Name

Live Link


All Time

Categories of Research



Is the Warburg Effect the Cause or the Effect of Cancer: A 21st Century View?


Biological NetworksCANCER BIOLOGY & Innovations in Cancer TherapyCell BiologyDisease BiologyGenome BiologyImaging-based Cancer Patient ManagementInternational Global Work in PharmaceuticalLiver & Digestive Diseases ResearchMetabolomicsMolecular Genetics & PharmaceuticalNutritionPharmaceutical Industry Competitive IntelligencePharmaceutical R&D InvestmentPopulation Health ManagementProteomicsStem Cells for Regenerative MedicineTechnology Transfer: Biotech and Pharmaceutical | Tagged Adenosine triphosphateATPGlycolysisHypoxia-inducible factorsKrebLactate dehydrogenaseMammalian target of rapamycinMitochondrionWarburg Effect

WordCloud for Article #1 – ABOVE the image your place: WC #, Article name, Who create the WC, see Example


Is the Warburg Effect the Cause or the Effect of Cancer: A 21st Century View?

Article #1: WordCloud by DM


Article Title (Live Link)All Time ViewsCategories of Research
Big Data in Genomic Medicine695Bio Instrumentation in Experimental Life Sciences ResearchChemical Biology and its relations to Metabolic DiseaseChemical GeneticsComputational Biology/Systems and BioinformaticsGenome BiologyGenomic Testing: Methodology for DiagnosisMolecular Genetics & PharmaceuticalPersonalized and Precision Medicine & Genomic ResearchPopulation Health Management, Genetics & PharmaceuticalStatistical Methods for Research EvaluationTechnology Transfer: Biotech and Pharmaceutical
Unraveling Retrograde Signaling Pathways57Biological Networks, Gene Regulation and EvolutionCell Biology, Signaling & Cell CircuitsComputational Biology/Systems and BioinformaticsDisease Biology, Small Molecules in Development of Therapeutic DrugsGenome BiologyInternational Global Work in PharmaceuticalPersonalized and Precision Medicine & Genomic ResearchPharmaceutical Industry Competitive Intelligence
Genomics of Bacterial and Archaeal Viruses69Biological Networks, Gene Regulation and EvolutionComputational Biology/Systems and BioinformaticsDisease Biology, Small Molecules in Development of Therapeutic DrugsGenome BiologyInfectious Disease & New Antibiotic TargetsInternational Global Work in PharmaceuticalMolecular Genetics & PharmaceuticalPharmaceutical Industry Competitive IntelligencePopulation Health Management, Genetics & PharmaceuticalScientist: Career considerationsTechnology Transfer: Biotech and Pharmaceutical
Genetics and Male Endocrinology103Biological Networks, Gene Regulation and EvolutionGenome BiologyGenomic Testing: Methodology for DiagnosisMolecular Genetics & PharmaceuticalPersonalized and Precision Medicine & Genomic ResearchPopulation Health Management, Genetics & PharmaceuticalReproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics

Article #1

Big Data in Genomic Medicine

Article #1: Word Cloud by NT

Article #2

Unraveling Retrograde Signaling Pathways

Article #2: Word Cloud by NT

Article #3

Genomics of Bacterial and Archaeal Viruses

Article #3: Word Cloud by NT

Article #4

Genetics and Male Endocrinology

Article #4: Word Cloud by NT


Table for Article #3

WordCloud for Article #3


Table for Article #4

WordCloud for Article #4


List of Contributors to Volume One

Larry Bernstein, MD, FCAP,  Senior Editor 

Introduction 1.1, 1.2, 1.4, 1.5, 2.2, 2.6, 3.1, 3.2, 3.3, 3.6, 4.6, 4.8, 5.8, 5.9, 5.10, 6.1, 6.2, 6.3, 6.5, 6.7, 6.8, 6.9, 6.10, 6.11, 6.12, 6.13, 6.14, 6.16, 6.17, 8.5, 8.6, 9.6, 10.4, 10.5, 10.6, 10.7, 11.1, 11.7, 11.10, 11.11, 12.2, 12.3, 12.4, 12.6, 12.8, 13.8, 13.9, 14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15.5, 15.8, 15.9, 15.9.4, 15.11, 16.1, 16.2, 16.3, 16.4, 16.5, 17.2, 18.1, 18.2, 18.5, 18.6, 20.2, 20.3, 20.4, 20.5, 20.6, Introduction-21, Summary-21, Volume Summary, Epilogue

Stephen J. Williams, PhD, Editor

2.3, 2.7, 6.15, 7.6, 8.8, 11.8, 12.5, 12.7, 15.3, 20.7, Introduction-21

Aviva Lev-Ari, PhD, RN, Editor-in-Chief, BioMed e-Books Series

1.6, 2.1, 2.5, 3.4, 3.5, 3.7, 3.8, 4.1, 4.4, 4.5, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 6.18, 7.1, 7.2, 7.3, 7.4, 7.5, 8.1, 8.2, 8.3, 8.7, 8.9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.8, 10.1, 10.2, 10.3, 10.8, 11.2, 11.3, 11.4, 11.5, 11.9, 12.1, 13.5 13.7, 15.1, 15.2, 15.4, 15.6, 15.7, 15.9.1, 15.9.2, 15.9.3, 15.9.5, 15.10, 17.1, 18.3, 18.4, 19.4, 19.5, 20.1, 20.8, 21.1.1, 21.1.2, 21.1.3, 21.1.4, 21.2.1, 21.2.2, 21.2.3, 21.2.4, 21.3.1, 21.3.2, 21.4.2

Sudipta Saha, PhD
1.3, 6.6, 11.6, 13.2, 13.3, 13.4, 19.1, 19.2, 19.6, 19.7, 19.8, 19.9, 19.10

Ritu Saxena, PhD
4.2, 6.4, 9.7, 13.6, 14.1, 17.3, 17.4, 17.5, 19.3

Tilda Barlyia, PhD
8.4, 13.1, 14.2

Anamika Sarkar, PhD

Marcus W Feldman, PhD, Professor of Computational BiologyStanford University, Department of Biology


Demet Sag, PhD

4.7, 4.9, 4.10

electronic Table of Contents

Chapter 1

1.1 Advances in the Understanding of the Human Genome The Initiation and Growth of Molecular Biology and Genomics – Part I

1.2 CRACKING THE CODE OF HUMAN LIFE: Milestones along the Way – Part IIA

1.3 DNA – The Next-Generation Storage Media for Digital Information

1.4 CRACKING THE CODE OF HUMAN LIFE: Recent Advances in Genomic Analysis and Disease – Part IIC

1.5 Advances in Separations Technology for the “OMICs” and Clarification of Therapeutic Targets

1.6 Genomic Analysis: FLUIDIGM Technology in the Life Science and Agricultural Biotechnology

Chapter 2

2.1 2013 Genomics: The Era Beyond the Sequencing of the Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

2.2 DNA structure and Oligonucleotides

2.3 Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single Human Cell 

2.4 Genomics and Evolution

2.5 Protein-folding Simulation: Stanford’s Framework for Testing and Predicting Evolutionary Outcomes in Living Organisms – Work by Marcus Feldman

2.6 The Binding of Oligonucleotides in DNA and 3-D Lattice Structures

2.7 Finding the Genetic Links in Common Disease: Caveats of Whole Genome Sequencing Studies

Chapter 3

3.1 Big Data in Genomic Medicine

3.2 CRACKING THE CODE OF HUMAN LIFE: The Birth of Bioinformatics & Computational Genomics – Part IIB 

3.3 Expanding the Genetic Alphabet and linking the Genome to the Metabolome

3.4 Metabolite Identification Combining Genetic and Metabolic Information: Genetic Association Links Unknown Metabolites to Functionally Related Genes

3.5 MIT Scientists on Proteomics: All the Proteins in the Mitochondrial Matrix identified

3.6 Identification of Biomarkers that are Related to the Actin Cytoskeleton

3.7 Genetic basis of Complex Human Diseases: Dan Koboldt’s Advice to Next-Generation Sequencing Neophytes

3.8 MIT Team Researches Regulatory Motifs and Gene Expression of Erythroleukemia (K562) and Liver Carcinoma (HepG2) Cell Lines

Chapter 4

4.1 ENCODE Findings as Consortium

4.2 ENCODE: The Key to Unlocking the Secrets of Complex Genetic Diseases

4.3 Reveals from ENCODE Project will Invite High Synergistic Collaborations to Discover Specific Targets  

4.4 Human Variome Project: encyclopedic catalog of sequence variants indexed to the human genome sequence

4.5 Human Genome Project – 10th Anniversary: Interview with Kevin Davies, PhD – The $1000 Genome

4.6 Quantum Biology And Computational Medicine

4.7 The Underappreciated EpiGenome

4.8 Unraveling Retrograde Signaling Pathways

4.9  “The SILENCE of the Lambs” Introducing The Power of Uncoded RNA

4.10  DNA: One man’s trash is another man’s treasure, but there is no JUNK after all

Chapter 5

5.1 Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1 

5.2 Computational Genomics Center: New Unification of Computational Technologies at Stanford

5.3 Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3

5.4 Cancer Genomics – Leading the Way by Cancer Genomics Program at UC Santa Cruz

5.5 Genome and Genetics: Resources @Stanford, @MIT, @NIH’s NCBCS

5.6 NGS Market: Trends and Development for Genotype-Phenotype Associations Research

5.7 Speeding Up Genome Analysis: MIT Algorithms for Direct Computation on Compressed Genomic Datasets

5.8  Modeling Targeted Therapy

5.9 Transphosphorylation of E-coli Proteins and Kinase Specificity

5.10 Genomics of Bacterial and Archaeal Viruses

Chapter 6

6.1  Directions for Genomics in Personalized Medicine

6.2 Ubiquinin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

6.3 Mitochondrial Damage and Repair under Oxidative Stress

6.4 Mitochondria: More than just the “Powerhouse of the Cell”

6.5 Mechanism of Variegation in Immutans

6.6 Impact of Evolutionary Selection on Functional Regions: The imprint of Evolutionary Selection on ENCODE Regulatory Elements is Manifested between Species and within Human Populations

6.7 Cardiac Ca2+ Signaling: Transcriptional Control

6.8 Unraveling Retrograde Signaling Pathways

6.9 Reprogramming Cell Fate

6.10 How Genes Function

6.11 TALENs and ZFNs

6.12 Zebrafish—Susceptible to Cancer

6.13 RNA Virus Genome as Bacterial Chromosome

6.14 Cloning the Vaccinia Virus Genome as a Bacterial Artificial Chromosome 

6.15 Telling NO to Cardiac Risk- DDAH Says NO to ADMA(1); The DDAH/ADMA/NOS Pathway(2)

6.16  Transphosphorylation of E-coli proteins and kinase specificity

6.17 Genomics of Bacterial and Archaeal Viruses

6.18  Diagnosing Diseases & Gene Therapy: Precision Genome Editing and Cost-effective microRNA Profiling

Chapter 7

7.1 Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders @ http://pharmaceuticalintelligence.com

7.2 Consumer Market for Personal DNA Sequencing: Part 4

7.3 GSK for Personalized Medicine using Cancer Drugs Needs Alacris Systems Biology Model to Determine the In Silico Effect of the Inhibitor in its “Virtual Clinical Trial”

7.4 Drugging the Epigenome

7.5 Nation’s Biobanks: Academic institutions, Research institutes and Hospitals – vary by Collections Size, Types of Specimens and Applications: Regulations are Needed

7.6 Personalized Medicine: Clinical Aspiration of Microarrays

Chapter 8

8.1 Personalized Medicine as Key Area for Future Pharmaceutical Growth

8.2 Inaugural Genomics in Medicine – The Conference Program, 2/11-12/2013, San Francisco, CA

8.3 The Way With Personalized Medicine: Reporters’ Voice at the 8th Annual Personalized Medicine Conference, 11/28-29, 2012, Harvard Medical School, Boston, MA

8.4 Nanotechnology, Personalized Medicine and DNA Sequencing

8.5 Targeted Nucleases

8.6 Transcript Dynamics of Proinflammatory Genes

8.7 Helping Physicians identify Gene-Drug Interactions for Treatment Decisions: New ‘CLIPMERGE’ program – Personalized Medicine @ The Mount Sinai Medical Center

8.8 Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing[1]

8.9 Diagnosing Diseases & Gene Therapy: Precision Genome Editing and Cost-effective microRNA Profiling

Chapter 9

9.1 Personal Tale of JL’s Whole Genome Sequencing

9.2 Inspiration From Dr. Maureen Cronin’s Achievements in Applying Genomic Sequencing to Cancer Diagnostics

9.3 Inform Genomics Developing SNP Test to Predict Side Effects, Help MDs Choose among Chemo Regimens

9.4 SNAP: Predict Effect of Non-synonymous Polymorphisms: How Well Genome Interpretation Tools could Translate to the Clinic

9.5  LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

9.6 The Initiation and Growth of Molecular Biology and Genomics – Part I

9.7 Personalized Medicine-based Cure for Cancer Might Not Be Far Away

9.8 Personalized Medicine: Cancer Cell Biology and Minimally Invasive Surgery (MIS)

 Chapter 10

10.1 Pfizer’s Kidney Cancer Drug Sutent Effectively caused REMISSION to Adult Acute Lymphoblastic Leukemia (ALL)

10.2 Imatinib (Gleevec) May Help Treat Aggressive Lymphoma: Chronic Lymphocytic Leukemia (CLL)

10.3 Winning Over Cancer Progression: New Oncology Drugs to Suppress Passengers Mutations vs. Driver Mutations

10.4 Treatment for Metastatic HER2 Breast Cancer

10.5 Personalized Medicine in NSCLC

10.6 Gene Sequencing – to the Bedside

10.7 DNA Sequencing Technology

10.8 Nobel Laureate Jack Szostak Previews his Plenary Keynote for Drug Discovery Chemistry

Chapter 11

11.1 mRNA Interference with Cancer Expression

11.2 Angiogenic Disease Research Utilizing microRNA Technology: UCSD and Regulus Therapeutics

11.3 Sunitinib brings Adult acute lymphoblastic leukemia (ALL) to Remission – RNA Sequencing – FLT3 Receptor Blockade

11.4 A microRNA Prognostic Marker Identified in Acute Leukemia 

11.5 MIT Team: Microfluidic-based approach – A Vectorless delivery of Functional siRNAs into Cells.

11.6 Targeted Tumor-Penetrating siRNA Nanocomplexes for Credentialing the Ovarian Cancer Oncogene ID4

11.7 When Clinical Application of miRNAs?

11.8 How mobile elements in “Junk” DNA promote cancer. Part 1: Transposon-mediated tumorigenesis,

11.9 Potential Drug Target: Glycolysis Regulation – Oxidative Stress-responsive microRNA-320

11.10  MicroRNA Molecule May Serve as Biomarker

11.11 What about Circular RNAs?

Chapter 12

12.1 The “Cancer Establishments” Examined by James Watson, Co-discoverer of DNA w/Crick, 4/1953

12.2 Otto Warburg, A Giant of Modern Cellular Biology

12.3 Is the Warburg Effect the Cause or the Effect of Cancer: A 21st Century View?

12.4 Hypothesis – Following on James Watson

12.5 AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo

12.6 AKT signaling variable effects

12.7 Rewriting the Mathematics of Tumor Growth; Teams Use Math Models to Sort Drivers from Passengers

12.8 Phosphatidyl-5-Inositol signaling by Pin1

Chapter 13

13.1 Nanotech Therapy for Breast Cancer

13.2 BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

13.3 Exome sequencing of serous endometrial tumors shows recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes

13.4 Recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes in serous endometrial tumors

13.5 Prostate Cancer: Androgen-driven “Pathomechanism” in Early onset Forms of the Disease

13.6 In focus: Melanoma Genetics

13.7 Head and Neck Cancer Studies Suggest Alternative Markers More Prognostically Useful than HPV DNA Testing

13.8 Breast Cancer and Mitochondrial Mutations

13.9  Long noncoding RNA network regulates PTEN transcription

Chapter 14

14.1 HBV and HCV-associated Liver Cancer: Important Insights from the Genome

14.2 Nanotechnology and HIV/AIDS treatment

14.3 IRF-1 Deficiency Skews the Differentiation of Dendritic Cells

14.4 Sepsis, Multi-organ Dysfunction Syndrome, and Septic Shock: A Conundrum of Signaling Pathways Cascading Out of Control

14.5  Five Malaria Genomes Sequenced

14.6 Rheumatoid Arthritis Risk

14.7 Approach to Controlling Pathogenic Inflammation in Arthritis

14.8 RNA Virus Genome as Bacterial Chromosome

14.9 Cloning the Vaccinia Virus Genome as a Bacterial Artificial Chromosome

Chapter 15

15.1 Personalized Cardiovascular Genetic Medicine at Partners HealthCare and Harvard Medical School

15.2 Congestive Heart Failure & Personalized Medicine: Two-gene Test predicts response to Beta Blocker Bucindolol

15.3 DDAH Says NO to ADMA(1); The DDAH/ADMA/NOS Pathway(2)

15.4 Peroxisome Proliferator-Activated Receptor (PPAR-gamma) Receptors Activation: PPARγ Transrepression for Angiogenesis in Cardiovascular Disease and PPARγ Transactivation for Treatment of Diabetes

15.5 BARI 2D Trial Outcomes

15.6 Gene Therapy Into Healthy Heart Muscle: Reprogramming Scar Tissue In Damaged Hearts

15.7 Obstructive coronary artery disease diagnosed by RNA levels of 23 genes – CardioDx, a Pioneer in the Field of Cardiovascular Genomic  Diagnostics

15.8 Ca2+ signaling: transcriptional control

15.9 Lp(a) Gene Variant Association

15.9.1 Two Mutations, in the PCSK9 Gene: Eliminates a Protein involved in Controlling LDL Cholesterol

15.9.2. Genomics & Genetics of Cardiovascular Disease Diagnoses: A Literature Survey of AHA’s Circulation Cardiovascular Genetics, 3/2010 – 3/2013

15.9.3 Synthetic Biology: On Advanced Genome Interpretation for Gene Variants and Pathways: What is the Genetic Base of Atherosclerosis and Loss of Arterial Elasticity with Aging

15.9.4 The Implications of a Newly Discovered CYP2J2 Gene Polymorphism Associated with Coronary Vascular Disease in the Uygur Chinese Population

15.9.5  Gene, Meis1, Regulates the Heart’s Ability to Regenerate after Injuries.

15.10 Genetics of Conduction Disease: Atrioventricular (AV) Conduction Disease (block): Gene Mutations – Transcription, Excitability, and Energy Homeostasis

15.11 How Might Sleep Apnea Lead to Serious Health Concerns like Cardiac and Cancers?

Chapter 16

16.1 Can Resolvins Suppress Acute Lung Injury?

16.2 Lipoxin A4 Regulates Natural Killer Cell in Asthma

16.3 Biological Therapeutics for Asthma

16.4 Genomics of Bronchial Epithelial Dysplasia

16.5 Progression in Bronchial Dysplasia

Chapter 17

17.1 Breakthrough Digestive Disorders Research: Conditions Affecting the Gastrointestinal Tract.

17.2 Liver Endoplasmic Reticulum Stress and Hepatosteatosis

17.3 Biomarkers-identified-for-recurrence-in-hbv-related-hcc-patients-post-surgery

17.4  Usp9x: Promising Therapeutic Target for Pancreatic Cancer

17.5 Battle of Steve Jobs and Ralph Steinman with Pancreatic cancer: How We Lost

Chapter 18

18.1 Ubiquitin Pathway Involved in Neurodegenerative Disease

18.2 Genomic Promise for Neurodegenerative Diseases, Dementias, Autism Spectrum, Schizophrenia, and Serious Depression

18.3 Neuroprotective Therapies: Pharmacogenomics vs Psychotropic Drugs and Cholinesterase Inhibitors

18.4 Ustekinumab New Drug Therapy for Cognitive Decline Resulting from Neuroinflammatory Cytokine Signaling and Alzheimer’s Disease

18.5 Cell Transplantation in Brain Repair

18.6 Alzheimer’s Disease Conundrum – Are We Near the End of the Puzzle?

Chapter 19

19.1 Genetics and Male Endocrinology

19.2 Genomic Endocrinology and its Future

19.3 Commentary on Dr. Baker’s post “Junk DNA Codes for Valuable miRNAs: Non-coding DNA Controls Diabetes”

19.4 Therapeutic Targets for Diabetes and Related Metabolic Disorders

19.5 Secondary Hypertension caused by Aldosterone-producing Adenomas caused by Somatic Mutations in ATP1A1 and ATP2B3 (adrenal cortical; medullary or Organ of Zuckerkandl is pheochromocytoma)

19.6 Personal Recombination Map from Individual’s Sperm Cell and its Importance

19.7 Gene Trap Mutagenesis in Reproductive Research

19.8 Pregnancy with a Leptin-Receptor Mutation

19.9 Whole-genome Sequencing in Probing the Meiotic Recombination and Aneuploidy of Single Sperm Cells

19.10 Reproductive Genetic Testing

Chapter 20

20.1 Genomics & Ethics: DNA Fragments are Products of Nature or Patentable Genes?

20.2 Understanding the Role of Personalized Medicine

20.3 Attitudes of Patients about Personalized Medicine

20.4  Genome Sequencing of the Healthy

20.5   Genomics in Medicine – Tomorrow’s Promise

20.6  The Promise of Personalized Medicine

20.7 Ethical Concerns in Personalized Medicine: BRCA1/2 Testing in Minors and Communication of Breast Cancer Risk

 20.8 Genomic Liberty of Ownership, Genome Medicine and Patenting the Human Genome

Chapter 21

Recent Advances in Gene Editing Technology Adds New Therapeutic Potential for the Genomic Era:  Medical Interpretation of the Genomics Frontier – CRISPR – Cas9


21.1 Introducing CRISPR/Cas9 Gene Editing Technology – Works by Jennifer A. Doudna

21.1.1 Ribozymes and RNA Machines – Work of Jennifer A. Doudna

21.1.2 Evaluate your Cas9 gene editing vectors: CRISPR/Cas Mediated Genome Engineering – Is your CRISPR gRNA optimized for your cell lines?

21.1.3 2:15 – 2:45, 6/13/2014, Jennifer Doudna “The biology of CRISPRs: from genome defense to genetic engineering”

21.1.4  Prediction of the Winner RNA Technology, the FRONTIER of SCIENCE on RNA Biology, Cancer and Therapeutics  & The Start Up Landscape in BostonGene Editing – New Technology The Missing link for Gene Therapy?

21.2 CRISPR in Other Labs

21.2.1 CRISPR @MIT – Genome Surgery

21.2.2 The CRISPR-Cas9 System: A Powerful Tool for Genome Engineering and Regulation

Yongmin Yan and Department of Gastroenterology, Hepatology & Nutrition, University of Texas M.D. Anderson Cancer, Houston, USADaoyan Wei*

21.2.3 New Frontiers in Gene Editing: Transitioning From the Lab to the Clinic, February 19-20, 2015 | The InterContinental San Francisco | San Francisco, CA

21.2.4 Gene Therapy and the Genetic Study of Disease: @Berkeley and @UCSF – New DNA-editing technology spawns bold UC initiative as Crispr Goes Global

21.2.5 CRISPR & MAGE @ George Church’s Lab @ Harvard

21.3 Patents Awarded and Pending for CRISPR

21.3.1 Litigation on the Way: Broad Institute Gets Patent on Revolutionary Gene-Editing Method

21.3.2 The Patents for CRISPR, the DNA editing technology as the Biggest Biotech Discovery of the Century

2.4 CRISPR/Cas9 Applications

21.4.1  Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells using a bacterial CRISPR/Cas 

21.4.2 CRISPR: Applications for Autoimmune Diseases @UCSF

21.4.3 In vivo validated mRNAs


21.4.6 Level of Comfort with Making Changes to the DNA of an Organism

21.4.7 Who will be the the First to IPO: Novartis bought in to Intellia (UC, Berkeley) as well as Caribou (UC, Berkeley) vs Editas (MIT)??

21.4.8 CRISPR/Cas9 Finds Its Way As an Important Tool For Drug Discovery & Development


WordCloud Visualization of LPBI’s Top Sixteen Articles on CANCER in eight categories and by Views at All Time and their Research Categories in the Ontology of PharmaceuticalIntelligence.com

Curator: Stephen J. Williams, PhD and WordCloud Producers: Daniel Menzin, Noam Steiner-Tomer, Zach Day, Ofer Markman, PhD and Aviva Lev-Ari, PhD, RN

Introduction (From Cancer Volume 1): Cancer is the second most cause of medically related deaths in the developed world.  However, concerted efforts among most developed nations to eradicate the disease, such as increased government funding for cancer research and a mandated ‘war on cancer’ in the mid 70’s has translated into remarkable improvements in diagnosis, early detection, and cancer survival rates for many individual cancer.  For example, survival rate for breast and colon cancer have improved dramatically over the last 40 years.  In the UK, overall median survival times have improved from one year in 1972 to 5.8 years for patients diagnosed in 2007.  In the US, the overall 5 year survival improved from 50% for all adult cancers and 62% for childhood cancer  in 1972 to 68% and childhood cancer rate improved to 82% in 2007. However, for some cancers, including lung, brain, pancreatic and ovarian cancer, there has been little improvement in survival rates since the “war on cancer” has started.

Many of the improvements in survival rates are a direct result of the massive increase in the knowledge of tumor biology obtained through ardent basic research.  Breakthrough discoveries regarding oncogenes, cancer cell signaling, survival, and regulated death mechanisms, tumor immunology, genetics and molecular biology, biomarker research, and now nanotechnology and imaging, have directly led to the advances we now we in early detection, chemotherapy, personalized medicine, as well as new therapeutic modalities such as cancer vaccines and immunotherapies and combination chemotherapies.  Molecular and personalized therapies such as trastuzumab and aromatase inhibitors for breast cancer, imatnib for CML and GIST related tumors, bevacizumab for advanced colorectal cancer have been a direct result of molecular discoveries into the nature of cancer.

Purpose:  To Curate a listing of articles in CANCER representative of  the Agora of the LPBI Journal for the purpose of generating WordClouds for eventual Natural Language Processing.


For a full description of methodology please contact the LPBI Group at avivalev-ari@alum.berkeley.edu , LinkedIn, or through Twitter @pharma_BI.

Methods in Brief:

 A listing of all Cancer articles which had been viewed at least 131 times was generated.  They could either be authored, curated, written, or reported articles.  The initial list was generated by Daniel, Chief Technology Officer.  This listing was generated as an Excel worksheet.  (A Total of 1555 articles had views of at least 133 total all time views of which 352 were explicitly on CancerEach article was read and verified for cancer-related content).

Each Cancer article was then categorized  according to the STYLE in which it was written as follows

    • Authored; requires original thought, ideas, and multiple references; has a methodology
    • Curated; multiple disparate sources connected by a theme generated by the curator
    • Written: as a writer; only one or two references but having some input into content
    • Reported: an article which only reports on a topic or event; usually a new report or press announcement

After categorizing the STYLE,  the AUTHORED, CURATED, AND WRITTEN articles (263 articles) were further sub-categorized based on the following subject material categories:

    • Therapeutic 
    • Diagnosis 
    • Imaging 
    • Mechanisms of tumorigenesis 
    • Genomics 
    • Resistance and Adverse Events 
    • Patient Care and Personalized Care 
    • Cancer Models and Research 

Each article author or curated was also recorded in the Excel spreadsheet.  A mind map of each of the major authors and curators on the topic of Cancer was generated by curating common themes in the articles as well as opinion pieces written by each of the main editors of the Cancer Volumes (I and II).  The mind-map guided the further selection of 16 articles which were representative of the above sub-categories and reflective of the editor(s) theory of cancer etiology and vision of paradigm changes within the field.  WordClouds were generated from these listing of 16 representative articles of the Agora of Cancer offerings within the LPBI database.



Article Selection and Categorization

Of the 352 CANCER articles, there were 69 AUTHORED, 178 CURATED, 16 WRITTEN, and 89 REPORTED articles. Sub-categorization of the Authored, Curated, and Written articles yielded the following 

    • Therapeutic (69 articles)
    • Diagnosis (36 articles)
    • Imaging (16 articles)
    • Mechanisms of tumorigenesis (40 articles)
    • Genomics (69 articles)
    • Resistance and Adverse Events (12 articles)
    • Patient Care and Personalized Care (12 articles)
    • Cancer Models and Research (12 articles)

This resulted in 263 article which were either authored, curated or written.  These 263 articles were then used for further sub-selection based on  the Mind Map generated (as described below). 

Generation of a Mind Map of Editors of Cancer Volume 1 and 2

In the Vision of Dr. Larry H. Bernstein:

A multidisciplinary approach has led us to a unique multidisciplinary or systems view of cancer, with different fields of study offering their unique expertise, contributions, and viewpoints on the etiology of cancer.  Diverse fields in immunology, biology, biochemistry, toxicology, molecular biology, virology, mathematics, social activism and policy, and engineering have made such important contributions to our understanding of cancer, that without cooperation among these diverse fields our knowledge of cancer would never had evolved as it has.


In the Vision of Dr. Stephen J. Williams

This ebook highlights some of the recent trends and discoveries in cancer research and cancer treatment, with particular attention how new technological and informatics advancements have ushered in paradigm shifts in how we think about, diagnose, and treat cancer.  The book is organized with the 8 hallmarks of cancer in mind, concepts which are governing principles of cancer from Drs. Hanahan and Weinberg (Hallmarks of Cancer).

Maintaining Proliferative Signals

Avoiding Immune Destruction

Evading Growth Suppressors

Resisting Cell Death

Becoming Immortal


Deregulating Cellular Energy

Activating Invasion and Metastasis

Therefore the reader is asked to understand how each of these underlying principles are being translated to current breakthrough discoveries, in association with the basic biological knowledge we have amassed through diligent research and how these principals and latest research can be used by the next generation of cancer scientist and oncologist to provide the future breakthroughs.  As the past basic research had provided a new platform for the era of genomics in oncology, it is up to this next generation of scientists and oncologists to provide the basic research for the next platform which will create the future breakthroughs to combat this still deadly disease.

In the Vision of Dr. Dror Nir

The concept of personalized medicine has been around for many years. Recent advances in cancer treatment choice, availability of treatment modalities, including “adaptable” drugs and the fact that patients’ awareness increases, put medical practitioners under pressure to better clinical assessment of this disease prior to treatment decision and quantitative reporting of treatment outcome. In practice, this translates into growing demand for accurate, noninvasive, nonuser-dependent probes for cancer detection and localization. The advent of medical-imaging technologies such as image-fusion, functional-imaging and noninvasive tissue characterisation is playing an imperative role in answering this demand thus transforming the concept of personalized medicine in cancer into practice. The leading modality in that respect is medical imaging. To date, the main imaging systems that can provide reasonable level of cancer detection and localization are: CT, mammography, Multi-Sequence MRI, PET/CT and ultrasound. All of these require skilled operators and experienced imaging interpreters in order to deliver what is required at a reasonable level. It is generally agreed by radiologists and oncologists that in order to provide a comprehensive work-flow that complies with the principles of personalized medicine, future cancer patients’ management will heavily rely on computerized image interpretation applications that will extract from images in a standardized manner measurable imaging biomarkers leading to better clinical assessment of cancer patients.


Using these VISIONS of CANCER a mind map was generated for each of these authors/editors. Mind maps consisted of a thematic sentence to describe their individual VISION of CANCER and a second sentence describing what each author/editor saw as greatest PARADIGM SHIFT in their respective sub-disciplines of cancer (basic and clinical).  The MIND MAP is shown below:


CategoryArticle nameIntern Name
Therapeutic (69 articles)



Targeting the Wnt Pathway [7.11]



Therapeutic (69 articles)



Warburg Effect and Mitochondrial Regulation- 2.1.3Daniel
Therapeutic (69 articles)



Cancer Mutations Across the LandscapeDaniel
Therapeutic (69 articles)



Diagnosis (36 articles)



Targeting Cancer Neoantigens and Metabolic Change in T-cells









Diagnosis (36 articles)





In Search of Clarity on Prostate Cancer Screening, Post-Surgical Followup, and Prediction of Long Term Remission


Diagnosis (36 articles)







Imaging (16 articles)



State of the art in oncologic imaging of Prostate




Imaging (16 articles)



Mechanisms of tumorigenesis (40 articles)



Neuroblastoma: A review




Mechanisms of tumorigenesis (40 articles)



Is the Warburg Effect the Cause or the Effect of Cancer: A 21st Century View?Williams
Mechanisms of tumorigenesis (40 articles)



How Mobile Elements in “Junk DNA Promote Cancer – Part 1: Transposon-mediated Tumorigenesis”Daniel
Mechanisms of tumorigenesis (40 articles)



Genomics (69 articles)



Akt inhibition for cancer treatment, where do we stand today?Williams
Genomics (69 articles)



Thymosin alpha1 and melanomaWilliams
Genomics (69 articles)



AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In VivoWilliams
Genomics (69 articles)



Steroids, Inflammation, and CAR-T TherapyDaniel
Genomics (69 articles)



Resistance and Adverse Events (12 articles)



Predicting Tumor Response, Progression, and Time to RecurrenceWilliams
Resistance and Adverse Events (12 articles)



Patient Care and Personalized Care (12 articles)



Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders @ http://pharmaceuticalintelligence.comWilliams
Patient Care and Personalized Care (12 articles)



Cancer Models and Research (12 articles)



Humanized Mice May Revolutionize Cancer Drug DiscoveryWilliams
Cancer Models and Research (12 articles)




Article #1

Targeting the Wnt Pathway [7.11]

Article #1: Word Cloud by NT

Article #2

Warburg Effect and Mitochondrial Regulation- 2.1.3

Word Cloud by DM

Article #3

Cancer Mutations Across the Landscape

Word Cloud by DM

Article #4

Targeting Cancer Neoantigens and Metabolic Change in T-cells

Article #4: Word Cloud by NT

Article #6

State of the art in oncologic imaging of Prostate

Article #6: Word Cloud by NT

Article #8

Neuroblastoma: A Review

Article #8: Word Cloud by NT

Article #9

How Mobile Elements in “Junk DNA Promote Cancer – Part 1: Transposon-mediated Tumorigenesis”

Word Cloud by DM

Article #13

Steroids, Inflammation, and CAR-T Therapy

Word Cloud by DM







Authored by Dr. Williams:


Purpose: To Curate a listing of articles in CANCER for the purpose of generating WordClouds for eventual Natural Language Processing

Initial Request: Aviva requested 12 articles in CANCER to be used to generate a WordCloud for AI machine learning

Problem: Only 12 article only represents less than 1% of all CANCER OFFERINGS by LPBI and would severely limit the ability to generate a meaningful WordCloud. Dr Williams then used a methodology to curate a meaningful list which could be repeated on extended offerings and subjects.

Solution: Dr. Williams generated a listing of all Cancer articles which had been viewed at least 131 times. They could either be authored, curated, written, or reported articles. The initial list was generated by Daniel, Chief Technology Officer. This listing was generated as an Excel worksheet. (A Total of 1555 articles had views of at least 133 total all time views of which 352 were explicitly on Cancer. Each article was read for content).

  • Williams then categorized each article according to the STYLE in which it was written as follows
    • Authored; requires original thought, ideas, and multiple references; has a methodology
    • Curated; multiple disparate sources connected by a theme generated by the curator
    • Written: as a writer; only one or two references but having some input into content
    • Reported: an article which only reports on a topic or event; usually a new report or press announcement

Of the 352 CANCER articles, there were 69 AUTHORED, 178 CURATED, 16 WRITTEN, and 89 REPORTED articles

  • Williams, after categorizing the STYLE, then categorized the AUTHORED, CURATED, AND WRITTEN articles (263 articles) based on the following subject material categories:
    • Therapeutic (69 articles)
    • Diagnosis (36 articles)
    • Imaging (16 articles)
    • Mechanisms of tumorigenesis (40 articles)
    • Genomics (69 articles)
    • Resistance and Adverse Events (12 articles)
    • Patient Care and Personalized Care (12 articles)
    • Cancer Models and Research (12 articles)

The following tables represent the articles in each sub-category

Therapeutic (69 articles)

Akt inhibition for cancer treatment, where do we stand today?

Crucial role of Nitric Oxide in Cancer

Targeting Mitochondrial-bound Hexokinase for Cancer Therapy

The Development of siRNA-Based Therapies for Cancer

Nanotech Therapy for Breast Cancer

Thymosin alpha1 and melanoma

What can we expect of tumor therapeutic response?

β Integrin emerges as an important player in mitochondrial dysfunction associated Gastric Cancer

Personalized Medicine and Colon Cancer

Pancreatic Cancer: a discovery in Toulouse that would slow its progression

Quantitative Systems Pharmacology – Use in Oncology Clinical Development: Anna Georgieva Kondic, PhD

Predicting Tumor Response, Progression, and Time to Recurrence

Usp9x: Promising therapeutic target for pancreatic cancer

Targeting Epithelial To Mesenchymal Transition (EMT) As A Therapy Strategy For Pancreatic Cancer

VEGF activation and signaling, lysine methylation, and activation of receptor tyrosine kinase

Brain Cancer Vaccine in Development and other considerations

Paclitaxel vs Abraxane (albumin-bound paclitaxel)

Mesothelin: An early detection biomarker for cancer (By Jack Andraka)

Confined Indolamine 2, 3 dioxygenase (IDO) Controls the Hemeostasis of Immune Responses for Good and Bad

AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo

Targeting the Wnt Pathway [7.11]

Monoclonal Antibody Therapy and Market

Non-small Cell Lung Cancer drugs – where does the Future lie?

CD47: Target Therapy for Cancer

Peroxisome proliferator-activated receptor (PPAR-gamma) Receptors Activation: PPARγ transrepression for Angiogenesis in Cardiovascular Disease and PPARγ transactivation for Treatment of Diabetes

Cardio-oncology and Onco-Cardiology Programs: Treatments for Cancer Patients with a History of Cardiovascular Disease

Mitochondrial fission and fusion: potential therapeutic targets?

Heroes in Medical Research: Barnett Rosenberg and the Discovery of Cisplatin

Imatinib (Gleevec) May Help Treat Aggressive Lymphoma: Chronic Lymphocytic Leukemia (CLL)

Lung Cancer (NSCLC), drug administration and nanotechnology

Soft Tissue Sarcoma: an Overview

Steroids, Inflammation, and CAR-T Therapy

14th ANNUAL BIOTECH IN EUROPE FORUM For Global Partnering & Investment 9/30 – 10/1/2014 • Congress Center Basel – SACHS Associates, London

Moderna Therapeutics Deal with Merck: Are Personalized Vaccines here?

Good and Bad News Reported for Ovarian Cancer Therapy

Topoisomerase 1 inhibitors and cancer therapy

J.P. Morgan 34th Annual Healthcare Conference & Biotech Showcase™ January 11 – 15, 2016 in San Francisco

Bisphosphonates and Bone Metabolism

Cancer Immunotherapy

Signaling of Immune Response in Colon Cancer

Oncolytic Virus Immuno-Therapy: New Approach for a New Class of Immunotherapy Drugs

Angiogenesis Inhibitors [9.5]

Novel Approaches to Cancer Therapy [11.1]

Findings on Bacillus Calmette–Guérin (BCG) for Superficial Bladder Cancer

Are CXCR4 Antagonists Making a Comeback in Cancer Chemotherapy?

The 2nd ANNUAL Sachs Cancer Bio Partnering & Investment Forum Promoting Public & Private Sector Collaboration & Investment in Drug Development, 19th March 2014 • New York Academy of Sciences • USA

Bispecific and Trispecific Engagers: NK-T Cells and Cancer Therapy

Immune-Oncology Molecules In Development & Articles on Topic in @pharmaceuticalintelligence.com

Monoclonal Antibody Therapy: What is in the name or clear description?

Nanoparticle Delivery to Cancer Drug Targets

Autophagy-Modulating Proteins and Small Molecules Candidate Targets for Cancer Therapy: Commentary of Bioinformatics Approaches

Immunotherapy in Cancer: A Series of Twelve Articles in the Frontier of Oncology by Larry H Bernstein, MD, FCAP

2014 MassBio Annual Meeting 4/3 – 4/4 2014, Royal Sonesta Hotel, Cambridge, MA

AACR2016 – Cancer immunotherapy

Report on Cancer Immunotherapy Market & Clinical Pipeline Insight

CD-4 Therapy for Solid Tumors

In focus: Melanoma therapeutics

Allogeneic Stem Cell Transplantation [9.3]

Cyclic Dinucleotides and Histone deacetylase inhibitors

Cancer Innovations from across the Web

“””Thymosin alpha1 and melanoma””,168

NGS Market: Trends and Development for Genotype-Phenotype Associations Research”””

Myelodysplastic syndrome and acute myeloid leukemia following adjuvant chemotherapy

Cancer Cell Therapy: Global Start up Acquisitions in Oncolytic Viruses (OV) Therapeutics – a Pipeline of 70 OVs in Clinical Development and another 95 in Preclinical Programs

Cancer Vaccines: Targeting Cancer Genes for Immunotherapy – A Conference by Keystone Symposia on Molecular and Cellular Biology

IDO for Commitment of a Life Time: The Origins and Mechanisms of IDO, indolamine 2, 3-dioxygenase

The Delicate Connection: IDO (Indolamine 2, 3 dehydrogenase) and Cancer Immunology

Advances in Cancer Immunotherapy

COMBAT study: Combination of BL-8040 and KEYTRUDA® (pembrolizumab) for Pancreatic Cancer: Collaboration Agreement Merck, BioLineRx and MD Anderson Cancer Center

DIAGNOSIS (36 articles)

Nanotechnology: Detecting and Treating metastatic cancer in the lymph node

Acute Lymphoblastic Leukemia (ALL) and Nanotechnology

Role of Progesterone in Breast Cancer Progression

Today’s fundamental challenge in Prostate cancer screening

Sensors and Signaling in Oxidative Stress

City of Hope, Duarte, California – Combining Science with Soul to Create Miracles at a Comprehensive Cancer Center designated by the National Cancer Institute – An Interview with the Provost and Chief Scientific Officer of City of Hope, Steven T. Rosen, M.D.

In Focus: Identity of Cancer Stem Cells

Thermodynamic Modeling for Cancer Cells

Glypican-1 identifies cancer exosomes

Ultrasound-based Screening for Ovarian Cancer

Ovarian Cancer and fluorescence-guided surgery: A report

Diagnosing Lung Cancer in Exhaled Breath using Gold Nanoparticles

Pancreatic Cancer at the Crossroads of Metabolism

Virtual Biopsy – is it possible?

Prostate Cancer and Nanotecnology

Metabolomics based biomarker discoveries

Personalized Medicine: Cancer Cell Biology and Minimally Invasive Surgery (MIS)

Pancreatic Cancer Targeted Treatment?

Breast Cancer: Genomic profiling to predict Survival: Combination of Histopathology and Gene Expression Analysis

Targeting Cancer Neoantigens and Metabolic Change in T-cells

Cancer Immunotherapy Conference & Biomarkers for Cancer Immunotherapy Symposium, March 6-11, 2016 | Moscone North Convention Center | San Francisco, CA

New insights in cancer, cancer immunogenesis and circulating cancer cells

Circulating Biomarkers World Congress, March 23-24, 2015, Boston: Exosomes, Microvesicles, Circulating DNA, Circulating RNA, Circulating Tumor Cells, Sample Preparation

Prostate Cancer: Diagnosis and Novel Treatment – Articles of Note @PharmaceuticalIntelligence.com

Cancer Biomarkers

What about PDL-1 in oncotherapy diagnostics for NSCLC?

Novel biomarkers for targeting cancer immunotherapy

Hematological Cancer Classification

Cancer Biomarkers []

In Search of Clarity on Prostate Cancer Screening, Post-Surgical Followup, and Prediction of Long Term Remission

Biomarkers identified for recurrence in HBV-related HCC patients post surgery

Recent comprehensive review on the role of ultrasound in breast cancer management

Automated Breast Ultrasound System (‘ABUS’) for full breast scanning: The beginning of structuring a solution for an acute need!

“””The Molecular pathology of Breast Cancer Progression””,296

Medical MEMS BioMEMS and Sensor Applications”””

Battle of Steve Jobs and Ralph Steinman with Pancreatic cancer: How we lost

Metabolic drivers in aggressive brain tumors

IMAGING (16 articles)

Nanotechnology and MRI imaging

The unfortunate ending of the Tower of Babel construction project and its effect on modern imaging-based cancer patients’ management

Improving Mammography-based imaging for better treatment planning

State of the art in oncologic imaging of Colorectal cancers.

State of the art in oncologic imaging of Prostate.

Imaging Technology in Cancer Surgery

State of the art in oncologic imaging of lungs.

Causes and imaging features of false positives and false negatives on 18F-PET/CT in oncologic imaging

Clinical Trials on Schwannoma & Benign Intracranial Tumors Radiosurgery Treatment

Whole-body imaging as cancer screening tool; answering an unmet clinical need?

Improving Mammography-based imaging for better treatment planning

Imaging: seeing or imagining? (Part 1)

Knowing the tumor’s size and location, could we target treatment to THE ROI by applying imaging-guided intervention?

Imaging: seeing or imagining? (Part 2)

Tumor Imaging and Targeting: Predicting Tumor Response to Treatment: Where we stand?

State of the art in oncologic imaging of breast.

Mechanisms of tumorigenesis (40 articles)

Is the Warburg Effect the Cause or the Effect of Cancer: A 21st Century View?

In focus: Circulating Tumor Cells

Summary of Transcription, Translation ond Transcription Factors

Mitochondria: More than just the “powerhouse of the cell”

How Mobile Elements in “Junk DNA Promote Cancer – Part 1: Transposon-mediated Tumorigenesis”

Demythologizing sharks, cancer, and shark fins

A Synthesis of the Beauty and Complexity of How We View Cancer

Neuroblastoma: A review

Refined Warburg Hypothesis -2.1.2

Introduction – The Evolution of Cancer Therapy and Cancer Research: How We Got Here?

Epistemology of the Origin of Cancer: a New Paradigm

Role of Primary Cilia in Ovarian Cancer

Prologue to Cancer – e-book Volume One – Where are we in this journey?

“””The Molecular pathology of Breast Cancer Progression””, 325

Ultrasound-based Screening for Ovarian Cancer”””

The “Cancer establishments examined by James Watson 4/1953”

Lipids link to breast cancer

“””Thymosin alpha1 and melanoma””, 169

Amplifying Information Using S-Clustering and Relationship to Kullback-Liebler Distance: An Application to Myocardial Infarction”””

Wnt/β-catenin Signaling [7.10]

Cancer Signaling Pathways and Tumor Progression: Images of Biological Processes in the Voice of a Pathologist Cancer Expert

Mitochondrial Damage and Repair under Oxidative Stress

Nitric Oxide has a Ubiquitous Role in the Regulation of Glycolysis – with a Concomitant Influence on Mitochondrial Function


Ubiquitin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

Pancreatic Cancer and Crossing Roads of Metabolism

Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Warburg Effect Revisited – 2

Prostate Cancer Cells: Histone Deacetylase Inhibitors Induce Epithelial-to-Mesenchymal Transition

Naked Mole Rats Cancer-Free

In focus: Triple Negative Breast Cancer

Heat Shock Proteins (HSP) and Molecular Chaperones

Nonhematologic Cancer Stem Cells [11.2.3]

Mitochondria and Cancer: An overview of mechanisms

Growth Factors, Suppressors and Receptors in Tumorigenesis [7.1]

Upregulate Tumor Suppressor Pathways [7.5]

Nrf2 Role in Blocking DNA Damage

Prostate Cancer: Androgen-driven “Pathomechanism in Early-onset Forms of the Disease”

Cancer Metastasis

Halstedian model of cancer progression

Otto Warburg, A Giant of Modern Cellular Biology

Tang Prize for 2014: Immunity and Cancer

Genomics (69 articles)

Pancreatic Cancer: Genetics, Genomics and Immunotherapy

Summary of Signaling and Signaling Pathways

In focus: Melanoma Genetics

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

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

Stanniocalcin: A Cancer Biomarker.

The Underappreciated EpiGenome

Li -Fraumeni Syndrome and Pancreatic Cancer

“To Die or Not To Die” – Time and Order of Combination drugs for Triple Negative Breast Cancer cells: A Systems Level Analysis

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variation of a Single Human Cell

Metabolomics and prostate cancer

“The Molecular pathology of Breast Cancer Progression”, 172 Bioinformatic Tools for Cancer Mutational Analysis: COSMIC and Beyond”

Personalized Medicine in NSCLC

Notes On Tumor Heterogeneity: Targets and Mechanisms, from the 2015 AACR Meeting in Philadelphia PA

AstraZeneca’s WEE1 protein inhibitor AZD1775 Shows Success Against Tumors with a SETD2 mutation

A Primer on DNA and DNA Replication

Integrins, Cadherins, Signaling and the Cytoskeleton

The Molecular pathology of Breast Cancer Progression

Signaling transduction tutorial

Hematologic Malignancies [2.4.3]

Sunitinib brings Adult Acute Lymphoblastic Leukemia (ALL) to Remission – RNA Sequencing – FLT3 Receptor Blockade

Hypoxia Inducible Factor 1 (HIF-1)[7.9]

Observations on Human Papilloma Virus and Cancer

The role and importance of transcription factors

Differentiation Therapy – Epigenetics Tackles Solid Tumors

CRISPR-Cas9 Foundational Technology originated at UC, Berkeley & UCSF, Broad Institute is developing Biotech Applications — Intellectual Property emerging as Legal Potential Dispute

Bioinformatic Tools for Cancer Mutational Analysis: COSMIC and Beyond

Issues in Personalized Medicine: Discussions of Intratumor Heterogeneity from the Oncology Pharma forum on LinkedIn

The Human Proteome Map Completed

CRISPR/Cas9 Finds Its Way As an Important Tool For Drug Discovery & Development

Mitochondrial Isocitrate Dehydrogenase and Variants

Pathway Specific Targeting in Anticancer Therapies [7.7]

Protein-binding, Protein-Protein interactions & Therapeutic Implications [7.3]

Gene Editing with CRISPR gets Crisper

Delineating a Role for CRISPR-Cas9 in Pharmaceutical Targeting

RNA and the Transcription the Genetic Code

Role of Calcium, the Actin Skeleton, and Lipid Structures in Signaling and Cell Motility

Finding the Genetic Links in Common Disease: Caveats of Whole Genome Sequencing Studies

LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment: Part 2

Introduction to Metabolomics

CRACKING THE CODE OF HUMAN LIFE: Recent Advances in Genomic Analysis and Disease – Part IIC

Sirtuins [7.8]

Highlights from 8th Annual Personalized Medicine Conference, November 28-29, 2012, Harvard Medical School, Boston, MA

2019 Trends in Precision Medicine: A Perspective from Foundation Medicine

Loss of Gene Islands May Promote a Cancer Genome’s Evolution: A new Hypothesis on Oncogenesis

Warburg Effect and Mitochondrial Regulation- 2.1.3

Cancer Genomics – Leading the Way by Cancer Genomics Program at UC Santa Cruz

The Magic of the Pandora’s Box : Epigenetics and Stemness with Long non-coding RNAs (lincRNA)

HBV and HCV-associated Liver Cancer: Important Insights from the Genome

PostTranslational Modification of Proteins

Cancer Genomic Precision Therapy: Digitized Tumor’s Genome (WGSA) Compared with Genome-native Germ Line: Flash-frozen specimen and Formalin-fixed paraffin-embedded Specimen Needed

eProceeding 2019 Koch Institute Symposium – 18th Annual Cancer Research Symposium – Machine Learning and Cancer, June 14, 2019, 8:00 AM-5:00 PMET MIT Kresge Auditorium, 48 Massachusetts Ave, Cambridge, MA

Genomics and Epigenetics: Genetic Errors and Methodologies – Cancer and Other Diseases

Genomics and Metabolomics Advances in Cancer

Deciphering the Epigenome

Tumor Ammonia Recycling: How Cancer Cells Use Glutamate Dehydrogenase to Recycle Tumor Microenvironment Waste Products for Biosynthesis

Cancer Mutations Across the Landscape

BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

2016 World Medical Innovation Forum: CANCER, April 25-27, 2016, Partners HealthCare, Boston, at the Westin Hotel, Boston

Winning Over Cancer Progression: New Oncology Drugs to Suppress Passengers Mutations vs. Driver Mutations

Gene Amplification and Activation of the Hedgehog Pathway

Bioinformatics Tool Review: Genome Variant Analysis Tools

Gastric Cancer: Whole-genome reconstruction and mutational signatures

7th Annual Novel Strategies for Kinase Inhibitors Exploring New Therapeutic Areas September 24-25, 2013 | Boston, MA

Targeting Untargetable Proto-Oncogenes

Salivary Gland Cancer – Adenoid Cystic Carcinoma: Mutation Patterns: Exome- and Genome-Sequencing @ Memorial Sloan-Kettering Cancer Center

Heroes in Medical Research: Dr. Robert Ting, Ph.D. and Retrovirus in AIDS and Cancer

DNA: One man’s trash is another man’s treasure, but there is no JUNK after all

PIK3CA mutation in Colorectal Cancer may serve as a Predictive Molecular Biomarker for adjuvant Aspirin therapy

Resistance and Adverse Events (12 articles)

Tumor Associated Macrophages: The Double-Edged Sword Resolved?

Predicting Tumor Response, Progression, and Time to Recurrence

Development of Chemoresistance to Targeted Therapies: Alterations of Cell Signaling & the Kinome

Can IntraTumoral Heterogeneity Be Thought of as a Mechanism of Resistance?

Rapid regression of HER2 breast cancer

Liver Toxicity halts Clinical Trial of IAP Antagonist for Advanced Solid Tumors

Myc and Cancer Resistance

Mechanisms of Drug Resistance

New Generation of Platinated Compounds to Circumvent Resistance

Breast Cancer, drug resistance, and biopharmaceutical targets

Issues Need to be Resolved With ImmunoModulatory Therapies: NK cells, mAbs, and adoptive T cells

Curation of Recently Halted Oncology Trials Due to Serious Adverse Events – 2015

Patient and Personalized Care (12 articles)

The Experience of a Patient with Thyroid Cancer

Management of Follicular Lymphoma

Acoustic Neuroma, Neurinoma or Vestibular Schwannoma: Treatment Options

Can Mobile Health Apps Improve Oral-Chemotherapy Adherence? The Benefit of Gamification.

The Relation between Coagulation and Cancer affects Supportive Treatments

NIH Considers Guidelines for CAR-T therapy: Report from Recombinant DNA Advisory Committee

Ethical Concerns in Personalized Medicine: BRCA1/2 Testing in Minors and Communication of Breast Cancer Risk

Cancer and Nutrition

Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of Cancer Scientific Leaders @ http://pharmaceuticalintelligence.com

Environment and Cancer [11.3.4]

Hormonal Therapy, Complementary and Alternative Therapies – 9.4

Relation of Diet and Cancer

Research and Cancer Models (12 articles)

The SCID Pig: How Pigs are becoming a Great Alternate Model for Cancer Research

The SCID Pig II: Researchers Develop Another SCID Pig, And Another Great Model For Cancer Research

The Discovery and Properties of Avemar – Fermented Wheat Germ Extract: Carcinogenesis Suppressor

Zebrafish—Susceptible to Cancer

Humanized Mice May Revolutionize Cancer Drug Discovery

Heroes in Medical Research: Developing Models for Cancer Research

Recent Breakthroughs in Cancer Research at the Technion-Israel Institute of Technology- 2015

Guidelines for the welfare and use of animals in cancer research

Colon cancer and organoids

Organoid Development

New Ecosystem of Cancer Research: Cross Institutional Team Science

Koch Institute for Integrative Cancer Research @MIT – Summer Symposium 2014: RNA Biology, Cancer and Therapeutic Implications, June 13, 2014 8:30AM – 4:30PM, Kresge Auditorium @MIT

In the following now we will pick articles based on an even distribution between the subcategories

via Key Immune System Genes Identified to Explain High COVID Deaths and Spread in Northern Italy Versus Fewer Cases and Deaths in the South

14th Annual BioPharma & Healthcare Summit, Friday, September 4, 2020, 8 AM EST to 3-30 PM EST – Virtual Edition

Real Time Press Coverage: Aviva Lev-Ari, PhD, RN

Founder & Director, LPBI Group








USAIC has created an ecosystem committed to driving a global dialogue on BioPharma & Healthcare innovation, attracting a diverse mix of senior industry professionals and catalyzing partnerships, new ideas, networks and regulatory reform. This unique platform creates mutually beneficial opportunities and relationships for the global Life Sciences & Healthcare industry.

In these unprecedented times due to COVID-19, USAIC is offering Free Registration for its annual summit.

Click for free registration



Chair and Master of Ceremonies (Emcee)– Dr. Andrew Plump, President of R&D, Takeda Pharmaceuticals
Summit Theme: “From N of One to N of a Billion”

  • Moderated Fireside Chat- Kenneth Frazier, Chairman of the Board and Chief Executive Officer, Merck & Co. and Stelios Papadopoulos, Chairman of the Board, Biogen
  • Moderated Fireside Chat- Roy Vagelos, Chairman of the Board, Regeneron Pharmaceuticals and Mathai Mammen, Global Head of R&D, Janssen Pharmaceutical Companies of Johnson & Johnson
  • Moderated Fireside Chat- K. VijayRaghavan, Principal Scientific Advisor, Government of India and Amitabh Kant, CEO, National Institution for Transforming India (NITI)

Panel Discussions:

  • Covid-19: Where are we now? Where are we going?
  • Oncology: A never ending tunnel?
  • Rare Diseases: Breaking Barriers for a Healthy Brain
  • Digital & Data Sciences: Leveraging data and digital to achieve healthcare solutions
  • Industry & Investment Outlook
  • R&D Strategies and Trends: Innovation – The Big I

Program and speakers subject to change*

14th Annual BioPharma & Healthcare Summit, Friday, September 4, 2020, 8 AM EST to 3-30 PM EST – Virtual Edition


Kenneth Frazier
Chairman of the Board & CEO
Merck & Co.

Dr. Andrew Plump
President of R&D
Takeda Pharmaceuticals

Dr. Laurie Glimcher
President & CEO
Dana-Farber Cancer Institute

Dr. Roy Vagelos
Chairman of the Board

Dr. Stelios Papadopoulos
Chairman of the Board

Christopher Viehbacher
Managing Partner
Gurnet Point Capital

Dr. Mathai Mammen
Global Head of R&D
Janssen- Johnson & Johnson

Kiran Mazumdar Shaw
Chairperson & Managing Director

Dr. Hal Barron
President, R&D and CSO

Prof. K. Vijay Raghavan
Principal Scientific Advisor
Government of India

Dr. George Yancopoulos
Co-Founder, President & CSO

Dr. Elias Zerhouni
Professor Emeritus
Johns Hopkins University

Daphne Zohar
Founder & CEO
PureTech Health

Sanat Chattopadhyay
President- Merck Manufacturing Division
Merck & Co.

Dr. David Reese
Executive Vice President- R&D

Hari Bhartia
Founder & Co-Chairman
Jubilant Bhartia Group

Dr. Alfred Sandrock
Exe Vice President R&D & CMO

Dr. Najat Khan
Chief Operating Officer, Data Sciences
Janssen- Johnson & Johnson

Dr. Richard Hatchett
Chief Executive Officer

Amitabh Kant
Chief Executive Officer
NITI Aayog

Dr. Martin Mackay

Dr. Daniel Curran
Head of the Rare Diseases TA
Takeda Pharmaceuticals

Dr. Alise Reicin
Former President, Global Clinical Dev.

Dr. David Meeker
Chairman & CEO
Rhythm Pharmaceuticals

Dr. John Orloff
EVP and Head of R&D

Dr. Barry Bloom
Professor & former Dean
Harvard School of Public Health

Dr. Mandeep Bhandari
Joint Secretary
Ministry of Health, India

Arpa Garay
President, Commercial Analytics
Merck & Co.

Dr. Steve Uden

Dr. Philip Larsen
Global Head of Research
Bayer AG

Sastry Chilukuri
Executive Vice President

Dr. William Chin
Professor of Medicine, Emeritus
Harvard Medical School

Dr. Anne Heatherington
Head of Data Sciences Institute
Takeda Pharmaceuticals

Dr. V G Somani
Drugs Controller General of India
Government of India

Dr. Rajeev Venkayya
President-Global Vaccines

Dr. Raju Kucherlapati
Professor of Genetics
Harvard Medical School

Matt Wilsey
Co-Founder & Chairman
Grace Science Foundation

Muna Bhanji
SVP, Global Market Access
Merck & Co.

Dr. Maya Said
Chief Executive Officer

Rehan Verjee
EMD Serono
Pharmasia News Biospectrum India Online