Mapping each pre-existing condition’s association to short-term and long-term COVID-19 complications

(Jul 27 2021)

Originally posted in medRxiv

(Dec 4 2020)

AJ Venkatakrishnan, Colin Pawlowski, David Zemmour, Travis Hughes,...

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Authored by nference  Mayo Clinic

Understanding the relationships between pre-existing conditions and complications of COVID-19 infection is critical to identifying which patients will develop severe disease. Here, we leverage 1.1 million clinical notes from 1,903 hospitalized COVID-19 patients and deep neural network models to characterize ...

Correspondence: Venky Soundararajan (venky@nference.net)



COVID-19 vaccines dampen genomic diversity of SARS-CoV-2: Unvaccinated patients exhibit more antigenic mutational variance

Posted in medRxiv

(Jul 5 2021)

Michiel J.M. Niesen, Praveen Anand, Eli Silvert, Rohit Suratekar,...

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Authored by nference  Mayo Clinic

The raging COVID-19 pandemic in India and reports of “vaccine breakthrough infections” globally have raised alarm mandating the characterization of the immunoevasive features of SARS-CoV-2. Here, we systematically analyzed over 1.3 million SARSCoV-2 genomes from 178 countries ...

Correspondence: Venky Soundararajan (venky@nference.net)



Antigenic minimalism of SARS-CoV-2 is linked to surges in COVID-19 community transmission and vaccine breakthrough infections

Posted in medRxiv

(May 31 2021)

A.J. Venkatakrishnan, Praveen Anand, Patrick Lenehan, Pritha Ghosh,...

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Authored by nference  Mayo Clinic

The raging COVID-19 pandemic in India and reports of “vaccine breakthrough infections” globally have raised alarm mandating the characterization of the immunoevasive features of SARS-CoV-2. Here, we systematically analyzed over 1.3 million SARSCoV-2 genomes from 178 countries ...

Correspondence: Venky Soundararajan (venky@nference.net), A.J. Venkatakrishnan (aj@nference.net)



Real-world effectiveness of Ad26.COV2.S adenoviral vector vaccine for COVID-19

Posted in medRxiv

(Apr 30 2021)

Juan Corchado-Garcia, David Puyraimond-Zemmour, Travis Hughes, Tudor...

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Authored by nference Mayo Clinic

In light of the massive and rapid vaccination campaign against COVID-19, continuous real-world effectiveness and safety assessment of the FDA-authorized vaccines is critical to amplify transparency, build public trust, and ultimately improve ...
 
Correspondence: Venky Soundararajan (venky@nference.net), Tyler Wagner (tyler@nference.net)
 


Effects of tumor mutation burden on the antigen presentation pathway

Posted in bioRxiv

(Apr 14 2021)

Enrique M. Garcia-Rivera, Jiho Park, Aakash Desai, Romain Boidot,...

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Authored by nference  Mayo Clinic  Georges-Francois LeClerc Cancer Center  Genetic and Immunology Medical Institute  University of Burgundy Franche-Comte

We hypothesized that inactivation of antigen presenting genes (APGs) that result from increased TMBs would result in inherent resistance to immune checkpoint inhibitors. We observed that somatic mutations in APGs were associated with increasing TMBs across 9,418 tumor ...

Correspondence: Aaron Mansfield (mansfield.aaron@mayo.edu)



Hair loss in females and thromboembolism in males are significantly enriched in post-acute sequelae of COVID (PASC) relative to recent medical history

Posted in medRxiv

(Apr 13 2021)

Elliot Akama-Garren, Praveen Anand, Tudor Cristea-Platon, Patrick...

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Authored by nference  Mayo Clinic

The post-acute sequelae of COVID-19 (PASC), also referred to as the ‘long COVID’ syndrome, remains mostly uncharacterized. We leveraged machine-augmented curation of the physician notes to retrospectively contrast the occurrence of symptoms and diseases in COVID-19 patients in the post ...

Correspondence:  Samir Awasthi (samir@nference.net), Venky Soundararajan (venky@nference.net)




Case fatality rates for COVID-19 are higher than case fatality rates for motor vehicle accidents for individuals over 40 years of age

Posted in medRxiv

(Apr 13 2021)

Arjun Puranik, Michiel J.M. Niesen, Emily Lindemer, Patrick Lenehan,...

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Authored by nference

Is a person more likely to die if they get a COVID diagnosis or if they get into a motor vehicle accident? We find that COVID carries the higher case fatality risk for individuals in their 40s and up. In particular, the COVID case fatality risk 1.5-fold more than for motor vehicle accidents for age group 40-49 ...

Correspondence: Colin Pawlowski (colin@nference.net), Venky Soundararajan (venky@nference.net)



Female-male differences in COVID vaccine adverse events have precedence in seasonal flu shots: a potential link to sex-associated baseline gene expression patterns

Posted in medRxiv

(Apr 7 2021)

AJ Venkatakrishnan, Praveen Kumar-M, Eli Silvert, Enrique...

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Authored by nference  Mayo Clinic

Do men and women experience the same adverse events after getting COVID-19 vaccines? Analysis of over 30,000 vaccinated patients shows Increased reporting of nausea and fever among females and males, respectively. This is also observed for prior influenza vaccines, establishing that these ...

 

Correspondence: Venky Soundararajan (venky@nference.net)



COVID-associated pediatric hospitalization and ICU admission trends across a multi-state health system and the broader US population

Posted in medRxiv

(Apr 5 2021)

AJ Venkatakrishnan, Colin Pawlowski, John C. O'Horo, Andrew D....

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Authored by nference  Mayo Clinic

Public health concerns are emerging based on reports of new SARS-CoV-2 variant strains purportedly triggering a rise in COVID-associated hospitalizations and ICU admissions, particularly in younger patients and the pediatric population. However, analyzing health records of COVID ...

Correspondence: Venky Soundararajan (venky@nference.net)



Counties with lower insurance coverage are associated with both slower vaccine rollout and higher COVID-19 incidence across the United States

Posted in medRxiv

(Mar 26 2021)

Featured in Politico 

Emily Lindemer, Mayank Choudhary, Gregory Donadio, Colin Pawlowski,...

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Authored by nference

We set out to determine the interplay of racial and socioeconomic factors on vaccine coverage and new COVID-19 cases across the US. Our findings demonstrated that the factor most strongly associated with both poor vaccine coverage and high incidence rates was the percent of a county’s ...

Correspondence: Colin Pawlowski (colin@nference.net), Venky Soundararajan (venky@nference.net)



Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC)

Published in eLife

(Aug 17 2020)

Featured in Medical Xpress

Colin Pawlowski, Tyler Wagner, Arjun Puranik, Karthik Murugadoss, ...

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Authored by nference  Mayo Clinic  Janssen

Temporal inference from laboratory testing results and triangulation with clinical outcomes extracted from unstructured electronic health record (EHR) provider notes is integral to advancing precision medicine. Here, we studied 246 SARS-CoV-2 PCR-positive (COVIDpos) patients and propensity-matched ...

Correspondence: Venky Soundararajan (venky@nference.net)


 
 

Real-time biomedical knowledge synthesis of the exponentially growing world wide web using unsupervised neural networks

Posted in bioRxiv

(Apr 4 2020)

Tyler Wagner, Samir Awasthi, Gayle Wittenberg, AJ Venkatakrishnan,...

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Authored by nference  Mayo Clinic  Janssen

Decoding disease mechanisms for addressing unmet clinical need demands the rapid assimilation of the exponentially growing biomedical knowledge. These are either inherently unstructured and non-conducive to current computing paradigms or siloed into structured databases requiring ...

Correspondence:  Venky Soundararajan (venky@nference.net)



Recapitulation and retrospective prediction of biomedical associations using temporally-enabled word embeddings

Posted in bioRxiv

(May 7 2019)

Jiho Park, Agustin Lopez-Marquez, Arjun Puranik, Ajit Rajasekharan, ...

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Authored by nference

Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Whereas other carcinogen-related tumors are associated with a high tumor mutation burden, mesothelioma is not. We observed that inter- or intrachromosomal rearrangements ...
Correspondence: Enrique Garcia-Rivera (enrique@nference.net)


Publications