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

Published in npj Digital Medicine

(Jul 27 2021)

Originally posted in medRxiv

(Dec 4 2020)

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

more

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,...

more

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)


Building a best-in-class de-identification tool for electronic medical records through ensemble learning

Published in Cell Patterns

(May 12 2021)

Originally Posted in medRxiv

(Feb 23 2021)

Karthik Murugadoss, Ajit Rajasekharan, Bradley Malin, Vineet...

more

Authored by nference  Mayo Clinic  Vanderbilt University Medical Center

The natural language portions of an electronic health record (EHR) communicate critical information about disease and treatment progression. However, the presence of personally identifying information in this data constrains its broad reuse. In the United States, the Health Insurance Portability ...
Correspondence: Venky Soundararajan (venky@nference.net), Sankar Ardhanari (sankar@nference.net)

FDA-authorized COVID-19 vaccines are effective per real-world evidence synthesized across a multi-state health system

Published in Cell Med

(Jun 28 2021)

Originally Posted in OSF (Feb 17 2021) and medRxiv (Feb 27 2021)

Colin Pawlowski, Patrick Lenehan, Arjun Puranik, Vineet Agarwal, AJ...

more

Authored by nference  Mayo Clinic

Large Phase 3 clinical trials of the two FDA-authorized COVID-19 vaccines, mRNA-1273 (Moderna) and BNT162b2 (Pfizer/BioNTech), have demonstrated efficacies of 94.1% (n = 30,420, 95% CI: 89.3-96.8) and 95% (n = 43,448, 95% CI: 90.3-97.6) in preventing symptomatic COVID-19, respectively ...

Correspondence: Venky Soundararajan (venky@nference.net)


Real-time analysis of a mass vaccination effort via an Artificial Intelligence platform confirms the safety of FDA-authorized COVID-19 vaccines

Published in Cell Med

(Jun 28 2021)

Originally Posted in medRxiv

(Feb 27 2021)

Reid McMurry, Patrick J. Lenehan, Samir Awasthi, Eli Silvert, Arjun...

more
more

Authored by nference  Mayo Clinic

As the COVID-19 vaccination campaign unfolds as one of the most rapid and widespread in history, it is important to continuously assess the real world safety of the FDA-authorized vaccines. Curation from large-scale electronic health records (EHRs) allows for near real-time safety evaluations that were not previously possible ...

Correspondence: Venky Soundararajan (venky@nference.net)


Anemia during SARS-CoV-2 infection is associated with rehospitalization after viral clearance

Published in iScience (Cell Press)

(Jun 24 2021)

Originally Posted in medRxiv

(Jan 19 2021)

Patrick Lenehan, Eshwan Ramudu, AJ Venkatakrishnan, Gabriela Berner, 

more

Authored by nference  Mayo Clinic

Patients with COVID-19 can experience symptoms and complications after viral clearance. It is important to identify clinical features of patients who are likely to experience these prolonged effects. We conducted a retrospective study to compare longitudinal laboratory test measurements (hemoglobin, hematocrit ...
Correspondence: Venky Soundararajan (venky@nference.net)

Cerebral Venous Sinus Thrombosis is not Significantly Linked to COVID-19 Vaccines or Non-COVID Vaccines in a Large Multi-State Health System

Published in Journal of Stroke and Cerebrovascular Diseases

(Jun 16 2021)

Originally Posted in medRxiv 

(Apr 23 2021)

Colin Pawlowski, John Rincón-Hekking, Samir Awasthi, Viral Pandey, ...

more

Authored by nference  Mayo Clinic

 

This real-world evidence-based study finds that CVST is rare and is not significantly associated with COVID-19 vaccination in our patient cohort. Limitations include the rarity of CVST in our dataset, a relatively small number of J&J COVID-19 vaccination events ...

Correspondence: Venky Soundararajan (venky@nference.net) 


 
 

A Literature-Derived Knowledge Graph Augments the Interpretation of Single Cell RNA-seq Datasets

Published in Genes

(Jun 10 2021)

Originally Posted in bioRxiv 

(Apr 4 2021)
Deeksha Doddahonnaiah, Patrick J. Lenehan, Travis K. Hughes, David...
more

Authored by nference 

The COVID-19 pandemic demands assimilation of all biomedical knowledge to decode mechanisms of pathogenesis. Despite the recent renaissance in neural networks, a platform for the real-time synthesis of the exponentially growing biomedical literature and deep omics insights is unavailable ...

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,...

more

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...

more

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,...

more

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...

more

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,...

more

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...

more

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....

more

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,...

more

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)


Pre-existing conditions are associated with COVID-19 patients' hospitalization, despite confirmed clearance of SARS-CoV-2 virus

Published in Lancet eClinicalMedicine

(Mar 23 2021)

Originally Posted in medRxiv

(Nov 3 2020)

Colin Pawlowski, AJ Venkatakrishnan, Eshwan Ramudu, Christian Kirkup...

more

Authored by nference  Mayo Clinic

The current diagnostic gold-standard for SARS-CoV-2 clearance from infected patients is two consecutive negative PCR test results. However, there are anecdotal reports of hospitalization from protracted COVID ...

 

Correspondence: Venky Soundararajan (venky@nference.net)


Plasma IL-6 levels following corticosteroid therapy as an indicator of ICU length of stay in critically ill COVID-19 patients

Published in Nature Cell Death Discovery

(Mar 15 2021)

Originally Posted in medRxiv

(Jul 3 2020)

Samir Awasthi, Tyler Wagner, AJ Venkatakrishnan, Arjun Puranik,...

more

Authored by nference  Mayo Clinic

Intensive Care Unit (ICU) admissions and mortality in severe COVID-19 patients are driven by “cytokine storms” and acute respiratory distress syndrome (ARDS). Interim clinical trial results suggest that the corticosteroid dexamethasone displays superior 28-day survival in severe COVID-19 patients requiring ventilation or oxygen ...

Correspondence: Venky Soundararajan (venky@nference.net)


Enoxaparin is associated with lower rates of thrombosis, kidney injury, and mortality than unfractionated heparin in hospitalized COVID patients

Published in Lancet eClinicalMedicine

(Mar 9 2021)

Originally Posted in medRxiv

(Oct 11 2020)

Colin Pawlowski, AJ Venkatakrishnan, Christian Kirkup, Gabriela...

more

Authored by nference  Mayo Clinic

Although anticoagulants such as unfractionated heparin and low molecular weight heparin (LMWH, e.g. enoxaparin) are both being used for therapeutic mitigation of COVID associated coagulopathy (CAC), differences in their clinical outcomes remain to be investigated ...
Correspondence: Venky Soundararajan (venky@nference.net)

Healthcare disparities among anticoagulation therapies for severe COVID-19 patients in the multi-site VIRUS registry

Published in Journal of Medical Virology

(Mar 5 2021)

Originally Posted in medRxiv

(Nov 10 2020)

Christian Kirkup, Colin Pawlowski, Arjun Puranik, Ian Conrad, John...

more

Authored by nference  Mayo Clinic  University of Cincinnati Beth Israel Deaconess Medical Center Banner University Medical Center  Kuban State Medical University Cox Medical Center Stamford Health St. Joseph's Candler Health System

COVID-19 patients are at an increased risk of thrombosis and various anticoagulants are being used in patient management without an established standard-of-care. Here, we analyze hospitalized and ICU patient outcomes from the Viral Infection and Respiratory illness Universal Study (VIRUS) registry ...

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


Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations

Published in Nature Scientific Reports

(Feb 26 2021)

Originally Posted in medRxiv

(Jul 29 2020)

Colin Pawlowski, Arjun Puranik, Hari Bandi, AJ Venkatakrishnan,...

more

Authored by nference  Mayo Clinic

Multiple clinical studies are ongoing to assess whether existing vaccines may afford protection against SARS-CoV-2 infection through trained immunity. In this exploratory study, we analyze immunization ...

Correspondence: Venky Soundararajan (venky@nference.net)


Long-term SARS-CoV-2 RNA shedding and its temporal association to IgG seropositivity

Published in Nature Cell Death Discovery

(Dec 2 2020)

Originally Posted in medRxiv

(Jul 7 2020)

Vineet Agarwal, AJ Venkatakrishnan, Arjun Puranik, Christian Kirkup,...

more

Authored by nference  Mayo Clinic

Longitudinal characterization of SARS-CoV-2 PCR testing from COVID-19 patient’s nasopharynx and its juxtaposition with blood-based IgG-seroconversion diagnostic assays is critical to understanding SARS-CoV-2 infection durations. Here, we retrospectively analyze 851 SARS-CoV-2-positive ...

Correspondence: Venky Soundararajan (venky@nference.net)

Hospital Room

Benchmarking evolutionary tinkering underlying human–viral molecular mimicry shows multiple host pulmonary–arterial peptides mimicked by SARS-CoV-2

Published in Nature Cell Death Discovery

(Oct 2 2020)

Featured in Paperity

AJ Venkatakrishnan, Nikhil Kayal, Praveen Anand, Andrew D. Badley,...

more

Authored by nference  Mayo Clinic  Harvard Medical School

The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. Here, we report 33 distinct 8-mer/9-mer peptides that are identical between SARS-CoV-2 and the human reference proteome. We benchmark this observation against other viral–human ...

Correspondence: 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, ...

more

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)


 
 

Human cancers express TRAILshort, a dominant negative TRAIL splice variant, which impairs immune effector cell killing of tumor cells

Published in Clinical Cancer Research

(Jul 13 2020)

Fatma Aboulnasr, Ashton Krogman, Rondell P Graham, Nathan W Cummins, 

more

Authored by nference  Mayo Clinic  Fusion Antibodies

Conclusion: These results identify TRAILshort in primary human malignancies, and suggest that TRAILshort blockade can augment the effector function of autologous immune effector cells ...

Correspondence: Andrew D. Badley (badley.andrew@mayo.edu)


Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis

Published in eLife

(Jul 7 2020)

Originally Posted in medRxiv

(Jun 11 2020)

Tyler Wagner, FNU Shweta, Karthik Murugadoss, Samir Awasthi, AJ...

more

Authored by nference Mayo Clinic

The COVID-19 pandemic demands assimilation of all biomedical knowledge to decode mechanisms of pathogenesis. Despite the recent renaissance in neural networks, a platform for the real-time synthesis of the exponentially growing biomedical literature and deep omics insights is unavailable ...

Correspondence: Andrew Badley (badley.andrew@mayo.edu), Venky Soundararajan (venky@nference.net) 


 
 
 

SARS-CoV-2 strategically mimics proteolytic activation of human ENaC

Published in eLife

(May 26 2020)

Originally Posted in bioRxiv

(Apr 30 2020)

Featured in The Scientist

Praveen Anand, Arjun Puranik, Murali Aravamudan, AJ Venkatakrishnan,...

more

Authored by nference

Molecular mimicry of host proteins is an evolutionary strategy adopted by viruses to evade immune surveillance and exploit host cell systems. We report that SARS-CoV-2 has evolved a unique S1/S2 cleavage site (RRARSVAS), absent in any previous coronavirus sequenced, that results in mimicry ...
Correspondence: AJ Venkatakrishnan (aj@nference.net), Venky Soundararajan (venky@nference.net)

 
 
 

Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors

Published in eLife

(May 28 2020)

Originally Posted in bioRxiv

(Mar 29 2020)

Featured in S T A T

AJ Venkatakrishnan, Arjun Puranik, Akash Anand, David Zemmour, Xiang...

more

Authored by nference Janssen

The COVID-19 pandemic demands assimilation of all biomedical knowledge to decode mechanisms of pathogenesis. Despite the recent renaissance in neural networks, a platform for the real-time synthesis of the exponentially growing biomedical literature and deep omics insights is unavailable ...

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,...

more

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)


Patient segmentation using machine-learning based literature and genomic data synthesis uncovers novel cohorts of NSCLC and mesothelioma patients

Published in Cancer Research

(Jul 19 2019)

Enrique Garcia-Rivera, Aaron S. Mansfield, Karthik Murugadoss,...

more

Authored by nference  Mayo Clinic

Current unbiased approaches to mine the large amounts of patient-level data on mutations, structural variations and gene expression result in an unwieldy amount of interactions and correlations, which cannot be parsed to identify disease drivers. Here we present an approach to encode mutational and structural variant ...

Correspondence:  Enrique Garcia-Rivera (enqrique@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, ...

more

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)

Neoantigenic potential of complex chromosomal rearrangements in mesothelioma

Published in Journal of Thoracic Oncology

(Oct 10 2018)

Virginia P. Van Keulen, Tobias Peikert, James B. Smadbeck, Julia B....

more

Authored by nference  Mayo Clinic

We observed that inter- or intra-chromosomal rearrangements were present in every specimen and were frequently in a pattern of chromoanagenesis such as chromoplexy or chromothripsis. Transcription of rearrangement-related junctions was predicted to result in many potential neoantigens ...
Correspondence: Aaron Mansfield (mansfield.aaron@mayo.edu)

Global connectivity of hub residues in Oncoprotein structures encodes genetic factors dictating personalized drug response to targeted Cancer therapy

Published in Nature Scientific Reports

(Dec 3 2014)

Venky Soundararajan, Murali Aravamudan

more

Authored by nference

Our results establish global connectivity analysis as a potent assay of protein functional modulation. This sets the stage for unearthing disease-causal exome mutations and motivates forecast of clinical drug response on a patient-by-patient basis. We suggest incorporation of structure-guided genetic inference assays into pharmaceutical and healthcare Oncology workflows ...

Correspondence: Venky Soundararajan (venky@nference.net) 

Global connectivity

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Hospital Room

Published in eLife

(May 26 2020)

Originally Posted in bioRxiv

(Apr 30 2020)

Featured in The Scientist

Global connectivity
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