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

Published in MDPI

(Aug 31 2021)

Originally 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)



Casirivimab-Imdevimab treatment is associated with reduced rates of hospitalization among high-risk patients with mild to moderate coronavirus disease-19

Published in EClinicalMedicine

(Aug 30 2021)

Raymund R. Razonable, Colin Pawlowski, John C. OHoro, Lori L....

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Authored by nference Mayo Clinic

Real-world clinical data to support the use of casirivimab–imdevimab for the treatment of outpatients with mild to moderate coronavirus disease-19 (COVID-19) is needed. This study aimed to assess the outcomes of casirivimab–imdevimab treatment of mild to moderate COVID-19.

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


 
 
 

Intravenous bamlanivimab use associates with reduced hospitalization in high-risk patients with mild to moderate COVID-19

(Aug 19 2020)

Ravindra Ganesh, Colin F. Pawlowski, John C. O'Horo, Lori L. Arndt,...

more

Authored by nference Mayo Clinic

Among high-risk patients with mild to moderate COVID-19, treatment with bamlanivimab was associated with a statistically significant lower rate of hospitalization compared with usual care ...

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


 
 
 

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,...

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)



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...

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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

(Jun 24 2021)

Originally Posted in medRxiv

(Jan 19 2021)

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

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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

(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) 


 
 
 

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)


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

(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

(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

(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

(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

(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

(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

(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) 


 
 
 

Neoantigenic potential of complex chromosomal rearrangements in mesothelioma

(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

(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


Publications















Hospital Room





Published in eLife

(May 26 2020)

Originally Posted in bioRxiv

(Apr 30 2020)

Featured in The Scientist




Global connectivity