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

(March 23, 2021)

Originally Posted in medRxiv

(November 3, 2020)

Colin PawlowskiAJ VenkatakrishnanEshwan RamuduChristian Kirkup...

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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

(March 15, 2021)

Originally Posted in medRxiv

(July 03, 2020)

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

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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)


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

(March 9, 2021)

Originally Posted in medRxiv

(October 11, 2020)

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

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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)
 

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

(March 5, 2021)

Originally Posted in medRxiv

(Nov. 10, 2020)

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

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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

(February 26, 2021)

Originally Posted in medRxiv

(July 29, 2020)

Colin PawlowskiArjun PuranikHari BandiAJ Venkatakrishnan...

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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)

 

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

(December 2, 2020)

Originally Posted in medRxiv

(July 07, 2020)

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

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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

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

(October 2, 2020)

AJ VenkatakrishnanNikhil KayalPraveen AnandAndrew D. Badley...

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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)

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)


 
 

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

(July 13, 2020)

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

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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)



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

Published in eLife

(May 26, 2020)

Originally Posted in bioRxiv

(April 30, 2020)

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

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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

(March 29, 2020 )

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

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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) 


 
 

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

Published in Cancer Research

(July 19, 2019)

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

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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)



Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma

(October 10, 2018)

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

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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)

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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

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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






Published in Nature Cell ...

(December 2, 2020)

Originally Posted in medR...

(July 07, 2020)
Hospital Room




Published in eLife

(May 26, 2020)

Originally Posted in bioR...

(April 30, 2020)




Global connectivity