nference Publications

Publications

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

(June 16, 2021)

Originally Posted in medRxiv

(Apr. 23, 2021)

Featured in BioWorld · Fierce Biotech · Star Tribune

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

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)

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

Published in Genes

(June 10, 2021)

Originally Posted in bioRxiv (Apr. 4, 2021)

Deeksha Doddahonnaiah, Patrick J. Lenehan, Travis K. Hughes, David...

Authored by nference

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)

Featured in The Scientist · American Society of Microbiology (ASM) · The Telegraph · Deccan Herald

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

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)

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

Published in Patterns (Cell Press)

(May 12, 2021)

Originally Posted in medRxiv

(Feb. 23, 2021)

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

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)

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

Posted in medRxiv

(Apr. 30, 2021)

Featured in World Health Organization (WHO) · News Medical Life Science · Business Insider · Prevention

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

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,...

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...

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)

Featured in News Medical Life Sciences

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

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...

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. Badley

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)

A literature-derived knowledge graph augments the interpretation of single cell RNA-seq datasets

Posted in bioRxiv

(Apr. 4, 2021)

Deeksha Doddahonnaiah, Patrick Lenehan, Travis Hughes, David Zemmour...

Authored by nference

Single cell RNA-sequencing has enabled the profiling of cellular heterogeneity across diverse tissues and pathologies at unprecedented levels. However, the plethora of knowledge contained within biomedical literature has not yet been leveraged systematically to aid in the annotation and interpretation ...

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,...

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)

Featured in The Washington Post

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

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, ...

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)

Featured in The Washington Post

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

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 ...

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)

Featured in Reuters · The Washington Post

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

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)

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

Posted in medRxiv

(Feb. 27, 2021)

Originally Posted in OSF Preprints

(Feb. 17, 2021)

Featured in Bloomberg

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

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)

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)

Featured in Scientific American · New York Times

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

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)

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

Posted in medRxiv

(Feb. 27, 2021)

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

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 prior to or during COVID-19 is a risk factor for rehospitalization after SARS-CoV-2 clearance

Posted in medRxiv

(Jan. 19, 2021)

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

Authored by nference Mayo Clinic

As the number of new and recovering cases continues to rise, it is increasingly important to understand the long-term impacts of COVID-19 beyond the time of active SARS-CoV-2 infection. However, the clinical and molecular biomarkers characterizing patients who are likely to experience longer lasting effects ...

Correspondence: Venky Soundararajan (venky@nference.net)

Augmented curation of clinical notes of COVID-19 and influenza patients reveals that long-term neuropsychiatric and coagulopathic symptoms are more associated with COVID-19

Posted in medRxiv

(Jan. 5, 2021)

Jacob T. Martin, Elliot Akama-Garren, Arjun Puranik, Saran...

Authored by nference Mayo Clinic

Here we demonstrate the use of an augmented curation platform for identifying the symptoms enriched in COVID patients. By contrasting Electronic Health Record (EHR)-derived symptoms of COVID-19-positive versus COVID-19-negative patients for the week preceding the PCR testing date ...

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

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

Posted in medRxiv

(Dec. 4, 2020)

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

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)

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,...

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)

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)

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

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, ...

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,

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

(Apr. 30, 2020)

Featured in The Scientist

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

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...

Authored by nference Janssen

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, ...

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, ...

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, ...

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....

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

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)