Publications

• Identifying commonalities and differences between EHR representations of PASC and ME/CFS in the RECOVER EHR cohort.
  Commun Med (Lond) Volume: 5 Page(s): 109
  04/11/2025 Authors: Powers JP; McIntee TJ; Bhatia A; Madlock-Brown CR; Seltzer J; Sekar A; Jain N; Hornig M; Seibert E; Leese PJ
• The Recent Increase in Invasive Bacterial Infections: A Report From the National COVID Cohort Collaborative.
  Pediatr Infect Dis J Volume: 44 Page(s): 217 - 227
  03/01/2025 Authors: Martin B; DeWitt PE; Russell S; Haendel M; Sanchez-Pinto N; Albers DJ; Jhaveri RR; Moffitt R; Bennett TD; N3C Consortium
• Long-COVID incidence proportion in adults and children between 2020 and 2024.
  Clin Infect Dis
  02/05/2025 Authors: Mandel H; Yoo YJ; Allen AJ; Abedian S; Verzani Z; Karlson EW; Kleinman LC; Mudumbi PC; Oliveira CR; Muszynski JA
• Association of glycemic control with Long COVID in patients with type 2 diabetes: findings from the National COVID Cohort Collaborative (N3C).
  BMJ Open Diabetes Res Care Volume: 13
  02/04/2025 Authors: Soff S; Yoo YJ; Bramante C; Reusch JEB; Huling JD; Hall MA; Brannock D; Sturmer T; Butzin-Dozier Z; Wong R
• Effect of nirmatrelvir/ritonavir (Paxlovid) on hospitalization among adults with COVID-19: An electronic health record-based target trial emulation from N3C.
  PLoS Med Volume: 22 Page(s): e1004493
  01/01/2025 Authors: Bhatia A; Preiss AJ; Xiao X; Brannock MD; Alexander GC; Chew RF; Davis H; Fitzgerald M; Hill E; Kelly EP
• Finding Long-COVID: temporal topic modeling of electronic health records from the N3C and RECOVER programs.
  NPJ Digit Med Volume: 7 Page(s): 296
  10/21/2024 Authors: O'Neil ST; Madlock-Brown C; Wilkins KJ; McGrath BM; Davis HE; Assaf GS; Wei H; Zareie P; French ET; Loomba J
• The Recent Increase in Invasive Bacterial Infections: A Report From the National COVID Cohort Collaborative.
  Pediatr Infect Dis J
  10/09/2024 Authors: Martin B; DeWitt PE; Russell S; Haendel M; Sanchez-Pinto N; Albers DJ; Jhaveri RR; Moffitt R; Bennett TD; N3C Consortium
• The Intersections of COVID-19, HIV, and Race/Ethnicity: Machine Learning Methods to Identify and Model Risk Factors for Severe COVID-19 in a Large U.S. National Dataset.
  AIDS Behav Volume: 28 Page(s): 5 - 21
  10/01/2024 Authors: Kunz M; Rott KW; Hurwitz E; Kunisaki K; Sun J; Wilkins KJ; Islam JY; Patel R; Safo SE; National Covid Cohort Collaborative (N3C) Consortium
• Associations of County-Level Social Determinants of Health with COVID-19 Related Hospitalization Among People with HIV: A Retrospective Analysis of the U.S. National COVID Cohort Collaborative (N3C).
  AIDS Behav Volume: 28 Page(s): 136 - 148
  10/01/2024 Authors: Islam JY; Hurwitz E; Li D; Camacho-Rivera M; Sun J; Safo S; Ross JM; Wilkins K; Hassan S; Hill EL
• Impact of HIV on COVID-19 Outcomes: A Propensity Score Matching Analysis with Varying Age Differences.
  AIDS Behav Volume: 28 Page(s): 124 - 135
  10/01/2024 Authors: Guo S; Zhang J; Yang X; Weissman S; Olatosi B; Patel RC; Li X; N3C Consortium
• A Case Demonstration of the Open Health Natural Language Processing Toolkit From the National COVID-19 Cohort Collaborative and the Researching COVID to Enhance Recovery Programs for a Natural Language Processing System for COVID-19 or Postacute Sequelae of SARS CoV-2 Infection: Algorithm Development and Validation.
  JMIR Med Inform Volume: 12 Page(s): e49997
  09/09/2024 Authors: Wen A; Wang L; He H; Fu S; Liu S; Hanauer DA; Harris DR; Kavuluru R; Zhang R; Natarajan K
• Effect of Paxlovid Treatment During Acute COVID-19 on Long COVID Onset: An EHR-Based Target Trial Emulation from the N3C and RECOVER Consortia.
  medRxiv
  07/31/2024 Authors: Preiss A; Bhatia A; Aragon LV; Baratta JM; Baskaran M; Blancero F; Brannock MD; Chew RF; Diaz I; Fitzgerald M
• Insights from an N3C RECOVER EHR-based cohort study characterizing SARS-CoV-2 reinfections and Long COVID.
  Commun Med (Lond) Volume: 4 Page(s): 129
  07/11/2024 Authors: Hadley E; Yoo YJ; Patel S; Zhou A; Laraway B; Wong R; Preiss A; Chew R; Davis H; Brannock MD
• Finding Long-COVID: Temporal Topic Modeling of Electronic Health Records from the N3C and RECOVER Programs.
  medRxiv
  06/11/2024 Authors: O'Neil ST; Madlock-Brown C; Wilkins KJ; McGrath BM; Davis HE; Assaf GS; Wei H; Zareie P; French ET; Loomba J
• Association of Premorbid GLP-1RA and SGLT-2i Prescription Alone and in Combination with COVID-19 Severity.
  Diabetes Ther Volume: 15 Page(s): 1169 - 1186
  05/01/2024 Authors: Klein KR; Abrahamsen TJ; Kahkoska AR; Alexander GC; Chute CG; Haendel M; Hong SS; Mehta H; Moffitt R; Strmer T
• Long COVID incidence in adults and children between 2020 and 2023: a real-world data study from the RECOVER Initiative.
  Res Sq
  04/26/2024 Authors: Mandel H; Yoo Y; Allen A; Abedian S; Verzani Z; Karlson E; Kleinman L; Mudumbi P; Oliveira C; Muszynski J
• Clinically relevant orthotopic pancreatic cancer models for adoptive T cell transfer therapy.
  J Immunother Cancer Volume: 12
  01/08/2024 Authors: Horvat NK; Karpovsky I; Phillips M; Wyatt MM; Hall MA; Herting CJ; Hammons J; Mahdi Z; Moffitt RA; Paulos CM
• FaStaNMF: A Fast and Stable Non-Negative Matrix Factorization for Gene Expression.
  IEEE/ACM Trans Comput Biol Bioinform Volume: 21 Page(s): 1633 - 1644
  01/01/2024 Authors: Sweeney MD; Torre-Healy LA; Ma VL; Hall MA; Chrastecka L; Yurovsky A; Moffitt RA
• Sample average treatment effect on the treated (SATT) analysis using counterfactual explanation identifies BMT and SARS-CoV-2 vaccination as protective risk factors associated with COVID-19 severity and survival in patients with multiple myeloma.
  Blood Cancer J Volume: 13 Page(s): 180
  12/07/2023 Authors: Mitra AK; Mukherjee UK; Mazumder S; Madhira V; Bergquist T; Shao YR; Liu F; Song Q; Su J; Kumar S
• Risk factors associated with post-acute sequelae of SARS-CoV-2: an N3C and NIH RECOVER study.
  BMC Public Health Volume: 23 Page(s): 2103
  10/25/2023 Authors: Hill EL; Mehta HB; Sharma S; Mane K; Singh SK; Xie C; Cathey E; Loomba J; Russell S; Spratt H
• National Trends in Anticoagulation Therapy for COVID-19 Hospitalized Adults in the United States: Analyses of the National COVID Cohort Collaborative.
  J Infect Dis Volume: 228 Page(s): 895 - 906
  10/03/2023 Authors: Lee E; Bates B; Kuhrt N; Andersen KM; Visaria A; Patel R; Setoguchi S; N3C Consortium
• Risk of post-acute sequelae of SARS-CoV-2 infection associated with pre-coronavirus disease obstructive sleep apnea diagnoses: an electronic health record-based analysis from the RECOVER initiative.
  Sleep Volume: 46
  09/08/2023 Authors: L Mandel H; Colleen G; Abedian S; Ammar N; Charles Bailey L; Bennett TD; Daniel Brannock M; Brosnahan SB; Chen Y; Chute CG
• Thirty-Day Mortality and Complication Rates in Total Joint Arthroplasty After a Recent COVID-19 Diagnosis: A Retrospective Cohort in the National COVID Cohort Collaborative (N3C).
  J Bone Joint Surg Am Volume: 105 Page(s): 1362 - 1372
  09/06/2023 Authors: Pincavitch JD; Pisquiy JJ; Wen S; Bryan N; Ammons J; Makwana P; Dietz MJ; on behalf of the National COVID Cohort Collaborative (N3C) Consortium
• Risk for stillbirth among pregnant individuals with SARS-CoV-2 infection varied by gestational age.
  Am J Obstet Gynecol Volume: 229 Page(s): 288.e1 - 288.e13
  09/01/2023 Authors: Lyu T; Liang C; Liu J; Hung P; Zhang J; Campbell B; Ghumman N; Olatosi B; Hikmet N; Zhang M
• Early Empiric Antibiotic Use in Patients Hospitalized With COVID-19: A Retrospective Cohort Study.
  Crit Care Med Volume: 51 Page(s): 1168 - 1176
  09/01/2023 Authors: Widere JC; Davis CL; Loomba JJ; Bell TD; Enfield KB; Barros AJ; N3C Consortium
• Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype.
  Nat Commun Volume: 14 Page(s): 5226
  08/26/2023 Authors: Oh K; Yoo YJ; Torre-Healy LA; Rao M; Fassler D; Wang P; Caponegro M; Gao M; Kim J; Sasson A
• Geographic and Temporal Trends in COVID-Associated Acute Kidney Injury in the National COVID Cohort Collaborative.
  Clin J Am Soc Nephrol Volume: 18 Page(s): 1006 - 1018
  08/01/2023 Authors: Yoo YJ; Wilkins KJ; Alakwaa F; Liu F; Torre-Healy LA; Krichevsky S; Hong SS; Sakhuja A; Potu CK; Saltz JH
• Hormone replacement therapy and COVID-19 outcomes in solid organ transplant recipients compared with the general population.
  Am J Transplant Volume: 23 Page(s): 1035 - 1047
  07/01/2023 Authors: Vinson AJ; Anzalone A; Schissel M; Dai R; French ET; Olex AL; Mannon RB; National COVID Cohort Collaborative
• De-black-boxing health AI: demonstrating reproducible machine learning computable phenotypes using the N3C-RECOVER Long COVID model in the All of Us data repository.
  J Am Med Inform Assoc Volume: 30 Page(s): 1305 - 1312
  06/20/2023 Authors: Pfaff ER; Girvin AT; Crosskey M; Gangireddy S; Master H; Wei W-Q; Kerchberger VE; Weiner M; Harris PA; Basford M
• Long COVID risk and pre-COVID vaccination in an EHR-based cohort study from the RECOVER program.
  Nat Commun Volume: 14 Page(s): 2914
  05/22/2023 Authors: Brannock MD; Chew RF; Preiss AJ; Hadley EC; Redfield S; McMurry JA; Leese PJ; Girvin AT; Crosskey M; Zhou AG
• Clinical encounter heterogeneity and methods for resolving in networked EHR data: a study from N3C and RECOVER programs.
  J Am Med Inform Assoc Volume: 30 Page(s): 1125 - 1136
  05/19/2023 Authors: Leese P; Anand A; Girvin A; Manna A; Patel S; Yoo YJ; Wong R; Haendel M; Chute CG; Bennett T
• Effect of Nirmatrelvir/Ritonavir (Paxlovid) on Hospitalization among Adults with COVID-19: an EHR-based Target Trial Emulation from N3C.
  medRxiv
  05/04/2023 Authors: Bhatia A; Preiss AJ; Xiao X; Brannock MD; Alexander GC; Chew RF; Fitzgerald M; Hill E; Kelly EP; Mehta HB
• Risk of severe acute respiratory syndrome coronavirus 2 infection among women with polycystic ovary syndrome.
  Fertil Steril Volume: 119 Page(s): 847 - 857
  05/01/2023 Authors: Alur-Gupta S; Boland MR; Dokras A; N3C Consortium
• Vaccination Against SARS-CoV-2 Decreases Risk of Adverse Events in Patients who Develop COVID-19 Following Cancer Surgery.
  Ann Surg Oncol Volume: 30 Page(s): 1305 - 1308
  03/01/2023 Authors: Verhagen NB; Koerber NK; Szabo A; Taylor B; Wainaina JN; Evans DB; Kothari AN; N3C Consortium
• A method for comparing multiple imputation techniques: A case study on the U.S. national COVID cohort collaborative.
  J Biomed Inform Volume: 139 Page(s): 104295
  03/01/2023 Authors: Casiraghi E; Wong R; Hall M; Coleman B; Notaro M; Evans MD; Tronieri JS; Blau H; Laraway B; Callahan TJ
• Coding long COVID: characterizing a new disease through an ICD-10 lens.
  BMC Med Volume: 21 Page(s): 58
  02/16/2023 Authors: Pfaff ER; Madlock-Brown C; Baratta JM; Bhatia A; Davis H; Girvin A; Hill E; Kelly E; Kostka K; Loomba J
• Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype model.
  Commun Biol Volume: 6 Page(s): 163
  02/10/2023 Authors: Torre-Healy LA; Kawalerski RR; Oh K; Chrastecka L; Peng XL; Aguirre AJ; Rashid NU; Yeh JJ; Moffitt RA
• SARS-CoV-2 Reinfection is Preceded by Unique Biomarkers and Related to Initial Infection Timing and Severity: an N3C RECOVER EHR-Based Cohort Study.
  medRxiv
  01/05/2023 Authors: Hadley E; Yoo YJ; Patel S; Zhou A; Laraway B; Wong R; Preiss A; Chew R; Davis H; Chute CG
• Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes.
  EBioMedicine Volume: 87 Page(s): 104413
  01/01/2023 Authors: Reese JT; Blau H; Casiraghi E; Bergquist T; Loomba JJ; Callahan TJ; Laraway B; Antonescu C; Coleman B; Gargano M
• Are fewer cases of diabetes mellitus diagnosed in the months after SARS-CoV-2 infection? A population-level view in the EHR-based RECOVER program.
  J Clin Transl Sci Volume: 7 Page(s): e90
  01/01/2023 Authors: Reddy NV; Yeh H-C; Tronieri JS; Strmer T; Buse JB; Reusch JE; Johnson SG; Wong R; Moffitt R; Wilkins KJ
• A framework for future national pediatric pandemic respiratory disease severity triage: The HHS pediatric COVID-19 data challenge.
  J Clin Transl Sci Volume: 7 Page(s): e175
  01/01/2023 Authors: Bergquist T; Wax M; Bennett TD; Moffitt RA; Gao J; Chen G; Telenti A; Maher MC; Bartha I; Walker L
• Are fewer cases of diabetes mellitus diagnosed in the months after SARS-CoV-2 infection?
  medRxiv
  12/04/2022 Authors: Reddy NV; Yeh H-C; Tronieri JS; Strmer T; Buse JB; Reusch JE; Johnson SG; Wong R; Moffitt R; Wilkins KJ
• Meta-analysis of single-cell RNA expression in genetically engineered mouse models of pancreatic ductal adenocarcinoma reveals inter-model heterogeneity
  Volume: 82 Page(s): 38 - 39
  11/15/2022 Authors: Yoo YJ; Oh KH; Torre-Healy LA; Moffitt RA
• Effect of SARS-CoV-2 Infection and Infection Severity on Longer-Term Glycemic Control and Weight in People With Type 2 Diabetes.
  Diabetes Care Volume: 45 Page(s): 2709 - 2717
  11/01/2022 Authors: Wong R; Vaddavalli R; Hall MA; Patel MV; Bramante CT; Casarighi E; Johnson SG; Lingam V; Miller JD; Reusch J
• Long COVID Risk and Pre-COVID Vaccination: An EHR-Based Cohort Study from the RECOVER Program.
  medRxiv
  10/07/2022 Authors: Brannock MD; Chew RF; Preiss AJ; Hadley EC; McMurry JA; Leese PJ; Girvin AT; Crosskey M; Zhou AG; Moffitt RA
• PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project.
  Bioinformatics Volume: 38 Page(s): 4434 - 4436
  09/15/2022 Authors: Ruan E; Nemeth E; Moffitt R; Sandoval L; Machiela MJ; Freedman ND; Huang W-Y; Wong W; Chen K-L; Park B
• COVID-19-associated AKI in hospitalized US patients: incidence, temporal trends, geographical distribution, risk factors and mortality.
  medRxiv
  09/02/2022 Authors: Yoo YJ; Wilkins KJ; Alakwaa F; Liu F; Torre-Healy LA; Krichevsky S; Hong SS; Sakhuja A; Potu CK; Saltz JH
• Coding Long COVID: Characterizing a new disease through an ICD-10 lens.
  medRxiv
  09/02/2022 Authors: Pfaff ER; Madlock-Brown C; Baratta JM; Bhatia A; Davis H; Girvin A; Hill E; Kelly L; Kostka K; Loomba J
• Acute Upper Airway Disease in Children With the Omicron (B.1.1.529) Variant of SARS-CoV-2-A Report From the US National COVID Cohort Collaborative.
  JAMA Pediatr Volume: 176 Page(s): 819 - 821
  08/01/2022 Authors: Martin B; DeWitt PE; Russell S; Sanchez-Pinto LN; Haendel MA; Moffitt R; Bennett TD
• Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C).
  J Am Med Inform Assoc Volume: 29 Page(s): 1350 - 1365
  07/12/2022 Authors: Thomas JA; Foraker RE; Zamstein N; Morrow JD; Payne PRO; Wilcox AB; N3C Consortium
• Identifying who has long COVID in the USA: a machine learning approach using N3C data.
  Lancet Digit Health Volume: 4 Page(s): e532 - e541
  07/01/2022 Authors: Pfaff ER; Girvin AT; Bennett TD; Bhatia A; Brooks IM; Deer RR; Dekermanjian JP; Jolley SE; Kahn MG; Kostka K
• Harmonizing units and values of quantitative data elements in a very large nationally pooled electronic health record (EHR) dataset.
  J Am Med Inform Assoc Volume: 29 Page(s): 1172 - 1182
  06/14/2022 Authors: Bradwell KR; Wooldridge JT; Amor B; Bennett TD; Anand A; Bremer C; Yoo YJ; Qian Z; Johnson SG; Pfaff ER
• NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study.
  Virol J Volume: 19 Page(s): 84
  05/15/2022 Authors: Reese JT; Coleman B; Chan L; Blau H; Callahan TJ; Cappelletti L; Fontana T; Bradwell KR; Harris NL; Casiraghi E
• Spatial Characterization of Tumor-Infiltrating Lymphocytes and Breast Cancer Progression.
  Cancers (Basel) Volume: 14
  04/26/2022 Authors: Fassler DJ; Torre-Healy LA; Gupta R; Hamilton AM; Kobayashi S; Van Alsten SC; Zhang Y; Kurc T; Moffitt RA; Troester MA
• Synergies between centralized and federated approaches to data quality: a report from the national COVID cohort collaborative.
  J Am Med Inform Assoc Volume: 29 Page(s): 609 - 618
  03/15/2022 Authors: Pfaff ER; Girvin AT; Gabriel DL; Kostka K; Morris M; Palchuk MB; Lehmann HP; Amor B; Bissell M; Bradwell KR
• Glycemic Control and Clinical Outcomes in U.S. Patients With COVID-19: Data From the National COVID Cohort Collaborative (N3C) Database.
  Diabetes Care Volume: 45 Page(s): 1099 - 1106
  02/24/2022 Authors: Wong R; Hall M; Vaddavalli R; Anand A; Arora N; Bramante CT; Garcia V; Johnson S; Saltz M; Tronieri JS
• Short- and Long-Term Recovery after Moderate/Severe AKI in Patients with and without COVID-19.
  Kidney360 Volume: 3 Page(s): 242 - 257
  02/24/2022 Authors: Sun S; Annadi RR; Chaudhri I; Munir K; Hajagos J; Saltz J; Hoai M; Mallipattu SK; Moffitt R; Koraishy FM
• Characteristics, Outcomes, and Severity Risk Factors Associated With SARS-CoV-2 Infection Among Children in the US National COVID Cohort Collaborative.
  JAMA Netw Open Volume: 5 Page(s): e2143151
  02/01/2022 Authors: Martin B; DeWitt PE; Russell S; Anand A; Bradwell KR; Bremer C; Gabriel D; Girvin AT; Hajagos JG; McMurry JA
• Temporal Events Detector for Pregnancy Care (TED-PC): A rule-based algorithm to infer gestational age and delivery date from electronic health records of pregnant women with and without COVID-19.
  PLoS One Volume: 17 Page(s): e0276923
  01/01/2022 Authors: Lyu T; Liang C; Liu J; Campbell B; Hung P; Shih Y-W; Ghumman N; Li X; National COVID Cohort Collaborative Consortium
• NSAID use and clinical outcomes in COVID-19 patients: A 38-center retrospective cohort study.
  medRxiv
  12/22/2021 Authors: Reese JT; Coleman B; Chan L; Blau H; Callahan TJ; Cappelletti L; Fontana T; Bradwell KR; Harris NL; Casiraghi E
• Characterizing Long COVID: Deep Phenotype of a Complex Condition.
  EBioMedicine Volume: 74 Page(s): 103722
  12/01/2021 Authors: Deer RR; Rock MA; Vasilevsky N; Carmody L; Rando H; Anzalone AJ; Basson MD; Bennett TD; Bergquist T; Boudreau EA
• Associations between HIV infection and clinical spectrum of COVID-19: a population level analysis based on US National COVID Cohort Collaborative (N3C) data.
  Lancet HIV Volume: 8 Page(s): e690 - e700
  11/01/2021 Authors: Yang X; Sun J; Patel RC; Zhang J; Guo S; Zheng Q; Olex AL; Olatosi B; Weissman SB; Islam JY
• Use of Hydroxychloroquine, Remdesivir, and Dexamethasone Among Adults Hospitalized With COVID-19 in the United States : A Retrospective Cohort Study.
  Ann Intern Med Volume: 174 Page(s): 1395 - 1403
  10/01/2021 Authors: Mehta HB; An H; Andersen KM; Mansour O; Madhira V; Rashidi ES; Bates B; Setoguchi S; Joseph C; Kocis PT
• Mortality Tracker: the COVID-19 case for real time web APIs as epidemiology commons.
  Bioinformatics Volume: 37 Page(s): 2073 - 2074
  08/04/2021 Authors: Almeida JS; Shiels M; Bhawsar P; Patel B; Nemeth E; Moffitt R; Closas MG; Freedman N; Berrington A
• Use of hydroxychloroquine, remdesivir, and dexamethasone among adults hospitalized with COVID-19 in the United States: Results from the National COVID Cohort Collaborative (N3C)
  Volume: 30 Page(s): 27 - 27
  08/01/2021 Authors: Mehta HB; An H; Andersen KM; Mansour O; Madhira V; Rashidi ES; Bates B; Setoguchi S; Joseph C; Kocis P
• Children with SARS-CoV-2 in the National COVID Cohort Collaborative (N3C).
  medRxiv
  07/23/2021 Authors: Martin B; DeWitt PE; Russell S; Anand A; Bradwell KR; Bremer C; Gabriel D; Girvin AT; Hajagos JG; McMurry JA
• Clinical Characterization and Prediction of Clinical Severity of SARS-CoV-2 Infection Among US Adults Using Data From the US National COVID Cohort Collaborative.
  JAMA Netw Open Volume: 4 Page(s): e2116901
  07/01/2021 Authors: Bennett TD; Moffitt RA; Hajagos JG; Amor B; Anand A; Bissell MM; Bradwell KR; Bremer C; Byrd JB; Denham A
• Association Between Glucagon-Like Peptide 1 Receptor Agonist and Sodium-Glucose Cotransporter 2 Inhibitor Use and COVID-19 Outcomes.
  Diabetes Care Volume: 44 Page(s): 1564 - 1572
  07/01/2021 Authors: Kahkoska AR; Abrahamsen TJ; Alexander GC; Bennett TD; Chute CG; Haendel MA; Klein KR; Mehta H; Miller JD; Moffitt RA
• A distinct microglial subset at the tumor-stroma interface of glioma.
  Glia Volume: 69 Page(s): 1767 - 1781
  07/01/2021 Authors: Caponegro MD; Oh K; Madeira MM; Radin D; Sterge N; Tayyab M; Moffitt RA; Tsirka SE
• Pancreatic cancer prognosis is predicted by an ATAC-array technology for assessing chromatin accessibility.
  Nat Commun Volume: 12 Page(s): 3044
  05/24/2021 Authors: Dhara S; Chhangawala S; Chintalapudi H; Askan G; Aveson V; Massa AL; Zhang L; Torres D; Makohon-Moore AP; Lecomte N
• Reciprocal regulation of pancreatic ductal adenocarcinoma growth and molecular subtype by HNF4 and SIX1/4.
  Gut Volume: 70 Page(s): 900 - 914
  05/01/2021 Authors: Camolotto SA; Belova VK; Torre-Healy L; Vahrenkamp JM; Berrett KC; Conway H; Shea J; Stubben C; Moffitt R; Gertz J
• Challenges in defining Long COVID: Striking differences across literature, Electronic Health Records, and patient-reported information.
  medRxiv
  03/26/2021 Authors: Rando HM; Bennett TD; Byrd JB; Bramante C; Callahan TJ; Chute CG; Davis HE; Deer R; Gagnier J; Koraishy FM
• The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.
  J Am Med Inform Assoc Volume: 28 Page(s): 427 - 443
  03/01/2021 Authors: Haendel MA; Chute CG; Bennett TD; Eichmann DA; Guinney J; Kibbe WA; Payne PRO; Pfaff ER; Robinson PN; Saltz JH
• The National COVID Cohort Collaborative: Clinical Characterization and Early Severity Prediction.
  medRxiv
  01/23/2021 Authors: Bennett TD; Moffitt RA; Hajagos JG; Amor B; Anand A; Bissell MM; Bradwell KR; Bremer C; Byrd JB; Denham A
• Detecting Miscoded Diabetes Diagnosis Codes in Electronic Health Records for Quality Improvement: Temporal Deep Learning Approach.
  JMIR Med Inform Volume: 8 Page(s): e22649
  12/17/2020 Authors: Rashidian S; Abell-Hart K; Hajagos J; Moffitt R; Lingam V; Garcia V; Tsai C-W; Wang F; Dong X; Sun S
• Cholesterol Pathway Inhibition Induces TGF- Signaling to Promote Basal Differentiation in Pancreatic Cancer.
  Cancer Cell Volume: 38 Page(s): 567 - 583.e11
  10/12/2020 Authors: Gabitova-Cornell L; Surumbayeva A; Peri S; Franco-Barraza J; Restifo D; Weitz N; Ogier C; Goldman AR; Hartman TR; Francescone R
• Correction: Direct therapeutic targeting of immune checkpoint PD-1 in pancreatic cancer.
  Br J Cancer Volume: 123 Page(s): 495
  08/01/2020 Authors: Gao M; Lin M; Moffitt RA; Salazar MA; Park J; Vacirca J; Huang C; Shroyer KR; Choi M; Georgakis GV
• Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer.
  Am J Pathol Volume: 190 Page(s): 1491 - 1504
  07/01/2020 Authors: Le H; Gupta R; Hou L; Abousamra S; Fassler D; Torre-Healy L; Moffitt RA; Kurc T; Samaras D; Batiste R
• Irreversible JNK1-JUN inhibition by JNK-IN-8 sensitizes pancreatic cancer to 5-FU/FOLFOX chemotherapy.
  JCI Insight Volume: 5
  04/23/2020 Authors: Lipner MB; Peng XL; Jin C; Xu Y; Gao Y; East MP; Rashid NU; Moffitt RA; Herrera Loeza SG; Morrison AB
• Comparative single-cell RNA sequencing (scRNA-seq) reveals liver metastasis-specific targets in a patient with small intestinal neuroendocrine cancer.
  Cold Spring Harb Mol Case Stud Volume: 6
  04/01/2020 Authors: Rao M; Oh K; Moffitt R; Thompson P; Li J; Liu J; Sasson A; Georgakis G; Kim J; Choi M
• Association of Proteinuria and Hematuria with Acute Kidney Injury and Mortality in Hospitalized Patients with COVID-19.
  Kidney Blood Press Res Volume: 45 Page(s): 1018 - 1032
  01/01/2020 Authors: Chaudhri I; Moffitt R; Taub E; Annadi RR; Hoai M; Bolotova O; Yoo J; Dhaliwal S; Sahib H; Daccueil F
• Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer.
  Clin Cancer Res Volume: 26 Page(s): 82 - 92
  01/01/2020 Authors: Rashid NU; Peng XL; Jin C; Moffitt RA; Volmar KE; Belt BA; Panni RZ; Nywening TM; Herrera SG; Moore KJ
• De novo compartment deconvolution and weight estimation of tumor samples using DECODER.
  Nat Commun Volume: 10 Page(s): 4729
  10/18/2019 Authors: Peng XL; Moffitt RA; Torphy RJ; Volmar KE; Yeh JJ
• Keratin 17 identifies the most lethal molecular subtype of pancreatic cancer.
  Sci Rep Volume: 9 Page(s): 11239
  08/02/2019 Authors: Roa-Pea L; Leiton CV; Babu S; Pan C-H; Vanner EA; Akalin A; Bandovic J; Moffitt RA; Shroyer KR; Escobar-Hoyos LF
• Keratin 17 is a sensitive and specific biomarker of urothelial neoplasia.
  Mod Pathol Volume: 32 Page(s): 717 - 724
  05/01/2019 Authors: Babu S; Mockler DC; Roa-Pea L; Szygalowicz A; Kim NW; Jahanfard S; Gholami SS; Moffitt R; Fitzgerald JP; Escobar-Hoyos LF
• Deep Learning on Electronic Health Records to Improve Disease Coding Accuracy.
  AMIA Jt Summits Transl Sci Proc Volume: 2019 Page(s): 620 - 629
  01/01/2019 Authors: Rashidian S; Hajagos J; Moffitt RA; Wang F; Noel KM; Gupta RR; Tharakan MA; Saltz JH; Saltz MM
• Direct therapeutic targeting of immune checkpoint PD-1 in pancreatic cancer.
  Br J Cancer Volume: 120 Page(s): 88 - 96
  01/01/2019 Authors: Gao M; Lin M; Moffitt RA; Salazar MA; Park J; Vacirca J; Huang C; Shroyer KR; Choi M; Georgakis GV
• Expression of neuropilin-1 is linked to glioma associated microglia and macrophages and correlates with unfavorable prognosis in high grade gliomas.
  Oncotarget Volume: 9 Page(s): 35655 - 35665
  11/02/2018 Authors: Caponegro MD; Moffitt RA; Tsirka SE
• Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer.
  Cancer Discov Volume: 8 Page(s): 1112 - 1129
  09/01/2018 Authors: Tiriac H; Belleau P; Engle DD; Plenker D; Deschnes A; Somerville TDD; Froeling FEM; Burkhart RA; Denroche RE; Jang G-H
• Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine.
  Cancer Discov Volume: 8 Page(s): 1096 - 1111
  09/01/2018 Authors: Aguirre AJ; Nowak JA; Camarda ND; Moffitt RA; Ghazani AA; Hazar-Rethinam M; Raghavan S; Kim J; Brais LK; Ragon D
• Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial.
  Clin Cancer Res Volume: 24 Page(s): 1344 - 1354
  03/15/2018 Authors: Aung KL; Fischer SE; Denroche RE; Jang G-H; Dodd A; Creighton S; Southwood B; Liang S-B; Chadwick D; Zhang A
• Hexokinase 2 promotes tumor growth and metastasis by regulating lactate production in pancreatic cancer.
  Oncotarget Volume: 8 Page(s): 56081 - 56094
  08/22/2017 Authors: Anderson M; Marayati R; Moffitt R; Yeh JJ
• Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma.
  Cancer Cell Volume: 32 Page(s): 185 - 203.e13
  08/14/2017 Authors: Cancer Genome Atlas Research Network. Electronic address: andrew_aguirre@dfci.harvard.edu; Cancer Genome Atlas Research Network
• MYC activation cooperates with Vhl and Ink4a/Arf loss to induce clear cell renal cell carcinoma.
  Nat Commun Volume: 8 Page(s): 15770
  06/08/2017 Authors: Bailey ST; Smith AM; Kardos J; Wobker SE; Wilson HL; Krishnan B; Saito R; Lee HJ; Zhang J; Eaton SC
• Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.
  Cancer Cell Volume: 29 Page(s): 723 - 736
  05/09/2016 Authors: Zheng S; Cherniack AD; Dewal N; Moffitt RA; Danilova L; Murray BA; Lerario AM; Else T; Knijnenburg TA; Ciriello G
• Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma.
  Nat Genet Volume: 47 Page(s): 1168 - 1178
  10/01/2015 Authors: Moffitt RA; Marayati R; Flate EL; Volmar KE; Loeza SGH; Hoadley KA; Rashid NU; Williams LA; Eaton SC; Chung AH
• Local iontophoretic administration of cytotoxic therapies to solid tumors.
  Sci Transl Med Volume: 7 Page(s): 273ra14
  02/04/2015 Authors: Byrne JD; Jajja MRN; O'Neill AT; Bickford LR; Keeler AW; Hyder N; Wagner K; Deal A; Little RE; Moffitt RA
• Circulating tumor cells as a biomarker of response to treatment in patient-derived xenograft mouse models of pancreatic adenocarcinoma.
  PLoS One Volume: 9 Page(s): e89474
  01/01/2014 Authors: Torphy RJ; Tignanelli CJ; Kamande JW; Moffitt RA; Herrera Loeza SG; Soper SA; Yeh JJ
• Feasibility of multiplex quantum dot stain using primary antibodies from four distinct host animals.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2012 Page(s): 6576 - 6579
  01/01/2012 Authors: Tran JK; Hubbard EN; Stokes TH; Moffitt RA; Wang MD
• caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts.
  BMC Bioinformatics Volume: 12 Page(s): 383
  09/29/2011 Authors: Moffitt RA; Yin-Goen Q; Stokes TH; Parry RM; Torrance JH; Phan JH; Young AN; Wang MD
• Adaptive control model reveals systematic feedback and key molecules in metabolic pathway regulation.
  J Comput Biol Volume: 18 Page(s): 169 - 182
  02/01/2011 Authors: Quo CF; Moffitt RA; Merrill AH; Wang MD
• An analysis of scale and rotation invariance in the bag-of-features method for histopathological image classification.
  Med Image Comput Comput Assist Interv Volume: 14 Page(s): 66 - 74
  01/01/2011 Authors: Raza SH; Parry RM; Moffitt RA; Young AN; Wang MD
• Feasibility analysis of high resolution tissue image registration using 3-D synthetic data.
  J Pathol Inform Volume: 2 Page(s): S6
  01/01/2011 Authors: Sharma Y; Moffitt RA; Stokes TH; Chaudry Q; Wang MD
• Automatic batch-invariant color segmentation of histological cancer images.
  Proc IEEE Int Symp Biomed Imaging Volume: 2011 Page(s): 657 - 660
  01/01/2011 Authors: Kothari S; Phan JH; Moffitt RA; Stokes TH; Hassberger SE; Chaudry Q; Young AN; Wang MD
• k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction
  PHARMACOGENOMICS JOURNAL Page(s): S62 - S79
  10/01/2010 Authors: Parry RM; Jones W; Stokes TH; Phan JH; Moffitt RA; Fang H; Shi L; Oberthuer A; Fischer M; Tong W
• The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
  PHARMACOGENOMICS JOURNAL Page(s): S5 - S16
  10/01/2010 Authors: Shi L; Campbell G; Jones WD; Campagne F; Wen Z; Walker SJ; Su Z; Chu T-M; Goodsaid FM; Pusztai L
• k-Nearest neighbor models for microarray gene expression analysis and clinical outcome prediction.
  Pharmacogenomics J Volume: 10 Page(s): 292 - 309
  08/01/2010 Authors: Parry RM; Jones W; Stokes TH; Phan JH; Moffitt RA; Fang H; Shi L; Oberthuer A; Fischer M; Tong W
• The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
  Nat Biotechnol Volume: 28 Page(s): 827 - 838
  08/01/2010 Authors: Shi L; Campbell G; Jones WD; Campagne F; Wen Z; Walker SJ; Su Z; Chu T-M; Goodsaid FM; Pusztai L
• Molecular mapping of tumor heterogeneity on clinical tissue specimens with multiplexed quantum dots.
  ACS Nano Volume: 4 Page(s): 2755 - 2765
  05/25/2010 Authors: Liu J; Lau SK; Varma VA; Moffitt RA; Caldwell M; Liu T; Young AN; Petros JA; Osunkoya AO; Krogstad T
• WebPK, a web-based tool for custom pharmacokinetic simulation.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2010 Page(s): 1494 - 1497
  01/01/2010 Authors: Srimani J; Moffitt RA; Wang MD
• Automated classification of renal cell carcinoma subtypes using bag-of-features.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2010 Page(s): 6749 - 6752
  01/01/2010 Authors: Raza HS; Parry MR; Sharma Y; Chaudry Q; Moffitt RA; Young AN; Wang MD
• Diagnostic biomarkers for renal cell carcinoma: selection using novel bioinformatics systems for microarray data analysis.
  Hum Pathol Volume: 40 Page(s): 1671 - 1678
  12/01/2009 Authors: Osunkoya AO; Yin-Goen Q; Phan JH; Moffitt RA; Stokes TH; Wang MD; Young AN
• Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment.
  Trends Biotechnol Volume: 27 Page(s): 350 - 358
  06/01/2009 Authors: Phan JH; Moffitt RA; Stokes TH; Liu J; Young AN; Nie S; Wang MD
• Novel Immunohistochemical Biomarkers for Renal Cell Carcinoma Derived from Expression Microarray Data
  Volume: 89 Page(s): 202A - 202A
  01/01/2009 Authors: Young AN; Yin-Goen Q; Phan JH; Moffitt R; Wang MD; Osunkoya AO
• Development of an automatic quantification method for cancer tissue microarray study.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2009 Page(s): 3665 - 3668
  01/01/2009 Authors: Sanders TH; Stokes TH; Moffitt RA; Chaudry Q; Parry R; Wang MD
• Quality control of highly multiplexed proteomic immunostaining with quantum dots: correcting for crosstalk.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2009 Page(s): 6739 - 6742
  01/01/2009 Authors: Moffitt RA; Caldwell ML; Liu T; Liu J; Nie S; Wang MD
• Matrix Factorization Techniques for Analysis of Imaging Mass Spectrometry Data.
  Volume: 2008
  10/01/2008 Authors: Siy PW; Moffitt RA; Parry RM; Chen Y; Liu Y; Sullards MC; Merrill AH; Wang MD
• Simple quantification of multiplexed quantum dot staining in clinical tissue samples.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2008 Page(s): 1907 - 1910
  01/01/2008 Authors: Caldwell ML; Moffitt RA; Liu J; Parry RM; Sharma Y; Wang MD
• An agent-based stochastic tumor model for predicting mitotic arrest drug response.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2008 Page(s): 5458 - 5461
  01/01/2008 Authors: Fox BM; Moffitt RA; Wang MD
• chip artifact CORRECTion (caCORRECT): a bioinformatics system for quality assurance of genomics and proteomics array data.
  Ann Biomed Eng Volume: 35 Page(s): 1068 - 1080
  06/01/2007 Authors: Stokes TH; Moffitt RA; Phan JH; Wang MD
• Modified genetic algorithm for parameter selection of compartmental models.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2007 Page(s): 143 - 146
  01/01/2007 Authors: Shah NA; Moffitt RA; Wang MD
• Extending microarray quality control and analysis algorithms to Illumina chip platform.
  Annu Int Conf IEEE Eng Med Biol Soc Volume: 2007 Page(s): 4637 - 4640
  01/01/2007 Authors: Stokes TH; Han X; Moffitt RA; Wang MD
• Advances in molecular classification of renal neoplasms.
  Histol Histopathol Volume: 21 Page(s): 325 - 339
  03/01/2006 Authors: Yin-Goen Q; Dale J; Yang W-L; Phan J; Moffitt R; Petros JA; Datta MW; Amin MB; Wang MD; Young AN
• Improvement of SVM Algorithm for Microarray Analysis Using Intelligent Parameter Selection.
  Volume: 2005 Page(s): 4838 - 4841
  01/01/2005 Authors: Phan J; Moffitt R; Dale J; Petros J; Young A; Wang M
• Computationally predicting rate constants in pathway models.
  Conf Proc IEEE Eng Med Biol Soc Volume: 2005 Page(s): 5093 - 5096
  01/01/2005 Authors: Henning P; Moffitt R; Allegood J; Wang E; Merrill A; Wang M
• Effect of outlier removal on gene marker selection using support vector machines.
  Conf Proc IEEE Eng Med Biol Soc Volume: 2006 Page(s): 917 - 920
  01/01/2005 Authors: Moffitt R; Phan J; Hemby S; Wang M