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Bronze Contributor

Sharif S Aly

PeerJ Editor, Author & Reviewer

Summary

As a veterinary epidemiologist I specialize in dairy cattle infectious diseases and welfare. I received my veterinary medicine degree from Cairo University (1998), practiced for two years before completing the Food Animal Production Medicine Internship at the Caine Veterinary Teaching Center at the U of Idaho, followed by the Food Animal Reproduction and Herd Health Residency at U of California, Davis. I completed my masters and doctoral degrees at UC Davis in Preventive Veterinary Medicine and Epidemiology, respectively.

Animal Behavior Computational Biology Data Mining & Machine Learning Data Science Epidemiology Evidence Based Medicine Infectious Diseases Mathematical Biology Population Biology Statistics Veterinary Medicine

Editing Journals

PeerJ - the Journal of Life & Environmental Sciences

Past or current institution affiliations

UC Davis

Work details

Professor, Epidemiology and Biostatistics

University of California, Davis

May 2010

School of Veterinary Medicine, Department of Population Health and Reproduction

As a faculty member of the Dept. of Population Health and Reproduction, School of Veterinary Medicine, UC Davis, I develop quantitative and epidemiological methods to advance the health, welfare and productivity of food animals. I am enthusiastic about teaching epidemiology to veterinary and graduate students.

Professor, Epidemiology & Biostatistics

University of California, Davis

May 2010

Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine

The Dairy Epi Lab (Aly Lab) current research focuses on effectively surveying large populations, novel scoring systems, diagnostic strategies, and risk assessment development. Using such tools I collaborate with teams dedicated to calf and adult cow health, foodborne pathogens, and antimicrobial resistance.

Websites

PeerJ Contributions

December 23, 2021

Quantification of antibiotic resistance genes and mobile genetic in dairy manure

Yi Wang, Pramod Pandey, Colleen Chiu, Richard Jeannotte, Sundaram Kuppu, Ruihong Zhang, Richard Pereira, Bart C. Weimer, Nitin Nitin, Sharif S. Aly

https://doi.org/10.7717/peerj.12408 PubMed 35036113

August 12, 2021

Development of a multiplex qPCR assay for the simultaneous detection of Mycoplasma bovis, Mycoplasma species, and Acholeplasma laidlawii in milk

Kanika Chauhan, Sharif S. Aly, Terry W. Lehenbauer, Karen H. Tonooka, Kathy Glenn, Paul Rossitto, Maria L. Marco

https://doi.org/10.7717/peerj.11881 PubMed 34447623

July 16, 2021

Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach

Pranav S. Pandit, Deniece R. Williams, Paul Rossitto, John M. Adaska, Richard Pereira, Terry W. Lehenbauer, Barbara A. Byrne, Xunde Li, Edward R. Atwill, Sharif S. Aly

https://doi.org/10.7717/peerj.11732 PubMed 34316397

July 13, 2021

2018 Survey of antimicrobial drug use and stewardship practices in adult cows on California dairies: post-Senate Bill 27

Pius S. Ekong, Essam M. Abdelfattah, Emmanuel Okello, Deniece R. Williams, Terry W. Lehenbauer, Betsy M. Karle, Joan D. Rowe, Edith S. Marshall, Sharif S. Aly

https://doi.org/10.7717/peerj.11515 PubMed 34306824

July 13, 2021

2018 Survey of factors associated with antimicrobial drug use and stewardship practices in adult cows on conventional California dairies: immediate post-Senate Bill 27 impact

Pius S. Ekong, Essam M. Abdelfattah, Emmanuel Okello, Deniece R. Williams, Terry W. Lehenbauer, Betsy M. Karle, Joan D. Rowe, Sharif S. Aly

https://doi.org/10.7717/peerj.11596 PubMed 34306825

April 20, 2021

Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows

Essam M. Abdelfattah, Pius S. Ekong, Emmanuel Okello, Tapakorn Chamchoy, Betsy M. Karle, Randi A. Black, David Sheedy, Wagdy R. ElAshmawy, Deniece R. Williams, Daniela Califano, Luis Fernando Durán Tovar, Jonathan Ongom, Terry W. Lehenbauer, Barbara A. Byrne, Sharif S. Aly

https://doi.org/10.7717/peerj.11108 PubMed 33976962

January 15, 2020

Bayesian estimation of diagnostic accuracy of fecal culture and PCR-based tests for the detection of Salmonella enterica in California cull dairy cattle

John M. Adaska, Pius S. Ekong, Kristin A. Clothier, Deniece R. Williams, Paul V. Rossitto, Terry W. Lehenbauer, Edward R. Atwill, Xunde Li, Sharif S. Aly

https://doi.org/10.7717/peerj.8310 PubMed 31988800

November 19, 2019

Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies

Tapakorn Chamchoy, Deneice R. Williams, John M. Adaska, Randall J. Anderson, Sharif S. Aly

https://doi.org/10.7717/peerj.8081 PubMed 31763073

May 6, 2019

Molecular epidemiology of coagulase-negative Staphylococcus species isolated at different lactation stages from dairy cattle in the United States

Stephen N. Jenkins, Emmanuel Okello, Paul V. Rossitto, Terry W. Lehenbauer, John Champagne, Maria C.T. Penedo, Andréia G. Arruda, Sandra Godden, Paul Rapnicki, Patrick J. Gorden, Leo L. Timms, Sharif S. Aly

https://doi.org/10.7717/peerj.6749 PubMed 31119068

March 21, 2019

Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California

Richard Pereira, Deniece R. Williams, Paul Rossitto, John Adaska, Emmanuel Okello, John Champagne, Terry W. Lehenbauer, Xunde Li, Jennifer Chase, Tran Nguyen, Alda F. A. Pires, Edward R. Atwill, Sharif S. Aly

https://doi.org/10.7717/peerj.6546 PubMed 30923650

August 30, 2016

Epidemiology of Salmonella sp. in California cull dairy cattle: prevalence of fecal shedding and diagnostic accuracy of pooled enriched broth culture of fecal samples

Omran A. Abu Aboud, John M. Adaska, Deniece R. Williams, Paul V. Rossitto, John D. Champagne, Terry W. Lehenbauer, Robert Atwill, Xunde Li, Sharif S. Aly

https://doi.org/10.7717/peerj.2386 PubMed 27635350

January 2, 2014

Development of a novel clinical scoring system for on-farm diagnosis of bovine respiratory disease in pre-weaned dairy calves

William J. Love, Terry W. Lehenbauer, Philip H. Kass, Alison L. Van Eenennaam, Sharif S. Aly

https://doi.org/10.7717/peerj.238 PubMed 24482759

Academic Editor on

December 24, 2021

Spatiotemporal patterns of the COVID-19 epidemic in Mexico at the municipality level

Jean-François Mas, Azucena Pérez-Vega

https://doi.org/10.7717/peerj.12685 PubMed 35036159

December 20, 2021

Sequence characteristics and phylogenetic analysis of H9N2 subtype avian influenza A viruses detected from poultry and the environment in China, 2018

Xiaoyi Gao, Naidi Wang, Yuhong Chen, Xiaoxue Gu, Yuanhui Huang, Yang Liu, Fei Jiang, Jie Bai, Lu Qi, Shengpeng Xin, Yuxiang Shi, Chuanbin Wang, Yuliang Liu

https://doi.org/10.7717/peerj.12512 PubMed 35036116

November 24, 2021

The reporting of p values, confidence intervals and statistical significance in Preventive Veterinary Medicine (1997–2017)

Locksley L. McV. Messam, Hsin-Yi Weng, Nicole W. Y. Rosenberger, Zhi Hao Tan, Stephanie D. M. Payet, Mahishi Santbakshsing

https://doi.org/10.7717/peerj.12453 PubMed 34900418

August 19, 2021

Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.

Shakeel Hussain, Syed Mohsin Bukhari, Lixin Wang, Nimra Khalid, Zhijun Hou

https://doi.org/10.7717/peerj.11819 PubMed 34466282

August 4, 2021

Effects of delivery via pressure-adjustable pneumatic gas-powered dart gun of three antimicrobial drugs (ceftiofur crystalline free acid, tildopirosin, and tulathromycin) on drug disposition and meat quality in cattle

Thomas B. Hairgrove, Virginia Fajt, Ronald Gill, Rhonda Miller, Michael Miller, Travis Mays

https://doi.org/10.7717/peerj.11822 PubMed 34430074

July 2, 2021

Cytological analysis of tracheal wash and bronchoalveolar lavage fluid in health and respiratory disease in dromedary camels

Turke Shawaf, Abdullah Almubarak, Naser Alhumam, Faisal Almathen, Jamal Hussen

https://doi.org/10.7717/peerj.11723 PubMed 34249521

June 17, 2021

Application of a multilayer perceptron artificial neural network for identification of peach cultivars based on physical characteristics

Adel M. Al-Saif, Mahmoud Abdel-Sattar, Abdulwahed M. Aboukarima, Dalia H. Eshra

https://doi.org/10.7717/peerj.11529

May 14, 2021

Consequences of herbal mixture supplementation on milk performance, ruminal fermentation, and bacterial diversity in water buffaloes

Faizul Hassan, Zhenhua Tang, Hossam M. Ebeid, Mengwei Li, Kaiping Peng, Xin Liang, Chengjian Yang

https://doi.org/10.7717/peerj.11241 PubMed 34040891

April 12, 2021

Clinical validation of the short and long UNESP-Botucatu scales for feline pain assessment

Maíra Belli, Alice R. de Oliveira, Mayara T. de Lima, Pedro H.E. Trindade, Paulo V. Steagall, Stelio P.L. Luna

https://doi.org/10.7717/peerj.11225 PubMed 33954046

April 8, 2021

spa diversity of methicillin-resistant and -susceptible Staphylococcus aureus in clinical strains from Malaysia: a high prevalence of invasive European spa-type t032

Sherry Usun Jones, Kek Heng Chua, Ching Hoong Chew, Chew Chieng Yeo, Fatimah Haslina Abdullah, Norlela Othman, Boon Pin Kee, Suat Moi Puah

https://doi.org/10.7717/peerj.11195 PubMed 33889447

March 26, 2021

The prospective COVID-19 vaccine: willingness to pay and perception of community members in Ibadan, Nigeria

Olayinka Ilesanmi, Aanuoluwapo Afolabi, Obioma Uchendu

https://doi.org/10.7717/peerj.11153 PubMed 33828927

March 24, 2021

Using demographic data to understand the distribution of H1N1 and COVID-19 pandemics cases among federal entities and municipalities of Mexico

Yohanna Sarria-Guzmán, Jaime Bernal, Michele De Biase, Ligia C. Muñoz-Arenas, Francisco Erik González-Jiménez, Clemente Mosso, Arit De León-Lorenzana, Carmine Fusaro

https://doi.org/10.7717/peerj.11144 PubMed 33828926

March 4, 2021

CoViD-19: an automatic, semiparametric estimation method for the population infected in Italy

Livio Fenga

https://doi.org/10.7717/peerj.10819 PubMed 33717677

February 19, 2021

Regucalcin expression profiles in veal calf testis: validation of histological and molecular tests to detect sex steroids illicit administration

Alessandro Benedetto, Elena Biasibetti, Chiara Beltramo, Valentina Audino, Simone Peletto, Elena Maria Bozzetta, Marzia Pezzolato

https://doi.org/10.7717/peerj.10894 PubMed 33643712

February 9, 2021

Validity of the Polar Vantage M watch when measuring heart rate at different exercise intensities

Tricia Shumate, Magdalen Link, James Furness, Kevin Kemp-Smith, Vini Simas, Mike Climstein

https://doi.org/10.7717/peerj.10893 PubMed 33614295

February 5, 2021

Stage 1 registered report: spatiotemporal patterns of the COVID-19 epidemic in Mexico at the municipality level

Jean-François Mas

https://doi.org/10.7717/peerj.10622 PubMed 33604169

January 11, 2021

SMARTAR: an R package for designing and analyzing Sequential Multiple Assignment Randomized Trials

Xiaobo Zhong, Bin Cheng, Xinru Wang, Ying Kuen Cheung

https://doi.org/10.7717/peerj.10559 PubMed 33510969

January 7, 2021

Reproducing country-wide COVID-19 dynamics can require the usage of a set of SIR systems

Eugene B. Postnikov

https://doi.org/10.7717/peerj.10679 PubMed 33505808

October 26, 2020

Towards a unified generic framework to define and observe contacts between livestock and wildlife: a systematic review

Sonny A. Bacigalupo, Linda K. Dixon, Simon Gubbins, Adam J. Kucharski, Julian A. Drewe

https://doi.org/10.7717/peerj.10221 PubMed 33173619

October 6, 2020

Attention behaviours but not pain-related behaviours are modified by the presence of a twin in lambs undergoing castration by rubber ring

Andrew Inhyuk Cho, Caroline Lee, Alison Small

https://doi.org/10.7717/peerj.10081 PubMed 33083137

September 30, 2020

MULTI-DEEP: A novel CAD system for coronavirus (COVID-19) diagnosis from CT images using multiple convolution neural networks

Omneya Attallah, Dina A. Ragab, Maha Sharkas

https://doi.org/10.7717/peerj.10086 PubMed 33062453

September 28, 2020

Predicting CoVID-19 community mortality risk using machine learning and development of an online prognostic tool

Ashis Kumar Das, Shiba Mishra, Saji Saraswathy Gopalan

https://doi.org/10.7717/peerj.10083 PubMed 33062451

September 4, 2020

Risk factors for disease-related deterioration following diagnostic bronchoalveolar lavage procedures in diffuse lung disease: a case-control study

Yuko Usagawa, Kosaku Komiya, Mari Yamasue, Kazuhiko Hashinaga, Eri Mizukami, Kenji Umeki, Shin-ichi Nureki, Masaru Ando, Kazufumi Hiramatsu, Jun-ichi Kadota

https://doi.org/10.7717/peerj.9864 PubMed 32953276

August 7, 2020

A note on the effects of epidemic forecasts on epidemic dynamics

Nicholas R. Record, Andrew Pershing

https://doi.org/10.7717/peerj.9649 PubMed 32844061

1 Answer

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