Bioinformatics Tools Development Professors and Supervisors | ApplySharif

جست‌وجوی استاد و پژوهشگر

استاد راهنما، استاد دانشگاه یا پژوهشگر مناسب برای مسیر پژوهشی‌تان را پیدا کنید و با او ارتباط بگیرید.

نمایش ۶۹۱-۷۰۵ از ۷٬۱۸۷ استاد راهنما

اطلاعات این پروفایل‌ها از صفحات عمومی دانشگاه‌ها جمع‌آوری شده و ممکن است به‌روز نباشد.

Yana Safonovaمشاهده پروفایل

استادیار

Pennsylvania State UniversityUnited States

Yana Safonova is an Assistant Professor in Computer Science and Engineering at the Huck Institutes of the Life Sciences , Pennsylvania State University. Her research bridges computational biology with immunogenomics. Immunoglobulin Gene Analysis Genome Assembly Methodology Antibody Diversity Bioinformatics Tool Development Her research focuses on immunoglobulin genetics , vertebrate genome assembly , and computational immunology . Recent work includes developing tools for IGH locus reconstruction and analyzing germline gene diversity in model organisms. Key publication trends reveal expertise in antibody engineering , genomic immunology , and bioinformatics pipeline development for immunosequencing and genome analysis .

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Andrew Parnellمشاهده پروفایل

استاد

University College DublinIreland

Andrew Parnell is a Professor at the Hamilton Institute, Maynooth University, and a funded investigator in three Science Foundation Ireland (SFI) centres: Insight Centre for Data Analytics, I-Form Advanced Manufacturing Centre, and VistaMilk Centre for Precision Pasture-based Dairy. His research bridges theoretical and applied domains. Research Areas: His work focuses on statistics and machine learning for large structured datasets, applied to: Climatology (sea level rise, extremes, paleoclimate analysis) Manufacturing (anomaly detection, real-time tool wear analytics) Bioinformatics (prostate cancer identification, SNP analysis) Learning Analytics (student progress monitoring) Quantitative Ecology (diet estimation, sediment tracing) Radiocarbon Dating (chronology modeling in archaeology) Funding & Commercialisation: He has secured over €1 million in direct funding and contributes to industry-academia collaborations through roles in startups Prolego Scientific (Chief Scientific Officer) and Atturos (Scientific Advisor). Technical Contributions: He develops open-source R packages for non-specialist users, emphasizing practical statistical tools for interdisciplinary applications. Interdisciplinary Impact: His work spans environmental science, healthcare, agriculture, and industrial analytics, with publications in high-impact journals like Science and Nature Communications.

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Kathleen Curranمشاهده پروفایل

استاد

University College DublinIreland

Prof. Kathleen Curran is a Professor at University College Dublin (UCD) and director of the UCD machine learning in medical imaging and diagnostics innovative research lab ( https://www.ucd-ml-mi.com/ ). She serves as an Affiliated Principal Investigator in the Centre for Biomedical Engineering, an INSIGHT funded investigator, and a funded investigator in the Science Foundation Ireland centre for research training in machine learning (ML-Labs). Her research integrates artificial intelligence, computer vision, and clinical medicine to develop interpretable AI solutions for medical diagnostics. Key focus areas include fetal ultrasound imaging, cardiac MRI reconstruction, neuroimaging for Alzheimer's disease and multiple sclerosis, and biomarker discovery for conditions like lymphangioleiomyomatosis and placenta accreta spectrum. She pioneers techniques in diffusion models, explainable AI, and multi-modal learning to address challenges in low-data medical scenarios. Analysis of her recent publications reveals dominant trends in applying generative models for medical data augmentation, developing uncertainty-aware diagnostic systems, and creating interpretable clinical AI tools. Her work consistently targets high-impact clinical applications including fetal development monitoring, cardiovascular disease management, and neurological disorder detection, with strong emphasis on real-world clinical implementation. Scientific recognition includes: 2019 InterTrade Ireland FUSION Project Exemplar Award (with Axial Medical Printing Ltd.) Three Enterprise Ireland Commercialisation Fund awards as Principal Investigator Horizon Europe consortium funding for SMASH-HCM project (Stratification, Management, and Guidance of Hypertrophic Cardiomyopathy Patients using Hybrid Digital Twin Solutions) Prof. Curran leads significant research funding initiatives including Horizon Europe and multiple Enterprise Ireland awards. Her group actively collaborates with industry partners like Axial Medical Printing Ltd. and participates in national research centers such as INSIGHT and ML-Labs, driving translational AI research from bench to bedside. The UCD machine learning in medical imaging and diagnostics lab ( https://www.ucd-ml-mi.com/ ) serves as her primary research hub, fostering interdisciplinary collaborations between computer scientists, clinicians, and biomedical engineers to advance clinical AI solutions.

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Md. Abul Hassan Sameeمشاهده پروفایل

دانشیار

Baylor College of MedicineUnited States

Md. Abul Hassan Samee is an Associate Professor at Baylor College of Medicine , specializing in Integrative Physiology . He is affiliated with the Computational and Integrative Biomedical Research Center (CIBR) , THINC@BCM , and the Cardiovascular Research Institute (CVRI) . Education: Postdoctoral Fellowship at Gladstone Institutes, University of California San Francisco PhD in Computer Science from University of Illinois Urbana Champaign Research Interests: Development of machine learning algorithms for biological datasets Single-cell and spatial omics analysis Comparative genomics in regeneration and aging Computational models for cancer and neurodegenerative diseases Publications focus on spatial transcriptomics, cardiac regeneration, and interpretable AI in genomic research. Recent projects include SPaSE for pathology scores and GraphAge for epigenetic aging. Grants from the National Institutes of Health support his work on Alzheimer's disease and MYH7 variant interpretation.

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Fuad Abujaradمشاهده پروفایل

دانشیار

Yale UniversityUnited States

Fuad Abujarad is an Associate Professor of Emergency Medicine and Biostatistics at the Yale School of Public Health . His interdisciplinary research bridges Digital Health , Gerontechnology , and Health Informatics to address critical gaps in elder mistreatment detection and informed consent processes. PhD in Computer Science from Michigan State University (2010) MSc in Computer Science from Michigan State University (2005) His work focuses on developing Virtual cOaching in making Informed Choices on Elder Mistreatment Self-Disclosure (VOICES) – an NIH/NIA-funded digital screening tool for elder abuse – and Virtual Multimedia Interactive Informed Consent (VIC) , an AHRQ-funded mHealth solution to enhance patient comprehension. Additional projects span Personal Care Aides (PCA) workforce strengthening and Health Information Technology systems for abuse prevention. Recent publications highlight applications of his tools in dementia care , emergency departments , and primary care settings . Key trends include digital risk assessment , multimodal patient education , and fault-tolerant software design for healthcare systems. Merit of Achievements (2006) from Yale University Fulbright Fellowship (2004) Dr. Abujarad leads grants from NIA , AHRQ , CMS , RWJF , and National Institutes of Health . His lab collaborates with Michigan State University and Yale Cancer Center , emphasizing patient-centered design and real-time background check systems for long-term care worker vetting.

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John Manakمشاهده پروفایل

استاد

University of IowaUnited States

John Manak serves as Professor and Biomedical Sciences Program Director in the Department of Biology at the University of Iowa, conducting research at the intersection of genomics, genetics, and neurobiology. His work employs model organisms including Drosophila and Xenopus to investigate human genetic disorders and develop translational therapies. His academic background includes: PhD from Columbia University Dr. Manak's research focuses on identifying causative mutations for congenital anomalies such as spina bifida, branchio-oto-renal syndrome, renal agenesis, and cleft lip/palate. His lab discovered ISM1 as a critical craniofacial patterning gene and elucidated PRICKLE's role in epilepsy-ataxia syndromes using fly models. Current work explores glial immune responses and oxidative stress pathways in seizure progression, with potential for repurposing anti-inflammatory drugs as novel anti-epileptic therapies. Analysis of his 2019-2023 publications reveals consistent emphasis on copy-number variation analysis in craniofacial disorders and epilepsy mechanisms. Key trends include identification of novel clefting genes (COBLL1, RIC1, ARHGEF38), chromatin organization studies involving Dm-Myb, and translational approaches targeting neuroinflammation. His work bridges fundamental genetic discovery with clinical applications through integrated genomic and physiological analyses. No scientific awards were specified in the source material. As principal investigator, Dr. Manak mentors graduate students and postdoctoral researchers while securing research funding evidenced by his publication record in high-impact journals including Nature, PNAS, and Cell Reports. His leadership extends to directing the Biomedical Sciences Program and contributing to departmental research initiatives. His laboratory maintains active research programs utilizing Drosophila for epilepsy modeling, Xenopus for craniofacial studies, and mammalian systems for neuroprotection research. The lab collaborates extensively with University of Iowa core facilities including the Carver Center for Genomics and Carver Center for Imaging, employing techniques ranging from CRISPR-based gene editing to electrophysiological analysis of neural circuits.

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Paola Paciمشاهده پروفایل

دانشیار

Sapienza University of RomeItaly

Paola Paci is an Associate Professor at the Department of Computer, Control, and Management Engineering "Antonio Ruberti" of Sapienza University of Rome and an Affiliate Professor at the Department of Laboratory Medicine, Cardio-Metabolic Unit of Karolinska Institutet, Sweden. She has held visiting positions at Harvard Medical School and research roles at CNR's Institute for Systems Analysis and Computer Science. Her work bridges computational biology and network medicine. 2010: Second Level Master in Bioinformatics (Sapienza University of Rome) 2003: PhD in Physics (University of Pavia) 1999: MSc in Physics (Sapienza University of Rome) Paci develops algorithms for biomarker discovery and drug repurposing in network medicine. Her tools include SWIM for glioblastoma biomarkers, SPINNAKER for ceRNA interactions, SAveRUNNER for drug repurposing, and MIENTURNET for miRNA-target analysis. Recent work focuses on single-cell multi-omics, adverse drug effects, and pathogen spillover mechanisms. Her research spans 2025-2024 publications covering Alzheimer’s disease drug prioritization, COPD pathway analysis, obesity therapeutics avoiding hepatic steatosis, and neuroblastoma immunotherapy resistance. These works integrate network medicine with pharmacology, genomics, and systems biology. 2018: BITS Best Poster Award 2017: IEEE TCCLS Best Poster (700 USD) 2016: IEEE TCCLS Best Poster (500 USD) 2014: SYSBIO Award (10,000 EUR) 2010: Master Award (1,500 EUR) She teaches bioinformatics at Sapienza University and Campus Biomedico University, organized key IEEE workshops, directs training courses, and serves on editorial boards (Scientific Reports, Biotechnology Reports). Her affiliations include the Network Medicine Institute and GNB bioengineering society.

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Matthew Torresمشاهده پروفایل

دانشیار

Georgia Institute of TechnologyUnited States

Dr. Matthew Torres is an Associate Professor of Biological Sciences at the Georgia Institute of Technology and an Adjunct Faculty member. He leads the Torres Lab , where his team integrates mass spectrometry , bioinformatics , and yeast genetics to decode how post-translational modifications (PTMs) regulate G protein and MAP-Kinase signaling systems. His work spans from developing machine learning tools like SAPH-ire for PTM prediction to experimental validation of PTM roles in stress adaptation and signal transduction. Education: B.S. in Biology, Humboldt State University (1997) Ph.D. in Biochemistry, University of North Carolina at Chapel Hill (2007) Research Interests: His lab focuses on four major areas: Coordinated PTM-based regulation of dynamic signaling complexes Identification of novel signaling PTMs PTM networks in stress adaptation Technology development for regulatory PTM detection Scientific Awards: K99/R00 NIH Pathway to Independence Award (2010–2016) IBB Above and Beyond Award (2016) ASPET Early Career Award (2022) Lab and Mentorship: Dr. Torres has mentored over 20 graduate students and postdocs, many of whom have gone on to prestigious positions at institutions like Genentech, UCSF, MD Anderson, and Harvard. His lab is also involved in outreach programs including Project ENGAGES for high school students and science education for elementary and middle schools. Research Tools and Facilities: He is co-director of the Systems Mass Spectrometry Core (SYMS-C) at Georgia Tech, which supports advanced proteomics research across the university.

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Michael Baudisمشاهده پروفایل

استاد

University of ZurichSwitzerland

Bioinformatics
Tumorgenomics
Genomics
+۴ مورد دیگر

Michael Baudis is a Professor of Bioinformatics and Tumorgenomics at the Institute of Molecular Biology , Faculty of Science, University of Zurich. He leads the development of the Progenetix database, a global reference for cancer genomic copy number alterations, and contributes to international standards through his membership in the Global Alliance for Genomics and Health (GA4GH) . Research focuses on genomic data representation , cancer subtype classification , and data sharing protocols Key projects include Beacon networks , Phenopackets , and GA4GH standards Email: michael.baudis@uzh.ch His recent work explores short tandem repeat variations , attention-based deep learning for CNAs , and heterogeneity in cancer classifications . Methodological contributions include segment_liftover , CNARA , and pgxRpi for genomic data calibration and analysis.

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Paola Arlottaمشاهده پروفایل

استاد

Harvard UniversityUnited States

Paola Arlotta is the Golub Family Professor and Chair of the Department of Stem Cell and Regenerative Biology at Harvard University. She is a principal faculty member at the Harvard Stem Cell Institute, an Institute Member at the Broad Institute, and an Associate Member of the Stanley Center for Psychiatric Research. Her career spans groundbreaking work in cortical development and regenerative neuroscience. Education: M.S. in Biochemistry from the University of Trieste, Italy Ph.D. in Molecular Biology from the University of Portsmouth, UK Postdoctoral training in Neuroscience at Harvard Medical School Dr. Arlotta’s research focuses on defining molecular pathways that govern the differentiation of neural progenitors into cortical projection neurons, with a special interest in corticospinal neurons linked to ALS and spinal cord injury. Her lab bridges developmental neuroscience with stem cell engineering to study human-specific cortical development using 3D organoid models, aiming to uncover mechanisms of neurodevelopmental diseases. Scientific Contributions: 2024: Discovery of individual susceptibility to neurotoxicity in brain chimeroids 2024: Microglia’s role in fetal brain inflammation response 2022: Autism risk genes affect asynchronous neuron class development 2019: Reproducible generation of human cortical diversity in organoids Scientific Awards: Elected to the National Academy of Medicine for pioneering brain organoid research Her lab employs advanced techniques like single-cell RNA sequencing, FIN-seq for frozen tissue analysis, and in utero electroporation. She also explores neuronal reprogramming and myelin dynamics across axons, contributing to understanding cortical circuit assembly and repair.

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Curtis Huttenhowerمشاهده پروفایل

استاد

Harvard UniversityUnited States

Dr. Curtis Huttenhower is a Professor of Computational Biology and Bioinformatics at Harvard T.H. Chan School of Public Health , with dual appointments in the Department of Biostatistics and Department of Immunology and Infectious Diseases . His research focuses on computational methods for microbial community analysis, human microbiome public health implications, and machine learning applications in genomics. Education: B.S. (2000) from Rose-Hulman Institute of Tech, M.S. (2003) from Carnegie Mellon, Ph.D. (2008) from Princeton Major grants: NIH R21CA299494 (cancer virome), U24HL175772 (HVP consortium), OT2CA297578 (early-onset colorectal cancer prevention) His work spans functional metagenomics , microbiome diagnostics , and structured biological knowledge in machine learning . Recent studies include strain-level microbiome mapping and microbiome links to depression, diabetes, and cardiovascular disease . He contributes to open-source tools like MaAsLin and WAAFLE , and leads the Human Microbiome Project sub-cohort for inflammatory bowel disease microbiome characterization.

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Abby Hareمشاهده پروفایل

دانشیار

Bloomsburg University of PennsylvaniaUnited States

Abby Hare is an Associate Professor of Biology at the Department of Biological and Allied Health Sciences , Bloomsburg University of Pennsylvania . She earned her Ph.D. in microbiology and molecular genetics from Rutgers University and a B.S. in biochemistry and molecular biology from Ursinus College with a minor in biostatistics. Teaching: Genetics, Bioinformatics, Anatomy and Physiology, Concepts in Biology Research Focus: Identification and phenotypic characterization of rare genetic variants in neuropsychiatric disorders using genomic datasets and electronic health records. Research Trends: Her publications highlight interdisciplinary work bridging genomics , neurodevelopmental disorders , and clinical phenotyping . Key areas include copy number variants , gene-gene interactions in autism and language impairments, and environmental influences on mental health.

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Frederik Trinkmannمشاهده پروفایل

استاد

Heidelberg UniversityGermany

Prof. Dr. med. Frederik Trinkmann serves as Head of the Asthma Outpatient Clinic and Managing Senior Physician in Pneumology and Respiratory Medicine at Thoraxklinik Heidelberg. He holds academic appointments at Universitätsmedizin Mannheim and Universität Heidelberg, where he leads pulmonary research initiatives. His research spans Internal Medicine , Pulmonology , and Respiratory Medicine , with a focus on Small airway dysfunction in asthma/COPD Cardiopulmonary risk in chronic lung diseases Smoking-related respiratory effects Post-COVID lung sequelae Bioinformatics in pulmonary diagnostics His work has been recognized with multiple scientific awards, including the Kurt und Erika Palm-Stiftung Science Prize (2nd Place) and DGIM Poster Award . Key publications highlight trends in Advanced oscillometry for small airway assessment Sex-specific differences in weaning outcomes Real-world effectiveness of triple inhalation therapies Cytokine profiling in respiratory inflammation Machine learning for lung function diagnostics He actively contributes to clinical guidelines including the Ers-Deutschland S2k-Leitlinie for cough diagnosis . Scientific Collaborations: Principal Investigator, German Center for Lung Research (DZL) Leadership, Translational Research Section at Universitätsmedizin Mannheim Cooperation with European Respiratory Society (ERS)

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Kyle P. Quinnمشاهده پروفایل

استاد

University of Arkansas FayettevilleUnited States

Kyle P. Quinn is a Professor at the Department of Biomedical Engineering, College of Engineering, University of Arkansas. He leads a multidisciplinary research group developing quantitative biomarkers for non-invasive tissue diagnostics, with a focus on skin wound healing and aging. Education : Postdoctoral Fellow at Tufts University, Ph.D. from University of Pennsylvania, and B.S. from University of Wisconsin-Madison. Research Focus : Integrates biomedical optics, cell biology, biomechanics, and bioinformatics to create label-free diagnostic tools. Specializes in multiphoton microscopy, deep learning algorithms, and collagen microstructure analysis for chronic wound detection and skin aging studies. Article Trends : Recent work emphasizes AI-driven wound analysis, multiscale tissue modeling, metabolic imaging in skin and cancer, and engineering solutions for calcific valve disease. Scientific Awards Solomon R. Pollack Award for Graduate Bioengineering Research NIH Ruth L. Kirschstein Postdoctoral Fellowship NIH Pathway to Independence K99/R00 Award NIH R01 Grant NSF CAREER Award Grants : Externally funded by NIH (R00EB017723, R01AG056560, R01EB031032), Department of Defense (W81XWH-17-1-0194, W81XWH-17-C-0169), NSF (1846853), and Arkansas Biosciences Institute. Lab Information : The Quinn Lab recruits postdoctoral, graduate, and undergraduate researchers in biomedical optics, animal models, and data science. Lab facilities include advanced microscopy and computational tools for tissue analysis.

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Jeffery A Goldsteinمشاهده پروفایل

دانشیار

Northwestern UniversityUnited States

Jeffery A Goldstein, MD, PhD is an Associate Professor in the Department of Pathology at Northwestern University Feinberg School of Medicine, where he serves as Director of Perinatal Pathology with additional appointments in Autopsy Pathology. He is an attending physician at Northwestern Memorial Hospital with clinical and teaching responsibilities in perinatal and autopsy pathology. His educational background includes: PhD: University of Chicago (2012) MD: University of Chicago (2014) Residency: Vanderbilt University, Anatomic Pathology (2017) Fellowship: Northwestern University, McGaw Medical Center (Lurie Children's Hospital), Pediatric Pathology (2018) Dr. Goldstein is an early-stage investigator focusing on maternal-child health with particular expertise in placental pathology. His research integrates bioimaging, informatics, and machine learning to transform placental examination from a specialized, resource-intensive process into a widely accessible diagnostic tool. He develops AI algorithms that can analyze placental photographs and microscopic slides to detect abnormalities associated with infection, neonatal sepsis, and other pregnancy complications. His work bridges computational science with clinical pathology to address the significant gap that less than 20% of placentas receive clinical examination despite their diagnostic value for future maternal and child health. His research portfolio includes multiple innovative projects applying machine learning to placental diagnosis, deep phenotyping, and quantitative description of placental features in health and disease. His recent publications demonstrate applications of deep learning for fetal inflammatory response diagnosis, machine learning assessment of gestational age, and analysis of placental lesions in gestational diabetes. Dr. Goldstein holds board certifications in Anatomic Pathology and Pediatric Pathology from the American Board of Pathology. His clinical work focuses on microscopic examination of placental slides, which forms the foundation of his research. He is affiliated with several research centers including the Center for Reproductive Science, the Institute for Artificial Intelligence in Medicine (specifically the Center for Computational Imaging and Signal Analytics in Medicine), and the Northwestern University Clinical and Translational Sciences Institute (NUCATS). His work has been featured in Northwestern Medicine news regarding AI applications for placental analysis to detect neonatal and maternal problems.

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