About

Mohamed (Moh) Salem is an Associate Professor in the Department of Animal & Avian Sciences at the University of Maryland. His research focuses on aquaculture genomics and muscle biology, utilizing various genome-wide omics approaches such as transcriptomics, genomics, epigenomics, CRISPR, and proteomics to study complex biological systems related to muscle growth and development. He aims to understand the interactions between components of muscle tissue under different biological and environmental conditions, with particular interest in the genetic and phenotypic variations in muscle during degenerative and regenerative processes. His ultimate goal is to maximize the synthesis of high-quality muscle fibers. In addition to his work on muscle biology, Salem is dedicated to enhancing aquaculture production through genetic improvement of fish strains. His research includes identifying and characterizing genetic traits that influence growth, stress tolerance, disease resistance, and feed conversion efficiency, thereby facilitating the development of genetically improved strains for aquaculture. Salem has held leadership roles such as Chair of the 2017 USDA National Animal Genome Research Program and Co-chair of the NRSP8 grant proposal writing committee. He serves as an associate editor for several scientific journals, including BMC Genomics, the International Journal of Genomics, and Marine Biotechnology. His projects involve integrated genomics and metagenomics to improve fillet yield, genome assembly and annotation of rainbow trout, and the development of genomic tools like SNP markers to advance aquaculture breeding programs.

Research topics

• Fishery
• Genetics
• Biology
• Computer Science
• Artificial Intelligence
• Computational biology
• Engineering
• Evolutionary biology
• Ecology
• Structural engineering

Selected publications

• Splicing retention and enhancer divergence govern the evolutionary fate of ohnologues following whole-genome duplication in rainbow trout

  Scientific Reports · 2026-03-14

  articleOpen accessSenior authorCorresponding

  Whole-genome duplication (WGD) generates gene duplicates, or ohnologues, that enhance evolutionary potential while challenging regulatory coordination and functional balance. Although gene expression divergence after WGD is well studied, the long-term evolutionary dynamics of alternative splicing (AS) remain unclear. We investigated AS evolution in rainbow trout (Oncorhynchus mykiss), which experienced a salmonid-specific WGD ~ 100 million years ago. Using a high-quality genome assembly, transcriptomes from six tissues, and ChIP-seq profiling of histone modifications, we classified ohnologue pairs by expression divergence, splicing complexity, and epigenetic signatures. Most ohnologues were retained through conservation, with a gradual decline in AS diversity over time. The study provides evidence that AS initially evolved through accelerated divergence, while also underscoring the potential role of the independent model in its long-term evolutionary trajectory. Enhancer-associated histone marks, particularly H3K27ac, diverged markedly between neofunctionalized and independently splicing pairs, suggesting that enhancer rewiring may contribute to regulatory and functional divergence. Our results indicate that AS evolution after WGD is shaped by both selective pressures and epigenetic modulation, challenging the assumption of rapid splicing loss and the negligible role of the independent model. This study provides an integrated framework for understanding the evolution of splicing and regulatory landscapes after genome duplication, with implications for vertebrate genome evolution and functional innovation.

  PublisherOA PDFDOI

• Design, control and implementation of AI-driven autonomous snake robot for archeological site exploration

  International Journal of Dynamics and Control · 2026-05-21

  articleOpen accessSenior author

  Abstract For decades, archeological site exploration has presented major challenges due to narrow spaces, unstable structures, and the high sensitivity of historical artifacts. Recent advancements in robotic technologies have introduced highly capable and reliable alternatives for safe and efficient exploration in environments that are otherwise inaccessible or hazardous to humans. This paper presents mathematical modeling, design, control and implementation of a bio-inspired autonomous snake robot tailored for the exploration of confined environments, with a particular focus on archeological sites. Our primary contribution is a novel system integration approach designed specifically for highly confined and fragile heritage environments, successfully combining a modular alternating-joint architecture with a ROS-based control framework and an AI-driven perception system focused strictly on YOLOv11-based artifact and obstacle identification. A physical network model was developed using MATLAB Simscape to simulate the system dynamic behavior under varying payloads. The control architecture was implemented using the robot operating system (ROS), supporting real-time execution of multiple locomotion strategies through coordinated servo actuation. The system is validated through simulation and physical experiments, demonstrating stable undulatory locomotion, accurate mapping in confined environments, and reliable artifact detection under variable lighting and occlusion. The results indicate that snake-inspired robotic platforms provide a viable and scalable solution for autonomous exploration and documentation in sensitive heritage sites.

  PublisherOA PDFDOI

• Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

  BMC Genomics · 2025-02-17 · 18 citations

  reviewOpen access

  BACKGROUND: The innovations of the "Omics Era" have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities. MAIN TEXT: Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (1) advancing reference genome assembly quality; (2) integrating multi-omics data to enhance analysis of production and performance traits; (3) developing resources for the collection and integration of phenomics data; (4) creating pathways for applying and integrating genomics information across animal industries; and (5) providing training, extension, and outreach to support the application of genome to phenome. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability. CONCLUSION: This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

  PublisherOA PDFDOI

• Correction: Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

  BMC Genomics · 2025-03-17

  erratumOpen access
  PublisherOA PDFDOI

• Effects of Pestici4des on Fish Health

  Journal of sustainable research in applied sciences · 2025-06-29

  articleOpen access1st authorCorresponding

  تُستخدم المبيدات على نطاق واسع في المجالات الزراعية والصناعية والسكنية لمكافحة الآفات والأعشاب الضارة، إلا أن هذا الاستخدام أثار مخاوف كبيرة بشأن تأثيره على النظم البيئية المائية، لا سيما صحة الأسماك. تستعرض هذه المراجعة تأثيرات المبيدات على الأسماك، بما في ذلك السُمية الحادة والمزمنة، والتغيرات السلوكية، والاضطرابات التكاثرية، والتغيرات الكيميائية الحيوية. كما يناقش هذا البحث آليات عمل المبيدات، ومسارات دخولها إلى البيئات المائية، وانعكاس ذلك على جماعات الأسماك والنظم البيئية المائية. وتشير النتائج إلى أن المبيدات تشكل تهديدًا كبيرًا لصحة الأسماك وللتنوع البيولوجي المائي، مما يبرز الحاجة إلى تشريعات أكثر صرامة واستراتيجيات بديلة لإدارة الآفات.

  PublisherOA PDFDOI

• Assessment of Training Barriers Among Underserved Virginia Value-added Food Producers: A Proposed Structure for Improving Parity in Food Safety Educational Interventions

  Journal of Food Protection · 2025-05-03

  articleOpen access

  • Participants (27%) reported multiple barriers to attending food safety training. • Training location and frequency could affect participants’ attendance. • Factsheets were the preferred learning tool for food safety. • Participants (22%) reported not knowing who to ask about food safety concerns. • Most producers (90%) understood the importance of food safety in their business. Food manufacturing businesses, regardless of size, must comply with appropriate food safety education requirements, but guidance on effectively training small, minority-owned producers is lacking in key areas, such as preferred formats and knowledge of current perceived barriers to compliance. This study aimed to understand the greatest barriers to knowledge gain and behavior change for underserved value-added food producers in Virginia. An anonymous 10-question survey was administered to Virginia food producers through various channels, including email links, flyers, electronic tablets, or physical copies provided in person. The survey queried demographic information about the producer, factors that inhibited their learning, and suggestions for improved education and outreach. Responses (n=124) were analyzed using descriptive statistics and logistic regression in RStudio version 4.2.3. The results indicated that many producers identify location as the primary barrier to attending and learning about food safety, followed by the frequency of available training events. Additionally, the three preferred learning tools for producers were factsheets, interactive sessions with trainers and/or materials, and prerecorded videos. While there is no single method to meet all the needs related to food safety training for small producers, it is crucial for Cooperative Extension to consider these factors when planning food safety training and workshops to ensure broader outreach to more producers to achieve parity in food safety education.

  PublisherDOI

• <i>De novo</i> Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-13

  preprintOpen access

  Abstract Rainbow trout ( Oncorhynchus mykiss ) exhibit extensive genomic diversity shaped by domestication, life history, and geographic origin. To advance the development of a comprehensive pangenome reference, we present new de novo genome assemblies of two genetically and ecologically distinct lines: Whale Rock (WR; wild, landlocked, Central California) and Keithley Creek (KC; wild, resident, interior Columbia Basin), along with the previously published assemblies of the Arlee (domesticated, Northern California) and Swanson (semi-domesticated, resident, Alaska) lines. All assemblies provide nearly complete coverage of known genes (BUSCO 95.8–99.7%) and are similar in genome size (∼2.3 Gb), with scaffold N50 values between 3.4 Mb (KC) and 52.4 Mb (Swanson). Comparative whole-genome alignments revealed high sequence conservation (97–98% identity) among assemblies, but also evidence of extensive structural variation of at least 50 bp in length. Structural variant (SV) profiling identified tens of thousands of deletions, insertions, and complex rearrangements largely in noncoding sequences. In an initial assessment of the utility of having multiple de novo genome assemblies for rainbow trout, we found that two strains (Arlee and Swanson; domesticated) share SVs enriched in genes linked with growth, reproduction, and adaptation to domestication, such as GTP binding and ECM-receptor interaction. In comparison, the other two strains (WR and KC; wild origin) share SVs associated with reproductive timing such as GnRH signaling pathway. Both Arlee and WR also have unique SVs potentially related to their geographic origin and unique life history. Additionally, we identified SVs in key regions, such as a QTL for fillet yield on Omy17 and the maturation-associated SIX6/ERβ-GPHB5 locus on Omy25q, suggesting the importance of considering SVs when investigating the genomics of complex traits. Together, these assemblies and comparative analyses establish a foundation for a rainbow trout pangenome reference, illuminating how they can be utilized to reveal the structural genomic basis of domestication, adaptation, and other complex traits in O. mykiss .

  PublisherOA PDFDOI

• Splicing Retention and Enhancer Divergence Govern the Evolutionary Fate of Ohnologues Following Whole-Genome Duplication in Rainbow Trout

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-07

  preprintOpen accessSenior authorCorresponding

  ABSTRACT Whole-genome duplication (WGD) produces gene duplicates—known as ohnologues—that expand evolutionary potential while posing challenges for regulatory coordination and functional balance. While divergence in gene expression has been widely studied post-WGD, the long-term evolutionary dynamics of alternative splicing (AS) and its regulatory basis remain unresolved. Here, we investigate the evolution of AS in rainbow trout (Oncorhynchus mykiss), a species that underwent a salmonid-specific WGD ∼100 million years ago. Using a high-quality genome assembly, transcriptome data across six tissues, and ChIP-seq profiling of histone modifications, we classify ohnologue pairs based on their expression divergence, splicing complexity, and epigenetic signatures. We find that most ohnologues are retained through conservation, with a gradual reduction in AS diversity over time. Contrary to earlier models, a substantial fraction of ohnologues follows an independent splicing model, maintaining splicing complexity similar to their unduplicated ancestors. Strikingly, we show that enhancer-associated histone marks, particularly H3K27ac, diverge significantly between neofunctionalized and independently splicing gene pairs, implicating enhancer rewiring as a key driver of regulatory and functional divergence. These findings reveal that AS evolution after WGD is shaped by both selective pressures and epigenetic modulation, challenging assumptions of rapid splicing loss and highlighting the independent model as a dominant long-term fate. Our results provide a unified framework for understanding how splicing and regulatory landscapes evolve following genome duplication, with broad implications for vertebrate genome evolution and functional innovation.

  PublisherOA PDFDOI

• Chromosome level genome assembly and annotation of the Swanson rainbow trout homozygous line

  Scientific Data · 2025-02-26 · 2 citations

  articleOpen accessSenior author

  The genome of the Swanson doubled haploid (DH) YY male line of rainbow trout was de novo assembled using the Canu pipeline, high-coverage PacBio long-read sequence data, Bionano optical maps, and Hi-C proximity ligation sequence data, resulting in 29 major scaffolds aligning with the karyotype of the Swanson line (2 N = 58). This assembly, totaling 2.3 Gb with an N50 of 52.4 Mb, represents approximately 95% of the genome in 29 chromosome sequences with only 109 gaps between scaffolds. Notably, corrections to previous errors in the Swanson line genome assembly were made, including the identification of a double large inversion on the Omy05 chromosome (~57 Mb), the absence of the Omy20 inversion between the Arlee and Swanson assemblies, and the discovery of a ~6.7 Mb inversion on Omy26. This comprehensive assembly contributes to refining the rainbow trout reference genome and serves as a valuable resource for future genetic studies within this species.

  PublisherOA PDFDOI

• Molecular Signatures and Machine Learning Driven Stress Biomarkers for Rainbow Trout Aquaculture and Climate Adaptation

  2025-01-02

  preprintOpen accessSenior author

  Climate and husbandry-induced stressors pose significant threats to fish growth and survival. Therefore, identifying reliable biomarkers is crucial for mitigating stress and enhancing fish health. This study conducted a comprehensive transcriptomic analysis of stress responses in rainbow trout exposed to five different stress conditions—high and low temperatures, crowding, salinity, and low-quality water—for six hours. In total, 21,580 differentially expressed transcripts (DETs) were identified, with 16,959 being unique DETs. Among the conditions studied, heat stress and salinity triggered the most significant transcriptomic responses. Most DETs were specific to individual stressors, indicating distinct physiological responses. Only 39 DETs were commonly regulated across all conditions. The most significant unique DETs associated with heat stress were utilized in machine learning analyses to assess their effectiveness in distinguishing between control and heat-stressed fish from natural Redband trout populations. The logistic model tree (LMT) performed best using a set of 234 DETs. When the dataset was reduced to 50 or 2 DETs, the Random Forest model achieved optimal classification at several time points. Notably, the model consistently relied on two heat shock genes, hsp47, and HSPA4L, as key predictors across all time points (both short- and long-term stress) as well as the combined dataset. In contrast, core DETs (shared between conditions) were less effective in predicting phenotypes, achieving only 52.78% accuracy. The study concluded that molecular signatures are largely specific to individual stressors. It identified potential biomarkers for monitoring stress associated with climate change and recommended their application in breeding programs to enhance fish welfare, improve aquaculture productivity, and support species conservation efforts.

  PublisherOA PDFDOI

Frequent coauthors

• Timothy D. Leeds

  National Center for Cool and Cold Water Aquaculture

  129 shared

• Ali Ali

  University of Maryland, College Park

  113 shared

• Brett Kenney

  West Virginia University

  92 shared

• Daniela Lourenço

  University of Georgia

  89 shared

• Rafet Al-Tobasei

  Middle Tennessee State University

  48 shared

• Jianbo Yao

  Yuncheng University

  41 shared

• Pratima Chapagain

  Vanderbilt University

  30 shared

• Caird E. Rexroad

  27 shared

Labs

• Animal & Avian SciencesPI

Education

• PhD, Genetics and Developmental Biology

  West Virginia University

  2004

Awards & honors

• Associate of the USDA National Animal Genome Research Progra…
• Chair of the 2017 USDA National Animal Genome Research Progr…
• Co-chair of the NRSP8 grant proposal writing committee (2017…