miguel esteban pacheco

molecular biologist, bioinformatician, photographer

Hi, I’m Miguel. I’m a Postdoctoral Fellow in the Next-generation Sequencing (NGS) lab in the FDA Office of Oncologic Diseases. In the NGS lab, I use bioinformatic approaches to evaluate B-cell receptor sequencing technologies and explore fundamental questions about mutational dynamics in cultured cancer cell lines. My curiosity about nature extends beyond the lab, where I seek to capture the beauty of people, our planet, and the cosmos through photography.

Professional Summary

Capturing the immune repertoire

The adaptive immune receptor repertoire (AIRR) contains a wealth of information about an individual’s health. However, as approaches to capture the immune repertoire are emerging technologies, there remain obstacles to their utility in regulatory decision making. As a postdoctoral fellow, I’ve developed standards for benchmarking B-cell receptor sequencing (BCR-seq) assays as part of the BCR-SEQC Consortium led by the FDA. In this capacity, I’ve analyzed bulk and single-cell BCR-seq datasets and evaluated various quality control and performance metrics.

The ribosome: A sentinel for cellular stress

As a graduate student, I became captivated by RNA biology. During my tenure as a student in the Green Lab at JHMI, I focused my studies on the signaling roles carried out by the translational machinery of the cell, using yeast genetics and bioinformatic analyses to assemble a case study at the intersection of translational control and cellular stress.

NGS expertise from bench to command line

My graduate work highlights nuances in mechanisms of Integrated Stress Response (ISR) activation. By employing a combination of RNA-seq, mass spectrometry, and polysome profiling, I identify novel connections between ribosome collisions and the Integrated Stress Response. I show that induction of ribosome collisions using the translation inhibitor cycloheximide (CHX) leads to a partial mobilization of ISR-target genes:

Gcn4-dependent gene lists defined by analysis of data from Natarajan et al. 2001; displayed RNA-seq data is my own.

Scientific Publications

Pacheco ME, Xiao W, BCR-SEQC consortium. (2025). Resources for establishing reference materials for B cell receptor profiling analysis using NGS technologies. In preparation.
Kim KQ, Li JJ, Nanjaraj Urs AN, Pacheco ME, Lasehinde V, Denk T, Tesina P, Tomomatsu S, Matsuo Y, McDonald E, Beckmann R, Inada T, Green R, Zaher HS. (2024). Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes. Molecular Cell.
Pacheco M, D’Orazio K, Lessen L, Veltri A, Neiman Z, Loll-Krippleber R, Brown G, Green R. (2024). “Genetic screens in S. cerevisiae identify a role for 40S ribosome recycling factors TMA20/22 in nonsense-mediated decay.” G3.