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<meta name="author" content="Lior Pachter" />
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<p><span>Pachter Lab</span></p>
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<h1> <dt>Research themes and selected papers</dt> </h1>
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<ul>
<li><b>Transcriptional dynamics with the chemical master equation</b>: <a href="https://biophysics.readthedocs.io/en/latest/">lab biophysics homepage</a>. </li>
<li><b>Software tools for genomics</b>: <a href="https://github.com/pachterlab/gget">gget</a> for efficient querying of genomic reference databases (<a href="https://academic.oup.com/bioinformatics/article/39/1/btac836/6971843">paper</a>) and <a href="https://github.com/pachterlab/ffq">ffq</a> for metadata retrieval from sequence databases (<a href="https://academic.oup.com/bioinformatics/article/39/1/btac667/6971839">paper</a>). </li>
<li><b>Cell type and state</b>: Isoform cell-type specificity in the mouse primary motor cortex (<a href="https://www.nature.com/articles/s41586-021-03969-3">paper</a>); Cell types and states in the jellyfish <i>Clytia hemisphaerica</i> (<a href="https://www.science.org/doi/full/10.1126/sciadv.abh1683">paper</a>).</li>
<li><b>Single-cell genomics technology</b>: ClickTag multiplexing of single-cell RNA-seq samples using a one-pot, two-step chemical cross-linking reaction to barcode samples (<a href="https://www.nature.com/articles/s41587-019-0372-z">paper</a>).</li>
<li><b>Single-cell genomics analysis</b>: Examination of the foundations of RNA velocity (<a href="https://www.biorxiv.org/content/10.1101/2022.02.12.480214v1">preprint</a>); Benchmarking of count normalization methods (<a href="https://www.biorxiv.org/content/10.1101/2022.05.06.490859v1">preprint</a>); Mechanistic models for count normalization (<a href="https://www.biorxiv.org/content/10.1101/2022.06.11.495771v1">preprint</a>). </li>
<li><b>Spatial transcriptomics</b>: Review and analysis of the origins of the field (<a href="https://www.nature.com/articles/s41592-022-01409-2">paper / supplemental book</a>).</li>
<li><b>Open-source bioinstrumentation</b>: Low-cost hardware for biomedical applications, including the poseidon syringe pump system (<a href="https://www.nature.com/articles/s41598-019-48815-9">paper</a>) and the colosseum fraction collector (<a href="https://www.sciencedirect.com/science/article/pii/S2468067221000304">paper</a>). </li>
<li><b>Reference-free genomics</b>: Genome-wide association studies using k-mers (<a href="https://elifesciences.org/articles/32920">paper</a>).</li>
<li><b>Pseudoalignment</b>: Introduction of a new paradigm for quantification of targets from short read sequencing using read assignment instead of read alignment (<a href="https://www.nature.com/articles/nbt.3519">kallisto paper</a>).</li>
<li><b>Differential expression methods</b>: Methods for differential analysis of genes and isoforms (<a href="https://www.nature.com/articles/nmeth.4324?ref=https://githubhelp.com">sleuth paper</a>, <a href="https://www.nature.com/articles/nbt.2450">Cuffdiff</a>).</li>
<li><b>RNA structure</b>: Sequencing based characterization of RNA structure with SHAPE-seq (<a href="https://www.pnas.org/doi/abs/10.1073/pnas.1106501108">assay development</a>, <a href="https://www.pnas.org/doi/abs/10.1073/pnas.1106541108">methods paper</a>).</li>
<li><b>Transcript assembly and quantification of bulk RNA-seq data</b>: Software for spliced short read alignment (<a href="https://academic.oup.com/bioinformatics/article/25/9/1105/203994">Tophat paper</a>),processing of bulk RNA-seq data (<a href="https://www.nature.com/articles/nbt.1621">Cufflinks paper</a>, <a href="https://www.nature.com/articles/nmeth.2251">eXpress paper</a>), and a framework for studying isoform switching during cell differentiation (<a href="https://www.nature.com/articles/nbt.1621">paper</a>).</li>
<li><b>Phylogenetics</b>: Insights into the neighbor-joining algorithm (<a href="https://link.springer.com/article/10.1007/s00453-007-9116-4">paper</a>); Theory of the neighbor-net algorithm (<a href="https://www.sciencedirect.com/science/article/pii/S019688581000093X">paper</a>); A unifying framework for tree metric theorems (<a href="https://link.springer.com/article/10.1007/s00026-012-0173-2">paper</a>).</li>
<li><b>Algebraic statistics</b>: <a href="https://www.amazon.com/Algebraic-Statistics-Computational-Biology-Pachter/dp/0521857007">Book</a> on algebraic statistics for computational biology; Tropical geometry of statistical models (<a href="https://www.pnas.org/doi/abs/10.1073/pnas.0406010101">paper</a>).</li>
<li><b>Microbial genomics and metagenomics</b>: Bioinformatics for whole-genome shotgun sequencing of communities (<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0010024">paper</a>); the asthmatic microbiome (<a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008578">paper</a>).</li>
<li><b>Genome alignment</b>: genomic sequence alignment (<a href="https://genome.cshlp.org/content/13/1/97.short">AVID paper</a>) and multiple alignment (<a href="https://genome.cshlp.org/content/14/4/693.short">MAVID paper</a>, <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000392">FSA paper</a>).</li>
<li><b>Genome sequencing and annotation</b>: Mouse genome (<a href="https://www.nature.com/articles/nature01262">paper</a>), rat genome (<a href="https://www.nature.com/articles/nature02426">paper</a>), chicken genome (<a href="https://www.nature.com/articles/nature03154">paper</a>), human genome (<a href="https://www.nature.com/articles/nature05874">ENCODE pilot paper</a>), fly genome (<a href="https://www.nature.com/articles/nature06341">paper</a>); <i>De novo</i> annotation (<a href="https://genome.cshlp.org/content/13/3/496.short">SLAM paper</a>). </li>
<li><b>Combinatorics</b>: Pebbling graphs (<a href="http://www.people.vcu.edu/~ghurlbert/pebbling/papers/PaSnVo_OPG.pdf">paper</a>); Counting tilings (<a href="https://www.combinatorics.org/ojs/index.php/eljc/article/view/v4i1r29">paper</a>).</li>
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