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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<h1>Sachin Pundhir, Ph.D.</h1>
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<p><b>Research Publications</b>
<table border=0 cellpadding=5 cellspacing=5>
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<td valign="top" align="right">2020</td><td>
The ASXL1-G643W variant accelerates the development of CEBPA mutant acute myeloid leukemia.<br>
D'Altri T, Wilhelmson AS, Schuster MB, Wenzel A, Kalvisa A, <b>Pundhir S</b>, Hansen AM, Porse BT.<br>
<b><i>Haematologica</i></b> May 7:haematol.2019.235150 [PMID: 32381577] [<a href="https://haematologica.org/article/view/9741" target="_blank">PDF</a>].
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<td valign="top" align="right">2020</td><td>
Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans.<br>
Nepal C, Taranta A, Hadzhiev Y, <b>Pundhir S</b>, Mydel P, Lenhard B, Müller F, Andersen JB.<br>
<b><i>iScience</i></b> 23(4):101008 [PMID: 32268280] [<a href="https://www.cell.com/iscience/fulltext/S2589-0042(20)30192-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2589004220301929%3Fshowall%3Dtrue" target="_blank">PDF</a>].
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<td valign="top" align="right">2019</td><td>
The splicing factor RBM25 controls MYC activity in acute myeloid leukemia.<br>
Ge Y, Schuster MB, <b>Pundhir S</b>, Rapin N, Bagger FO, Sidiropoulos N, Hashem N, Porse BT.<br>
<b><i>Nature Communications</i></b> 10(1):172 [PMID: 30635567] [<a href="https://www.nature.com/articles/s41467-018-08076-y" target="_blank">PDF</a>].
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<td valign="top" align="right">2019</td><td>
Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML.<br>
Jakobsen JS, Laursen LG, Schuster MB, <b>Pundhir S</b>, Schoof E, Ge Y, d'Altri T, Vitting-Seerup K, Rapin N, Gentil C, Jendholm J, Theilgaard-Mönch K, Reckzeh K, Bullinger L, Döhner K, Hokland P, Fitzgibbon J, Porse BT.<br>
<b><i>Science Advances</i></b> Jul 10;5(7):eaaw4304 [PMID: 31309149] [<a href="https://advances.sciencemag.org/content/5/7/eaaw4304" target="_blank">PDF</a>].
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<td valign="top" align="right">2019</td><td>
Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism.<br>
Jacobsen MJ, Havgaard JH, Anthon C, Mentzel CMJ, Cirera S, Krogh PM, <b>Pundhir S</b>, Karlskov-Mortensen P, Bruun CS, Lesnik P, Guerin M, Gorodkin J, Jørgensen CB, Fredholm M, Barrès R.<br>
<b><i>Front Genet.</i></b> 10:1268 [PMID: 31921306] [<a href="https://doi.org/10.3389/fgene.2019.01268" target="_blank">PDF</a>].
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<td valign="top" align="right">2018</td><td>
Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment.<br>
Lauridsen FKB, Jensen TL, Rapin N, Aslan D, Wilhelmson AS, <b>Pundhir S</b>, Rehn M, Paul F, Giladi A, Hasemann MS, Serup P, Amit I, Porse BT.<br>
<b><i>Cell Reports</i></b> 24(3):766-780 [PMID: 30021172] [<a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30984-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124718309847%3Fshowall%3Dtrue" target="_blank">PDF</a>].
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<td valign="top" align="right">2018</td><td>
Enhancer and transcription factor dynamics during myeloid differentiation reveal an early differentiation block in Cebpa null progenitors.<br>
<b>Pundhir S</b>*, Lauridsen FB*, Schuster MB, Jakobsen J, Ge Y, Schoof E, Rapin N, Waage J, Hasemann M and Porse BT.<br>
<b><i>Cell Reports</i></b> 23(9):2744-2757 [PMID: 29847803] [<a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30745-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124718307459%3Fshowall%3Dtrue" target="_blank">PDF</a>] (*joint first authors).
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<td valign="top" align="right">2016</td><td>
Peak-valley-peak pattern of histone modifications delineate active regulatory elements and their directionality.<br>
<b>Pundhir S</b>, Bagger FO, Lauridsen FB, Rapin N and Porse BT.<br>
<b><i>Nucleic Acids Research</i></b> 44:4037-4051 [PMID: 27095194] [<a href="http://nar.oxfordjournals.org/content/44/9/4037.full.pdf+html" target="_blank">PDF</a>].
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<td valign="top" align="right">2016</td><td>
BloodSpot: A database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis.<br>
Bagger F, Sasivarevic D, Sohi S, Laursen L, <b>Pundhir S</b>, Sønderby C, Winther O, Rapin, N and Porse, B.<br>
<b><i>Nucleic Acids Research</i></b> 44:D917-24 [PMID: 26507857] [<a href="http://nar.oxfordjournals.org/content/44/D1/D917.full.pdf+html" target="_blank">PDF</a>].
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<td valign="top" align="right">2015</td><td>
Differential and coherent processing patterns from small RNAs.<br>
<b>Pundhir S</b> and Gorodkin J.<br>
<b><i>Scientific Reports (Nature)</i></b> 5:12062 [PMID: 26166713] [<a href="http://www.readcube.com/articles/10.1038/srep12062" target="_blank">PDF</a>].
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<td valign="top" align="right">2015</td><td>
Emerging applications of read profiles towards the functional annotation of the genome.<br>
<b>Pundhir S</b>, Poirazi Y and Gorodkin J.<br>
<b><i>Frontiers in Genetics</i></b> 6:118 [PMID: 26042150] [<a href="http://www.readcube.com/articles/10.3389/fgene.2015.00188" target="_blank">PDF</a>].
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<td valign="top" align="right">2014</td><td>
EssOilDB: A database of essential oils reflecting terpene composition and variability in the plant kingdom.<br>
Kumari S, <b>Pundhir S</b>, Priya P, Jeena G, Punetha A, Chawla K, Jafaree Z, Mondal S and Yadav G.<br>
<b><i>Database (Oxford)</i></b> 2014:bau120 [PMID: 25534749] [<a href="http://database.oxfordjournals.org/content/2014/bau120.full.pdf+html" target="_blank">PDF</a>].
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<td valign="top" align="right">2014</td><td>
Spatially conserved long non-coding RNA and cis-regulatory elements identified within Cd247 gene in human and mouse using high-throughput sequencing data from ENCODE project.<br>
<b>Pundhir S</b>, Hannibal T, Bang-Berthelsen C, Wegener A, Pociot F, Holmberg D and Gorodkin J.<br>
<b><i>Gene</i></b> 545(1):80-87 [PMID: 24797614] [<a href="http://www.sciencedirect.com/science/article/pii/S0378111914005368/pdfft?md5=547f875f1a0bba2a8747050ae6727824&pid=1-s2.0-S0378111914005368-main.pdf" target="_blank">PDF</a>].
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<td valign="top" align="right">2014</td><td>
Structured RNAs and synteny regions in the pig genome.<br>
Anthon C, Tafer H, Havgaard J, Thomsen B, Hedegaard J, Seemann S, <b>Pundhir S</b>, Kehr S, Bartschat S, Nielsen M, Nielsen R, Fredholm M, Stadler P, Gorodkin J.<br>
<b><i>BMC Genomics</i></b> 15:459 [PMID: 24917120] [<a href="http://download.springer.com/static/pdf/860/art%253A10.1186%252F1471-2164-15-459.pdf?originUrl=http%3A%2F%2Fbmcgenomics.biomedcentral.com%2Farticle%2F10.1186%2F1471-2164-15-459&token2=exp=1472378233~acl=%2Fstatic%2Fpdf%2F860%2Fart%25253A10.1186%25252F1471-2164-15-459.pdf*~hmac=24b07b2b258b0b84c8e4feddfb4b098fe8587377916f5b9662a6d484ebc17b8f" target="_blank">PDF</a>].
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<td valign="top" align="right">2013</td><td>
MicroRNA discovery by similarity search to a database of RNA-seq profiles.<br>
<b>Pundhir S</b> and Gorodkin J.<br>
<b><i>Frontiers in Genetics</i></b> 4:133 [PMID: 23874353] [<a href="http://www.readcube.com/articles/10.3389/fgene.2013.00133" target="_blank">PDF</a>].
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<td valign="top" align="right">2012</td><td>
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.<br>
Langenberger D*, <b>Pundhir S</b>*, Ekstrøm C, Stadler P, Hoffmann S and Gorodkin J.<br>
<b><i>Bioinformatics</i></b> 28(1):17-24 [PMID: 22053076] [<a href="http://bioinformatics.oxfordjournals.org/content/28/1/17.full.pdf+html" target="_blank">PDF</a>] (*joint first authors).
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<td valign="top" align="right">2012</td><td>
SSPred: a prediction server based on SVM for the identification and classification of protein involved in bacterial secretion systems.<br>
<b>Pundhir S</b> and Kumar A.<br>
<b><i>Bioinformation</i></b> 6(10):380-382 [PMID: 21904425] [<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163916/pdf/97320630006380.pdf" target="_blank">PDF</a>].
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<td valign="top" align="right">2008</td><td>
PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes.<br>
<b>Pundhir S</b>, Vijaywargiya H and Kumar A.<br>
<b><i>In Silico Biology</i></b> 8(3-4):223-234 [PMID: 19032158] [<a href="http://content.iospress.com/articles/in-silico-biology/isb00352?resultNumber=0&totalResults=1&start=0&q=sachin+pundhir&resultsPageSize=10&rows=10" target="_blank">PDF</a>].
</td>
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<!--tr>
<td valign="top" align="right">Submitted/ In preparation</td><td>
Enhancer and transcription factor dynamics along the granulocytic-monocytic lineage reveals an early differentiation block in Cebpa mutant progenitor. <br>
<b>Pundhir S</b>*, Lauridsen F*, Jakobsen J, Schoof E, Rapin N, Waage J, Hasemann M and Porse B. (*joint first authors).
</td>
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</table>
</p>
<!--p><b>Oral talks and poster presentations</b></p>
<ol>
<li>Application of read profiles in genome annotation. (2013) TBI Winterseminar, Bled,
Slovenia. [Oral presentation].</li><br>
<li><u>Pundhir S</u> and Gorodkin J. (2012) A computational framework to analyze RNA-seq data for differential read processing
patterns. ECCB Conference, Basel, Switzerland. [Poster presentation].</li><br>
<li>Comparative analysis of read processing patterns across 11 total RNA-seq datasets.
(2012) TBI Winterseminar, Bled, Slovenia. [Oral presentation].</li><br>
<li><u>Pundhir S</u>, <u>Langenberger D</u>, Ekstrøm CT, Stadler PF, Hoffmann S and Gorodkin J. (2011)
deepBlockAlign: A tool for aligning RNAseq profiles of read block patterns.
ISMB/ECCB Conference, Vienna, Austria. [Poster presentation].</li><br>
<li>Processing Patterns: Significance and Analysis. (2011) Herbstseminar
Bioinformatik, Vysoka Lipa, Czech Republic. [Oral presentation].</li><br>
<li>Identification and Classification of ncRNAs using Deep Sequencing data. (2011) TBI
Winterseminar, Bled, Slovenia. [Oral presentation].</li><br>
<li>In-silico identification and classification of non-coding RNA using high-throughput
sequences. (2010) Herbstseminar Bioinformatik, Vysoka Lipa, Czech Republic. [Oral presentation].</li><br>
<li><u>Pundhir S</u> and Kumar A. (2008) SSPred: a prediction server based on SVM for the
identification and classification of proteins involved in bacterial secretion systems.
International Conference on Bioinformatics (InCoB), Taipei, Taiwan, October 20-23, 2008. [Poster Presentation].</li><br>
<li><u>Pundhir S</u>, Vijaywargiya H and Kumar A. (2008) PredictBias: a server for the
identification of genomic and pathogenicity islands in prokaryotes. International
Conference on Bioinformatics (InCoB), Taipei, Taiwan, October 20-23, 2008. [Oral Presentation].</li><br>
<li><u>Pundhir S</u> and Kumar A. (2008) Bioinformatics and statistical genomics.
Genomic Med. 2(3-4): 217-240. (Abstract 040: SSPred: a prediction server based on
SVM for the identification and classification of protein involved in bacterial secretion
systems). [PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/19488836" target="_blank">19488836</a>]</li><br>
<li><u>Pundhir S</u> and Kumar A. (2006) In Silico Classification of bacterial virlience factors.
National Conference on Biotechnology, Science & Environment. Indore, India,
Dec. 28-29, 2006 (Best paper award). [Oral Presentation].</li><br>
<li><u>Pundhir S</u>, Vijayvargiya H and Kumar A. (2006) PredictBias: Detection of
pathogenic islands in pathogenic bacteria. International Conference on
Bioinformatics (InCoB), Delhi, India, December 18-20, 2006. [Poster Presentation].</li>
</ol-->
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