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T

Timothy P. L. Smith

USDA ARS

70H-index
424Paper Count
2.3WCitation Count
Published Papers 102
Publication Date
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Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet
errCell Genomics
IF9
err2026-08-06
err0
errOAAI
errJuhyun Kim; Benjamin D. Rosen; Sarah E. Fumagalli; Kristen L. Kuhn; Amy Long; Jeffrey J. Schoenebeck; Heather Schwartz; Lan Wu-Cavener; Aleksey V. Zimin; Douglas R. Cavener; Timothy P.L. Smith; Adam M. Phillippy; Sergey Koren; Arang Rhie
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errSave
Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome
errNature Communications
IF15.7
err2026-03-16
err0
errOAAI
errShangqian Xie; Kimberly M. Davenport; Mazdak Salavati; Alex Caulton; Emily L. Clark; Alan L. Archibald; Shannon M. Clarke; Rudiger Brauning; Alisha T. Massa; Michelle R. Mousel; Stephen N. White; Kim C. Worley; Gordon K. Murdoch; Gabrielle Becker; Morgan R. Stegmiller; Sarem F. Khilji; Katie A. Shira; Temitayo A. Olagunju; Tracy Hadfield; Stephanie D. McKay; Benjamin D. Rosen; Noelle E. Cockett; Timothy P. L. Smith; Brenda M. Murdoch
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errSave
Phased-assembly-driven pangenome graphs for structural variant genotyping and complex trait mapping in dairy cattle
errNature Communications
IF15.7
err2026-01-30
err0
errOAAI
errLiu Yang; Yahui Gao; Kristen L. Kuhn; Nayan Bhowmik; Wenli Li; Geoffrey Zanton; Lingzhao Fang; John B. Cole; Congjun Li; Ransom L. Baldwin, VI; Curtis P. Van Tassell; Benjamin D. Rosen; Li Ma; Timothy P. L. Smith; George E. Liu
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errSave
Population structure and domestication history of the Javan banteng
errCurrent Biology
IF7.5
err2026-01-19
err0
errOAAI
errXi Wang; Sabhrina Gita Aninta; Genís Garcia-Erill; Zilong Li; Anubhab Khan; Xiaodong Liu; Laura D. Bertola; Anik Budhi Dharmayanthi; null Yulianto; null Yonathan; Conor Rossi; Reagan Cauble-Sims; Benjamin D. Rosen; Darren E. Hagen; Michael P. Heaton; Timothy P.L. Smith; Johannes A. Lenstra; Nuno F.G. Martins; Mikkel-Holger S. Sinding; Muhammad Agil
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errSave
Insights into natural neocentromere evolution from a cattle T2T X chromosome
errNature Communications
IF15.7
err2025-11-28
err0
errOAAI
errPaulene S. Pineda; Callum MacPhillamy; Yan Ren; Tong Chen; Luan Zhong; David L. Adelson; Carey Dessaix; Jose Perez-Silva; Leanne Haggerty; Fergal J. Martin; Cynthia D. K. Bottema; Wayne S. Pitchford; Benjamin D. Rosen; Timothy P. L. Smith; Wai Y. Low
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errSave
The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression
errNature Communications
IF15.7
err2025-09-25
err0
errOAAI
errXi Wang; Casia Nursyifa; Sabhrina Gita Aninta; Genís Garcia-Erill; Laura D. Bertola; Anubhab Khan; Josiah Kuja; Kristian Hanghøj; Jonas Meisner; Thomas Bøggild; Corey J. A. Bradshaw; Amal Al-Chaer; Alam Putra Persada; Dwi Sendi Priyono; Yuli A. Tribudi; Pita Sudrajad; Cynthia Dewi Gaina; Yu Jiang; Johannes A. Lenstra; Reagan Cauble-Sims; Benjamin D. Rosen; Darren E. Hagen; Michael P. Heaton; Timothy P. L. Smith; Laurent Frantz; Greger Larson; Mikkel-Holger S. Sinding; Dedy Duryadi Solihin; Muhammad Agil; Bambang Purwantara; Rasmus Heller
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errSave
Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle
errJournal of Advanced Research
IF13
err2025-04-19
err0
errOAAI
errYahui Gao; Liu Yang; Kristen Kuhn; Wenli Li; Geoffrey Zanton; Mary Bowman; Pengju Zhao; Yang Zhou; Lingzhao Fang; John B. Cole; Benjamin D. Rosen; Li Ma; Congjun Li; Ransom L. Baldwin; Curtis P. Van Tassell; Zhe Zhang; Timothy P.L. Smith; George E. Liu
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errSave
Assembly and analysis of sequence from a spring and winter type Camelina sativa by whole genome PacBio HiFi technologies
errINDUSTRIAL CROPS AND PRODUCTS
IF6.2
err2024-12-01
err1
errOAAI
errOntano, Andrew; Dobrin, Barbara; Smith, Timothy; Abernathy, Brian; Kandel, Jinita Sthapit; Shaikh, Tm; Anderson, James, V; Vaughn, Justin; Raman, Mukhlesur; Horvath, David
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errSave
QTL mapping to identify loci and candidate genes associated with freezing tolerance trait in Camelina sativa
errINDUSTRIAL CROPS AND PRODUCTS
IF6.2
err2024-12-01
err0
errOAAI
errShaikh, T. M.; Rahman, Mukhlesur; Anderson, James, V; Kandel, Jinita S.; Roy, Jayant; Vaughn, Justin; Smith, Timothy; Abernathy, Brian; Ontano, Andrew; Dobrin, Barbara; Dorn, Kevin; Horvath, David P.
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errSave
Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content
errNATURE COMMUNICATIONS
IF15.7
err2024-09-27
err0
errOAAI
errOlagunju, Temitayo A.; Rosen, Benjamin D.; Neibergs, Holly L.; Becker, Gabrielle M.; Davenport, Kimberly M.; Elsik, Christine G.; Hadfield, Tracy S.; Koren, Sergey; Kuhn, Kristen L.; Rhie, Arang; Shira, Katie A.; Skibiel, Amy L.; Stegemiller, Morgan R.; Thorne, Jacob W.; Villamediana, Patricia; Cockett, Noelle E.; Murdoch, Brenda M.; Smith, Timothy P. L.
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errSave
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project
errGIGASCIENCE
IF3.9
err2024-09-09
err1
errOAAI
errPineda, Paulene S.; Flores, Ester B.; Villamor, Lilian P.; Parac, Connie Joyce M.; Khatkar, Mehar S.; Thu, Hien To; Smith, Timothy P. L.; Rosen, Benjamin D.; Ajmone-Marsan, Paolo; Colli, Licia; Williams, John L.; Low, Wai Yee
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errSave
The Ruminant Telomere-to-Telomere (RT2T) Consortium
errNATURE GENETICS
IF31.8
err2024-08-05
err1
PREAI
errKalbfleisch, Theodore S.; McKay, Stephanie D.; Murdoch, Brenda M.; Adelson, David L.; Almansa-Villa, Diego; Becker, Gabrielle; Beckett, Linda M.; Benitez-Galeano, Maria Jose; Biase, Fernando; Casey, Theresa; Chuong, Edward; Clark, Emily; Clarke, Shannon; Cockett, Noelle; Couldrey, Christine; Davis, Brian W.; Elsik, Christine G.; Faraut, Thomas; Gao, Yahui; Genet, Carine; Grady, Patrick; Green, Jonathan; Green, Richard; Guan, Dailu; Hagen, Darren; Hartley, Gabrielle A.; Heaton, Mike; Hoyt, Savannah J.; Huang, Wen; Jarvis, Erich; Kalleberg, Jenna; Khatib, Hasan; Koepfi, Klaus-Peter; Koltes, James; Koren, Sergey; Kuehn, Christa; Leeb, Tosso; Leonard, Alexander; Liu, George E.; Low, Wai Yee; Mcconnell, Hunter; Mcrae, Kathryn; Miga, Karen; Mousel, Michelle; Neibergs, Holly; Olagunju, Temitayo; Pennell, Matt; Petry, Bruna; Pewsner, Mirjam; Phillippy, Adam M.; Pickett, Brandon D.; Pineda, Paulene; Potapova, Tamara; Rachagani, Satyanarayana; Rhie, Arang; Rijnkels, Monique; Robic, Annie; Rodriguez Osorio, Nelida; Safonova, Yana; Schettini, Gustavo; Schnabel, Robert D.; Sirpu Natesh, Nagabhishek; Stegemiller, Morgan; Storer, Jessica; Stothard, Paul; Stull, Caleb; Tosser-Klopp, Gwenola; Traglia, German M.; Tuggle, Christopher K.; Van Tassell, Curtis P.; Watson, Corey; Weikard, Rosemarie; Wimmers, Klaus; Xie, Shangqian; Yang, Liu; Smith, Timothy P. L.; O'Neill, Rachel J.; Rosen, Benjamin D.
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errSave
Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology
errGIGASCIENCE
IF3.9
err2024-04-16
err1
errOAAI
errBeiki, Hamid; Murdoch, Brenda M.; Park, Carissa A.; Kern, Chandlar; Kontechy, Denise; Becker, Gabrielle; Rincon, Gonzalo; Jiang, Honglin; Zhou, Huaijun; Thorne, Jacob; Koltes, James E.; Michal, Jennifer J.; Davenport, Kimberly; Rijnkels, Monique; Ross, Pablo J.; Hu, Rui; Corum, Sarah; McKay, Stephanie; Smith, Timothy P. L.; Liu, Wansheng; Ma, Wenzhi; Zhang, Xiaohui; Xu, Xiaoqing; Han, Xuelei; Jiang, Zhihua; Hu, Zhi-Liang; Reecy, James M.
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errSave
Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations
errNATURE COMMUNICATIONS
IF15.7
err2024-04-12
err1
errOAAI
errLiu, Xiaodong; Lin, Long; Sinding, Mikkel-Holger S.; Bertola, Laura D.; Hanghoj, Kristian; Quinn, Liam; Garcia-Erill, Genis; Rasmussen, Malthe Sebro; Schubert, Mikkel; Pecnerova, Patricia; Balboa, Renzo F.; Li, Zilong; Heaton, Michael P.; Smith, Timothy P. L.; Pinto, Rui Resende; Wang, Xi; Kuja, Josiah; Bruniche-Olsen, Anna; Meisner, Jonas; Santander, Cindy G.; Ogutu, Joseph O.; Masembe, Charles; da Fonseca, Rute R.; Muwanika, Vincent; Siegismund, Hans R.; Albrechtsen, Anders; Moltke, Ida; Heller, Rasmus
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errSave
Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis
errGENOME BIOLOGY AND EVOLUTION
IF2.8
err2024-04-08
err0
errOAAI
errDe Jode, Aurelien; Faria, Rui; Formenti, Giulio; Sims, Ying; Smith, Timothy P.; Tracey, Alan; Wood, Jonathan M. D.; Zagrodzka, Zuzanna B.; Johannesson, Kerstin; Butlin, Roger K.; Leder, Erica H.
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errSave
African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival
errNATURE COMMUNICATIONS
IF15.7
err2024-01-03
err4
errOAAI
errBalboa, Renzo F.; Bertola, Laura D.; Brueniche-Olsen, Anna; Rasmussen, Malthe Sebro; Liu, Xiaodong; Besnard, Guillaume; Salmona, Jordi; Santander, Cindy G.; He, Shixu; Zinner, Dietmar; Pedrono, Miguel; Muwanika, Vincent; Masembe, Charles; Schubert, Mikkel; Kuja, Josiah; Quinn, Liam; Garcia-Erill, Genis; Staeger, Frederik Filip; Rakotoarivony, Rianja; Henrique, Margarida; Lin, Long; Wang, Xi; Heaton, Michael P.; Smith, Timothy P. L.; Hanghoj, Kristian; Sinding, Mikkel-Holger S.; Atickem, Anagaw; Chikhi, Lounes; Roos, Christian; Gaubert, Philippe; Siegismund, Hans R.; Moltke, Ida; Albrechtsen, Anders; Heller, Rasmus
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errSave
Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition
errFRONTIERS IN MICROBIOLOGY
IF4.5
err2023-12-15
err1
errOAAI
errWeinroth, Margaret D.; Clawson, Michael L.; Harhay, Gregory P.; Eppinger, Mark; Harhay, Dayna M.; Smith, Timothy P. L.; Bono, James L.
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errSave
The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species
errGENOME BIOLOGY
IF9.4
err2023-06-19
err14
errOAAI
errSmith, Timothy P. L.; Bickhart, Derek M.; Boichard, Didier; Chamberlain, Amanda J.; Djikeng, Appolinaire; Jiang, Yu; Low, Wai Y.; Pausch, Hubert; Demyda-Peyras, Sebastian; Prendergast, James; Schnabel, Robert D.; Rosen, Benjamin D.
errShare
errSave
Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies
errBMC GENOMICS
IF3.7
err2023-03-13
err3
errOAAI
errRen, Yan; Tseng, Elizabeth; Smith, Timothy P. L.; Hiendleder, Stefan; Williams, John L. L.; Low, Wai Yee
errShare
errSave
Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa
errPLANT GENOME
IF3.8
err2023-03-09
err3
errOAAI
errShaikh, T. M.; Rahman, Mukhlesur; Smith, Timothy; Anderson, James V.; Chao, Wun S.; Horvath, David P.
errShare
errSave

Research Directions

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Co-authors
Cooperation Journals
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Evan E. Eichler
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M
Marco A. Marra
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S
Steven J.M. Jones
H-index: 189 · Papers: 1.3K
P
Paul Flicek
H-index: 167 · Papers: 522
D
David Hume
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